Re: [PyMOL] command question RE printing out distances to text file
Hej Suzanne,
you will need to append the other two distances to the script to get them
printed.
Following your example that would be something like:
# calculate the distance and store it in dst
dst1=cmd.distance('tmp','B///297/cb','A///17-19/cb')
dst2=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the
selections in this line!
dst3=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the
selections in this line!
# and then for writing the output file
f.write("%8.3f\n"%dst1)
f.write("%8.3f\n"%dst2)
f.write("%8.3f\n"%dst3)
inserting these blocks in your script hopefully will do the trick.
Cheers,
Andreas
On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) <
suzanne-lapo...@ouhsc.edu> wrote:
> Another follow up question to this. I decided to use the measure distance
> python script on the pymol wiki to do this, and I was able to do it
> successfully with a range of residues, but my question is about the output
> txt file. When I run the script I get the correct distances (all 3 of
> them) to show on the GUI but the text file that is generated (distnew.txt)
> only lists one distance--so perhaps the script needs to be modified for
> this as well for the residues measured?
>
> The original script is at the link
> http://www.pymolwiki.org/index.php/Measure_Distance
> and my modified version is below. Suggestions appreciated! Thank you.
>
> # This script writes the distance from
> # atom mol1///25/ha to atom mol1///26/ha
> # out to the file "dist.txt"
> # Simply change your selections to see different distances.
>
> # import PyMOL's command namespace
> from pymol import cmd
>
> # open dist.txt for writing
> f=open('distnew.txt','w')
>
> # calculate the distance and store it in dst
> dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')
>
> # write the formatted value of the distance (dst)
> # to the output file
> f.write("%8.3f\n"%dst)
>
> # close the output file.
> f.close()
>
> From: Robert Campbell [robert.campb...@queensu.ca]
> Sent: Monday, June 09, 2014 10:04 AM
> To: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] command question RE printing out distances to text
> file
>
> Hi Suzanne,
>
> You can also get the distance printed in the external GUI or terminal
> window
> by using the "cmd.distance" version of the command. So either you can
> assign the distance to a variable and print it or you can print the result
> directly.
>
> Assuming you have two selections, sele1 and sele2 specifying the atoms of
> interest you can do:
>
> d = cmd.distance(sele1,sele2)
> print sele1,sele2,d
>
>
> Cheers,
> Rob
>
> On Mon, 2014-06-09
> 13:13 EDT, Thomas Holder wrote:
>
> > Hi Suzanne,
> >
> > you can use the get_distance command. It doesn't generate a distance
> > object but prints the distance to the external window.
> >
> >
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
> >
> > Cheers,
> > Thomas
> >
> > On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
> > wrote:
> >
> > > Fellow Pymol Users:
> > > I may have asked this question before...but if so have forgotten. I am
> > > measuring distances between 2 atoms in 2 different objects using the
> > > distance command, and it is working perfectly, but I wonder if there is
> > > a command I can use/add so that those distances can be printed in the
> > > external gui as well as being shown in the viewer. I will be doing lots
> > > of these at the same time and the screen will get crowded. Thank you in
> > > advance.
> >
>
>
>
>
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Dept. of Biomedical & Molecular Sciences
> Botterell Hall Rm 644
> Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821
>
> https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlc&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225
>
>
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> Find What Matters Most in Your Big Data with HPCC Systems
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> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>
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Re: [PyMOL] command question RE printing out distances to text file
One more addition to the reply:
I failed to notice that you are trying to input a range of residues '17-19'
Make sure to input single atom selections to get correct distances and not
an average:
A straightforward way to get that name is to click on the atom while in the
'editing mode' of pymol: pymol will print: "you clicked" followed by a name
that can be copy-pasted.
e.g. "You clicked /lys///LYS`2/CA -> (pk1)" can be used to copy-paste
/lys///LYS`2/CA
Another alternative is to use selections to identify one atom:
e.g.
cmd.distance('chain B and resi 297 and name CB','chain A and resi 17 and
name CB')
Then your example becomes:
from pymol import cmd
# open dist.txt for writing
f=open('distnew.txt','w')
# calculate the distance and store it in dst
dst1=cmd.distance('chain B and resi 297 and name CB','chain A and resi 17
and name CB')
dst2=cmd.distance('chain B and resi 297 and name CB','chain A and resi 18
and name CB')
dst3=cmd.distance('chain B and resi 297 and name CB','chain A and resi 19
and name CB')
# and then for writing the output file
f.write("%8.3f\n"%dst1)
f.write("%8.3f\n"%dst2)
f.write("%8.3f\n"%dst3)
f.close()
Cheers,
Andreas
On Tue, Jun 17, 2014 at 8:45 PM, Andreas Warnecke <
4ndreas.warne...@gmail.com> wrote:
> Hej Suzanne,
>
> you will need to append the other two distances to the script to get them
> printed.
> Following your example that would be something like:
>
> # calculate the distance and store it in dst
> dst1=cmd.distance('tmp','B///297/cb','A///17-19/cb')
> dst2=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the
> selections in this line!
> dst3=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the
> selections in this line!
>
> # and then for writing the output file
> f.write("%8.3f\n"%dst1)
> f.write("%8.3f\n"%dst2)
> f.write("%8.3f\n"%dst3)
>
> inserting these blocks in your script hopefully will do the trick.
>
> Cheers,
>
> Andreas
>
>
> On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) <
> suzanne-lapo...@ouhsc.edu> wrote:
>
>> Another follow up question to this. I decided to use the measure distance
>> python script on the pymol wiki to do this, and I was able to do it
>> successfully with a range of residues, but my question is about the output
>> txt file. When I run the script I get the correct distances (all 3 of
>> them) to show on the GUI but the text file that is generated (distnew.txt)
>> only lists one distance--so perhaps the script needs to be modified for
>> this as well for the residues measured?
>>
>> The original script is at the link
>> http://www.pymolwiki.org/index.php/Measure_Distance
>> and my modified version is below. Suggestions appreciated! Thank you.
>>
>> # This script writes the distance from
>> # atom mol1///25/ha to atom mol1///26/ha
>> # out to the file "dist.txt"
>> # Simply change your selections to see different distances.
>>
>> # import PyMOL's command namespace
>> from pymol import cmd
>>
>> # open dist.txt for writing
>> f=open('distnew.txt','w')
>>
>> # calculate the distance and store it in dst
>> dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')
>>
>> # write the formatted value of the distance (dst)
>> # to the output file
>> f.write("%8.3f\n"%dst)
>>
>> # close the output file.
>> f.close()
>>
>> From: Robert Campbell [robert.campb...@queensu.ca]
>> Sent: Monday, June 09, 2014 10:04 AM
>> To: pymol-users@lists.sourceforge.net
>> Subject: Re: [PyMOL] command question RE printing out distances to text
>> file
>>
>> Hi Suzanne,
>>
>> You can also get the distance printed in the external GUI or terminal
>> window
>> by using the "cmd.distance" version of the command. So either you can
>> assign the distance to a variable and print it or you can print the result
>> directly.
>>
>> Assuming you have two selections, sele1 and sele2 specifying the atoms of
>> interest you can do:
>>
>> d = cmd.distance(sele1,sele2)
>> print sele1,sele2,d
>>
>>
>> Cheers,
>> Rob
>>
>> On Mon, 2014-06-09
>> 13:13 EDT, Thomas Holder wrote:
>>
>> > Hi Suzanne,
>> >
>> > you can use the get_distance command. It doesn't ge
Re: [PyMOL] Set fullscreen and grid mode in batch script
Hej,
I haven't tested, but the grid_mode should work, all you need to do is
correct the underscore typo:
set grid_mode, 1 # without _
set grid_slot, 2, object2
set grid_slot, 1, object1
Picture size and quality is not controlled by viewport unless you are
making a movie, in that case set viewport, ray_trace_frames and
movie_quality:
cmd.viewport(800,600)
cmd.set('ray_trace_frames',1)
cmd.set('movie_quality',100)
#Then use either:
cmd.mpng('example')
#or
cmd.movie.produce('example.mpg',mode='ray', preserve=0, quality=100)
I your case, however, a single image is best made using png:
e.g.
cmd.png('example.png', '15cm', '10cm', dpi=300, ray=1)
this will give you a 15x10 cm image at 300 dpi, regardless of viewport.
http://www.pymolwiki.org/index.php/Png
About starting in fullscreen:
using the command line option '-e' should make pymol start in fullscreen
this will probably not work with '-c', but you can open your script from
another shortcut.
http://www.pymolwiki.org/index.php/Command_Line_Options
Hope this helps,
/Andreas
On Thu, Jun 19, 2014 at 5:33 AM, J.R. W wrote:
> Hi,
>
> What I’d like to do is set_grid_mode_1, ray trace, and then output a png
> in batch mode (-c)
>
>
> However if you code this in the .pml:
>
> set_grid_mode, 1
> set grid_slot, 2, object2
> set grid_slot, 1, object1
>
> viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific
>
> ray 1000,1000
> png somepic.png
> cmd.save("lookatthis.pse”)
>
> Grid mode* does not* show up in the picture and the viewport in the
> session is still the default window size. However, grid mode *does* work
> in the session.
>
> So my question(s) are this:
>
> 1. Can you use grid mode in batch mode scripts to output an image?
> 2. Can you encode a full screen GUI in the pymol session so when you open
> up the session, it is full screen?
>
> Using MacPyMOL latest release, can switch to X11 if necessary.
>
> Thanks so much!
>
> Jordan
>
>
>
>
> --
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Re: [PyMOL] side chain helper glycine
Hej, I'm not sure about the side chain helper options, but you can always selectively show displays. You could try something like: show_as cartoon, object show sticks, sele and not name N+C+O or: show_as cartoon, object show sticks, sele hide sticks, name N+C+O Either option should show the cartoon plus non-main chain atoms. Hope that works, /Andreas On Mon, Jun 23, 2014 at 8:13 PM, Christian Roth < christian.r...@bbz.uni-leipzig.de> wrote: > Hi there, > > I used the side chain helper option to create a binding site in the > protein. However I want include a glycine, which doesn't show up. Even > when I create an extra object with the glycine and an neighbouring > residue I didn't get the carbonyl oxygen atom of glycine and I don't > want to switch of the side chain helper function for all residues. > Is there a way to get that done without switching the helper function > completely off? > > Thanks in advance for your help > > Christian > > > > -- > HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions > Find What Matters Most in Your Big Data with HPCC Systems > Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. > Leverages Graph Analysis for Fast Processing & Easy Data Exploration > http://p.sf.net/sfu/hpccsystems > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing & Easy Data Exploration http://p.sf.net/sfu/hpccsystems___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Aligning multiple residue sets in two or more proteins
Hi Monica, I haven't tested, but maybe you could try: align PDB1 and (resi 80-120 or resi 160-220), PDB2 and (resi 80-120 or resi 160-220) I.e. expanding the selection to both streches. Running sequential alignments will replace existing ones. How this may help. /Andreas On Jul 2, 2014 1:24 PM, "Monica Mittal" wrote: > Dear all > I need to align lets say resi 80-120 and 160-220 from one protein to resi > 80-120 and 160-220 in second protein. How can i do this. > I tried following: > align PDB1 and resi 80-120, PDB2 and resi 80-120 > this is for one set but how to do for two sets 80-120 as well as 160-220 > simultaneously. > Thank you > Monica > > > -- > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to show atom index or atom serial when clicking on an atom?
Hej Jose,
This script may do what you need. The core is to use iterate over the
different identifiers. I'm not sure if there's a more convenient way,
though.
python
def get_macro_name(sele):
'''
will return the atom macro name of the first atom in selection
accepts non-macro selection style only
'''
from pymol import stored
# name macro
try:
sele='first (%s)'%sele # reduce sele to one atom
stored.macroname=''
cmd.iterate(sele, 'stored.macroname="/%s/%s/%s/%s`%s/" %(model,
segi, chain, resn, resi)')
return stored.macroname
except:
raise Exception(("Invalid selection:\n#\n"
"Error in get_resi_macro_name\n#"))
python end
print get_macro_name('resi 1 and name CA') # example
Hope this helps,
Andreas
On Mon, Jul 14, 2014 at 12:28 AM, Jose Borreguero
wrote:
> Dear pymol users,
>
> When I click in an atom (mouse->selection mode->atoms) I get the
> /chain_name/residue_name/atom_name info string. Is there a way to output
> the atom serial or atom index?
> My molecule has atoms with duplicate names within the same residue, so the
> info string chain_name/residue_name/atom_name does not uniquely identify an
> atom. I need to see the atom index or atom serial.
>
> Thanks in advance for your help!
> -Jose
>
>
> --
>
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[PyMOL] Fwd: Re: How to show atom index or atom serial when clicking on an atom?
-- Forwarded message --
From: "Andreas Warnecke" <4ndreas.warne...@gmail.com>
Date: Jul 14, 2014 1:03 AM
Subject: Re: [PyMOL] How to show atom index or atom serial when clicking on
an atom?
To: "Jose Borreguero"
Cc:
minor amendment, changin the iterate line to:
cmd.iterate(sele, 'stored.macroname="/%s/%s/%s/%s`%s/%s`%s" %(model, segi,
chain, resn, resi, name, alt)')
will break it down to atom name and alternative (if present).
On Mon, Jul 14, 2014 at 12:54 AM, Andreas Warnecke <
4ndreas.warne...@gmail.com> wrote:
> Hej Jose,
>
> This script may do what you need. The core is to use iterate over the
> different identifiers. I'm not sure if there's a more convenient way,
> though.
>
>
>
> python
> def get_macro_name(sele):
> '''
> will return the atom macro name of the first atom in selection
> accepts non-macro selection style only
> '''
> from pymol import stored
> # name macro
> try:
> sele='first (%s)'%sele # reduce sele to one atom
> stored.macroname=''
> cmd.iterate(sele, 'stored.macroname="/%s/%s/%s/%s`%s/" %(model,
> segi, chain, resn, resi)')
> return stored.macroname
> except:
> raise Exception(("Invalid selection:\n#\n"
> "Error in get_resi_macro_name\n#"))
> python end
>
> print get_macro_name('resi 1 and name CA') # example
>
>
>
> Hope this helps,
>
> Andreas
>
>
> On Mon, Jul 14, 2014 at 12:28 AM, Jose Borreguero
> wrote:
>
>> Dear pymol users,
>>
>> When I click in an atom (mouse->selection mode->atoms) I get the
>> /chain_name/residue_name/atom_name info string. Is there a way to output
>> the atom serial or atom index?
>> My molecule has atoms with duplicate names within the same residue, so
>> the info string chain_name/residue_name/atom_name does not uniquely
>> identify an atom. I need to see the atom index or atom serial.
>>
>> Thanks in advance for your help!
>> -Jose
>>
>>
>> --
>>
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>>
>
>
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Re: [PyMOL] Iterating through states of a topology object (trajectories) and writing out a distance
Hej Sajeewa,
it is hard to test this without the data, however, I think what you may be
looking for is defining the "state". Either you can set it in your script
using cmd.set('state', x) or define it in the get_distance function. Since
you use state=0, it will always use the object's current one. In your loop
you could use i+1 or numarray[i] for this, depending on the order of the
states (I assume it starts with 1, i starts with 0).
from pymol import cmd # you won't need to write pymol.cmd. further down
f = open("twoD_dist_ang.txt", "w")
for i in range(0,len(numarray)): # I assume numarray is a defined list
containing numbers?
cmd.reinitialize() # I'm not sure you need to reinitialize PyMOL every
time, you could use cmd.delete('all') if you want to get rid of objects
cmd.load('amn%d_xd1.pdb' %(numarray[i]))
ang=cmd.get_angle(atom1="179/C",atom2="206/N",atom3="996/N",state=
numarray[i]) # skip the str() formatting for later
dis=cmd.get_distance(atom1="993/CG",atom2="996/N",state=numarray[i])
f.write('%.3f\t%.3f\t%d\n' %(ang, dis, numarray[i])) # format using %f
syntax, %.3f gives you 3 digits
f.close()
If you want to go through the states of the object you can use a loop:
for state in range(1, cmd.count_states('topo')+1):
cmd.set('state', state, 'topo')
# and so on
Hope this works out, you could manually control check if the script is
doing its job correctly.
Cheers,
Andreas
On Thu, Jul 17, 2014 at 7:47 PM, Sajeewa Pemasinghe
wrote:
> Hi all,
>
> I have loaded a topology file by the name of "topo" into pymol and loaded
> the trajectory file on top of it. Now pymol says "amn1136_xd1.trj" appended
> into object "topo".
> CmdLoadTraj: 250 total states in the object.
>
> I want go through these states and write the distance between two atoms to
> a file.
>
> I already have a script that goes through and array of files and writes a
> distance and an angle to a file.
>
> f = open("twoD_dist_ang.txt", "w")
> for i in range(0,len(numarray)):
> pymol.cmd.reinitialize()
> pymol.cmd.load('amn%d_xd1.pdb' %(numarray[i]))
>
> ang=str(cmd.get_angle(atom1="179/C",atom2="206/N",atom3="996/N",state="0"))
> dis=str(cmd.get_distance(atom1="993/CG",atom2="996/N",state="0"))
> f.write (ang+'\t'+dis+'\t'+str(numarray[i])+'\n')
> f.close()
>
> I would really appreciate some advice on how to modify the above script to
> go through the states of the above topology object "topo".
>
> Best regards
>
> Sajeewa Dewage
>
>
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Re: [PyMOL] Faster installation of plugins during development
Hej Matthew,
1. The advantage of using the plugin manager is that it will automatically
import all the plugin in the 'plugins' folder of the 'pymol-script-repo'.
This should re-load you plugin if it is located in a folder managed by the
plugin manager. The loading of plugins located therein occurs
automatically.
You can add paths to the plugin manager either manually or using scripts
during startup as described in the link. This is the way I prefer to do it.
Check the examples and linked pages:
http://www.pymolwiki.org/index.php/Plugin_manager
Note that deliberate import of these plugins changes:
e.g. to import colorama.py post startup use:
import pmg_tk.startup.colorama
# this is shown in the info dialog of the Plugin manager
A simple restart of PyMOL should re-load your updated plugin with the
changes made, provided the path is added to its list. It may require a
__init__.py file if it is a module.
2. if you are testing a plugin you can always have it in a separate folder
that you add yourself.
I sometime use the following to test scripts (added in the
run_on_startup.py):
#
import sys
import os
sys.path.append(os.path.abspath(os.path.join(os.environ['PYMOL_PATH'],
'plugins_private'))) # contains a folder called private with a (empty)
__init__.py file
import private
#
3. Another (maybe deprecated?) way of running your code would be to use
'execfile'. This would correspond to running the python code in PyMOL.
#
import os
PYMOLPATH=os.environ['PYMOL_PATH']
#Append 'plugin' folder # Change to 'Pymol-script-repo' if required
PLUGINPATH=os.path.realpath(os.path.join(PYMOLPATH, 'plugins'))
# Run every script in the folder and max. one sub-folder that is '.py'
PLUGINPATH_LIST=[os.path.realpath(os.path.join(PLUGINPATH, name)) for name
in os.listdir(PLUGINPATH) if os.path.isdir(os.path.join(PLUGINPATH, name))]
PLUGINPATH_LIST=[PLUGINPATH]+PLUGINPATH_LIST
print 'paths for plugins: '
for p in PLUGINPATH_LIST: print p
print
'#---'
for d in PLUGINPATH_LIST:
print 'Initiating (sub)-directory: '+d
for f in os.listdir(d):
if f=='__init__.py': continue
if f.endswith('.py'):
print "Executing plugin: "+f
execfile(os.path.realpath(os.path.join(d, f)))
else:
if not os.path.isdir(os.path.join(d,f)):print 'skipping non .py
file: '+f
#
The drawback in 2 or 3 is that this will not work for true plugins that add
menus to PyMOL.
4. For simple script or short chunks of code I often copy-paste:
python
#code here
python end
into the pymol mini shell. This is great for testing part of the code.
In conclusion I recommend using option. 1 and restart PyMOL after making
changes to the script: The plugin manager is a very practical addition to
PyMOL and I love it. It just needs to be configured correctly, which is
something that changed in comparison to other PyMOL versions (cf. the link).
Just beware: removing a installed plugin may physically delete the file. So
be sure to backup your script should you decide to remove scripts or paths
that were added to the Plugin Manager.
Hope this will relieve some of the frustration.
Cheers,
Andreas
On Fri, Jul 18, 2014 at 5:41 PM, Matthew Baumgartner wrote:
> Hi,
> So i am working on a pymol plugin (shameless plug
>
Re: [PyMOL] directing output of "print"
Hej Harry,
This PyMOL wiki page may help you out further, it may be hard to find
without the underscore in the name:
http://www.pymolwiki.org/index.php/Get_Area
If you use the load_b=1 option, PyMOL will overwrite the b-factor.
You could select the atom by the overwritten b-factor, e.g.:
select mysele, b>5
Note this works for labeling, too.
label all, "%.2f"%b
You can use print to output the b-factor for each atom (the first part is
just to get the atom macro name):
cmd.iterate('all', 'print "/%s/%s/%s/%s`%s/%s`%s, %f" %(model, segi, chain,
resn, resi, name, alt, b)')
# note to replace 'all' by your selection name
Or if you prefer a file:
#
python
from pymol import stored
stored.b_load=[]
cmd.iterate('all', 'stored.b_load.append("/%s/%s/%s/%s`%s/%s`%s, %f"
%(model, segi, chain, resn, resi, name, alt, b))')
f=open('report.txt','w')
for x in stored.b_load:
f.write(x+"\n")
f.close()
python end
#
The report is comma separated and good for EXCEL import.
Hope this helps you out.
Cheers,
Andreas
On Wed, Jul 23, 2014 at 12:48 PM, Harry Mark Greenblatt <
harry.greenbl...@weizmann.ac.il> wrote:
> BS"D
>
> Dear All,
>
> I thought I saw something about using get_area to get a residue by
> residue value for solvent accessible surface area, instead of the a per
> atom list. But I can't seem to find that now. Any ideas?
>
> In relation to this, when using the load_b option, can one redirect the
> output of "b" to a file within the command line (iterate object, print b)?
>
> Thanks
> Harry
>
>
>
> -
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology
>
> Weizmann Institute of SciencePhone: 972-8-934-3625
> 234 Herzl St.Facsimile: 972-8-934-4159
>
> Rehovot, 76100
>
> Israel
>
>
> harry.greenbl...@weizmann.ac.il
>
>
>
>
>
>
>
>
>
> --
> Want fast and easy access to all the code in your enterprise? Index and
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Re: [PyMOL] Fwd: color by RMSF or RMSD
Hej Nidhi, I'm not familiar with the two scipts but the usage appears correct. You can check the arguments in PyMOL using e.g.: rmsf_states ? and/or: help rmsf_states I assume the color_b command is a simplification of the spectrum command, so you could also check out: http://www.pymolwiki.org/index.php/Spectrum If you want to display several states, you can set 'all_states' to on: set all_states, 1 # shows all states http://www.pymolwiki.org/index.php/All_states Alternatively, consider splitting the object states after you're done with them: http://www.pymolwiki.org/index.php/Split_states Hope this helps out. Cheers, Andreas On Wed, Jul 23, 2014 at 1:09 PM, Nidhi Jatana wrote: > > Dear Sir/Madam > I have generated five models for a protein and I wanted to check how the > models align to each other and color them by RMSD/RMSF. I wanted to know > what should be the ideal way to do it. Shall I use RMSF or RMSD for the > same? > > I tried doing this using rmsf_states.py and color_b.py scripts: > > >- First I merged the five pdb files with load command, generating a >multi-state model >- Next, I used rmsf_states.py script to generate b-factors (using >command: rmsf_states tasser, byres=1, reference_state=1) >- Next I used the color_b.py script to color the structures (using >command: color_b(selection='all', item='b', mode='hist', >gradient='bgr') ) > > Is this the correct way to do it? > > And there is one more query. When I am loading the multi-state model, I > could only see one structure, not all five? Can I visualize all 5? > > > Thanking you > > Regards > > -- > Nidhi Jatana > Senior Research Fellow > Bioinformatics Center > Sri Venkateswara College > (University of Delhi) > Dhaula Kuan > New Delhi-110021. > > > > > > > -- > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Coloring of helices
Hej, you can try to exclude the backbone from your selections using "not": select V27, (resi 27 and EXA) and not (name N+C+O) # I included the CA in this selection etc. This should select the residue atoms excluding the backbone (except CA). If you have hydrogens in the structure you may need to modify the selection to also exclude certain hydrogens: select V27, (resi 27 and EXA) and not ((name N+C+O) or ((neighbor (name N+C+CA+O)) and elem H)) Now you should be able to color and display the object sequentially, without overlap: show_as cartoon, all # secondary structure show sticks, V27 # shows the residue as sticks (including CA) color green, all # base color color red, V27 and not CA # colors the residue red (excluding the CA) Hope this solves the issue. Cheers, Andreas On Fri, Aug 22, 2014 at 12:33 AM, Markus Heller wrote: > Hi all, > > I'm stuck. I'm trying to create a figure where I show a helix bundle, > with select side chains shown as sticks. I would like the helices to be > green, and the side chains in different colors. Easy enough, *but* the > carbon color of the side chains supersedes the green color of the helices. > > I tried to duplicate the object and show sticks for one objects and > helices for the other, which works in terms of color, *but* now the > cartoon_side_chain_helper doesn't work, since I'm displaying sticks and > helices from 2 different objects. > > How do I go about this? > > Thanks and Cheers > Markus > > PS: Here's my attempt: > > # reset everything > delete all > > # white background > bg_color white > > # show valences > set valence, 1 > > # show valences inside rings, 0 = centered, 1 = inside > set valence_mode, 1 > > # antialias > set antialias = 1 > > # don't show backbone for cartoons > set cartoon_side_chain_helper, on > > # keep standard helix, strand, loop representations > # other options: cartoon loop, cartoon rect, > # cartoon oval , cartoon tube > cartoon automatic > > # Molscript-like edges for helices > set cartoon_fancy_helices = 1 > > # color inside of helices gray > set cartoon_highlight_color, gray > > # load the PDB file > > load example.pdb, EXA > > # duplicate protein > copy EXA_dup, EXA > > # hide everything > hide everything > > # select protein > select prot, polymer > > # show cartoon ribbon > show cartoon, EXA > > # select helices > select heli, (ss h and EXA) > select heli_dup, (ss h and EXA_dup) > > # color everything limon > color limon > > # select residue of interest > select V27, (resi 27 and EXA) > select S31, (resi 31 and EXA) > select A34, (resi 34 and EXA) > select H37, (resi 37 and EXA) > select W41, (resi 41 and EXA) > > # show sticks for ROIs > show sticks, (V27 or S31 or A34 or H37 or W41) > > # color ROIs > color atomic, (V27 or S31 or A34 or H37 or W41) > color yellow, (name C* and V27) > color orange, (name C* and S31) > color cyan, (name C* and A34) > color magenta, (name C* and H37) > color purple, (name C* and W41) > > # color helices properly > show cartoon, EXA_dup > color limon, EXA_dup > > # deselect all to avoid little pink squares > deselect > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) > 827-1147 > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | > www.cdrd.ca > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should > not disseminate, distribute, copy, or alter this email. > > > > > > -- > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Hbonds in grid mode
Hej, The reason for this happening is that the distances are a separate object. What you are looking for is grid_slot. Simply assign the distance and protein objects to the same slot. http://www.pymolwiki.org/index.php/Grid_mode http://www.pymolwiki.org/index.php/Grid_slot Cheers, Andreas On Fri, Aug 22, 2014 at 1:10 AM, Markus Heller wrote: > Hi, > > I've got another question where a google search came up empty. > > I'm displaying 4 proteins in grid mode. When I try to display H bonds > (dist Hbo, resi 37, resi 41, mode = 2), the H bonds are displayed in a > separate panel. > > How can I avoid this, i.e. how can I show H bonds without making them an > object which gets displayed in its own panel? > > Thanks again and Cheers! > Markus > > -- > Markus Heller, Ph.D. > NMR Scientist > CDRD - The Centre for Drug Research and Development > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) > 827-1147 > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | > www.cdrd.ca > > > > > > > Follow us: > > This email and any files transmitted with it are confidential and intended > solely for the addressee. If you are not the named addressee you should > not disseminate, distribute, copy, or alter this email. > > > > > > -- > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] drawing arows, CONE cgo doesn't work.
Hej, if you simply copy-paste the wiki entry into PyMOL you will get the error. This code is intended to be run as a block (e.g. from script) and creates e.g. problems with indentation, or other errors. A simple solution would be to wrap the commands to a block using "python" and "python end". Either you include them in what copy paste (the whole shabang): python # axes.pyfrom pymol.cgo import *from pymol import cmdfrom pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green,#blue for X, Y and Z obj = [ CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0., CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0., CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0, ] # add labels to axes object (requires pymol version 0.8 or greater, I# believe cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) # then we load it into PyMOLcmd.load_cgo(obj,'axes') python end OR you can enter the lines/ copy paste sequentially. If you are interested in arrows/ cones, have a look at the cgo_arrow script: http://www.pymolwiki.org/index.php/Cgo_arrow Hope this helps. Cheers, Andreas On Mon, Aug 25, 2014 at 5:48 PM, vincent Chaptal wrote: > Hi, > > I'm trying to draw arrows in Pymol 1.7.2 for mac, "à la > http://www.pymolwiki.org/index.php/Axes " > > When I run the script for the Axes_with_nice_cones, I have the error > message: > File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 464, > in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1 > CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, > 1.0, 1.0, 1.0] > > ^ > SyntaxError: invalid syntax > > > As a workaround, I tried to use the cylinder syntax (bellow, by replacing > CYLINDER by CONE), pymol loads the object but doesn't draw anything. > cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, > b1 ], "cone_a" ) > > > Can someone tell me what is going on and how I can draw a cgo CONE in > pymol? It looks very nice. > > Thank you > Vincent > > > > > -- > > Vincent Chaptal, PhD > > Institut de Biologie et Chimie des Protéines > > Drug-resistance modulation and mechanism Laboratory > > 7 passage du Vercors > > 69007 LYON > > FRANCE > > +33 4 37 65 29 01 > > http://www.ibcp.fr > > > > > -- > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Testing for incentive vs. open-source in scripts
Dear PyMOL users, I am wondering if there is any way of testing whether a PyMOL version is open-source or incentive for use in scripts. I'm thinking of something similar to 'cmd.get_version()'. The reason for this is that I am e.g. using the 'alter' command on custom properties in scripts, which is a feature that may not be available in all PyMOL versions. At the moment I avoid a crash by placing the code within a 'try' statement, but this will yield an error message. If I could actually test the incentive/open-source state this would allow me to use an 'if' statement instead and avoid the error message. I would welcome suggestions on how to approach this. Thanks, Andreas -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Testing for incentive vs. open-source in scripts
Hi all,
just to specify the issue: the problem is not the crash, because the script
continues due to the try statement. The issue is that PyMOL handles and
prints the exception from the 'alter' command into the console. I would
like to avoid that, either by testing incentive vs. open-source, or by
preventing PyMOL from printing the exception.
The cmd.get_version() command can be used to test the version of PyMOL, but
does to my knowledge not give information on the incentive/open-source
build (?).
It would be useful to have a way of testing this, though. Ideas anyone?
Currently, I solved the issue with the printing like this now, but I feel
it is inferior to actually testing the incentive/open-source state:
try:
originalstdout = sys.stdout # hijack the output
sys.stdout = sys.stdout = open('/dev/null', 'w') # dump
cmd.alter('...') # longer command omitted here - error usually printed
here
sys.stdout = originalstdout # reinstate the output
except: pass
Thanks for the suggestions,
Andreas
On Fri, Oct 3, 2014 at 2:59 PM, Gianluca Santoni
wrote:
> Version number is printed in the startup message, so it has to be stored
> somewere related to this function.
>
> On 10/3/14 2:23 PM, Tsjerk Wassenaar wrote:
> > Hi Andreas,
> >
> > Ah, I think the problem is PyMOL handling the error. It probably prints
> > the exception and then continuous anyway. So it actually doesn't allow
> > you to catch it off. So you would indeed need to get access to the
> > version. I don't know where that is stored from the top of my head.
> > Maybe Thomas knows.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Fri, Oct 3, 2014 at 2:09 PM, Andreas Warnecke
> > <4ndreas.warne...@gmail.com <mailto:4ndreas.warne...@gmail.com>> wrote:
> >
> > Hi,
> >
> > Thanks for the reply. I'm just having the issue that even if I place
> > the code in a try statement the error output shows in the PyMOL
> > console, but the script proceeds anyhow.
> > Is there anyway of intercepting/silencing this output?
> >
> > Thanks,
> >
> > Andreas
> >
> > On Fri, Oct 3, 2014 at 1:46 PM, Tsjerk Wassenaar > <mailto:tsje...@gmail.com>> wrote:
> >
> > Hi Andreas,
> >
> > A try/except block is actually a very pythonic way of dealing
> > with such issues. You can catch the error with an except clause,
> > that allows executing some code in case the other thing didn't
> > work out. Make sure to only catch the error that is raised by
> > what you're trying, otherwise you may interfere with the normal
> > functioning of things (like catching a termination signal).
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Oct 3, 2014 at 1:35 PM, Andreas Warnecke
> > <4ndreas.warne...@gmail.com <mailto:4ndreas.warne...@gmail.com>>
> > wrote:
> >
> > Dear PyMOL users,
> >
> > I am wondering if there is any way of testing whether a
> > PyMOL version is open-source or incentive for use in
> > scripts. I'm thinking of something similar to
> > 'cmd.get_version()'.
> >
> > The reason for this is that I am e.g. using the 'alter'
> > command on custom properties in scripts, which is a feature
> > that may not be available in all PyMOL versions. At the
> > moment I avoid a crash by placing the code within a 'try'
> > statement, but this will yield an error message. If I could
> > actually test the incentive/open-source state this would
> > allow me to use an 'if' statement instead and avoid the
> > error message.
> >
> > I would welcome suggestions on how to approach this.
> >
> > Thanks,
> >
> > Andreas
> >
> >
>
> --
> > Meet PCI DSS 3.0 Compliance Requirements with EventLog
> Analyzer
> > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI
> > DSS Reports
> > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download
> > White paper
> > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog
> >
Re: [PyMOL] Testing for incentive vs. open-source in scripts
Hi,
interesting!
I noticed that using:
'print cmd.get_version()' in Python/PyMOL
vs.
'get_version' in PyMOL
yields two distinct outputs:
PyMOL>print cmd.get_version()
('1.7.0.5', 1.705, 1705, 1399913511,
'3070a0a1f405c02c919f62ea8bd67c5a55b0adfd', 0)
PyMOL>get_version
version: 1.7.0.5 (1.705) 1705, Incentive Product
So I assume there is a cryptic way of translating the latter entries into
Open-source vs. Incentive?
I also need to revise the script before (as it still buggy and fails in the
open() line ), but the idea is to intercept the output and simply not print
it.
Thanks for pointing this out,
Andreas
On Fri, Oct 3, 2014 at 3:18 PM, Gianluca Santoni
wrote:
> I get this output from cmd.get_version
>
> Open pymol:
>
> version: 1.7.0.0 (1.700) 1700, Open-Source
>
> Incentive pymol:
> version: 1.7 (1.700) 1700, Incentive Product
>
>
> You could ude this, or not?
>
> On 10/3/14 3:06 PM, Andreas Warnecke wrote:
>
>> Hi all,
>>
>> just to specify the issue: the problem is not the crash, because the
>> script continues due to the try statement. The issue is that PyMOL
>> handles and prints the exception from the 'alter' command into the
>> console. I would like to avoid that, either by testing incentive vs.
>> open-source, or by preventing PyMOL from printing the exception.
>>
>> The cmd.get_version() command can be used to test the version of PyMOL,
>> but does to my knowledge not give information on the
>> incentive/open-source build (?).
>>
>> It would be useful to have a way of testing this, though. Ideas anyone?
>>
>> Currently, I solved the issue with the printing like this now, but I
>> feel it is inferior to actually testing the incentive/open-source state:
>>
>> try:
>> originalstdout = sys.stdout # hijack the output
>> sys.stdout = sys.stdout = open('/dev/null', 'w') # dump
>> cmd.alter('...') # longer command omitted here - error usually
>> printed here
>> sys.stdout = originalstdout # reinstate the output
>> except: pass
>>
>> Thanks for the suggestions,
>>
>> Andreas
>>
>> On Fri, Oct 3, 2014 at 2:59 PM, Gianluca Santoni
>> mailto:gianluca.sant...@ibs.fr>> wrote:
>>
>> Version number is printed in the startup message, so it has to be
>> stored
>> somewere related to this function.
>>
>> On 10/3/14 2:23 PM, Tsjerk Wassenaar wrote:
>> > Hi Andreas,
>> >
>> > Ah, I think the problem is PyMOL handling the error. It probably
>> prints
>> > the exception and then continuous anyway. So it actually doesn't
>> allow
>> > you to catch it off. So you would indeed need to get access to the
>> > version. I don't know where that is stored from the top of my head.
>> > Maybe Thomas knows.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Fri, Oct 3, 2014 at 2:09 PM, Andreas Warnecke
>> > <4ndreas.warne...@gmail.com <mailto:4ndreas.warne...@gmail.com>
>> <mailto:4ndreas.warne...@gmail.com
>> <mailto:4ndreas.warne...@gmail.com>>> wrote:
>> >
>> > Hi,
>> >
>> > Thanks for the reply. I'm just having the issue that even if I
>> place
>> > the code in a try statement the error output shows in the PyMOL
>> > console, but the script proceeds anyhow.
>> > Is there anyway of intercepting/silencing this output?
>> >
>> > Thanks,
>> >
>> > Andreas
>> >
>> > On Fri, Oct 3, 2014 at 1:46 PM, Tsjerk Wassenaar <
>> tsje...@gmail.com <mailto:tsje...@gmail.com>
>> > <mailto:tsje...@gmail.com <mailto:tsje...@gmail.com>>> wrote:
>> >
>> > Hi Andreas,
>> >
>> > A try/except block is actually a very pythonic way of
>> dealing
>> > with such issues. You can catch the error with an except
>> clause,
>> > that allows executing some code in case the other thing
>> didn't
>> > work out. Make sure to only catch the error that is raised
>> by
>> > what you're trying, otherwise you may interfere with the
>> normal
>> > functioning of things (like catching a termination signal).
>> >
>> > Hope it helps,
&
Re: [PyMOL] CONECT table
Hi, It appears that the following: Select gluco, bound_to resn NDG Show sticks, gluco does not work. I'm not sure if the glycosylation is handled as a separate residue, but you could try: select glucoasp, byres (neighbor (resn NDG)) show sticks, glucoasp FYI: There are pages on selection algebra on the Pymol wiki that may give more inspiration. Hope this gets you started, /Andreas On Oct 7, 2014 10:02 PM, "Markus Heller" wrote: > D'uh. Thanks for pointing this out. > > Follow-up question: I want to show my glycosylated protein as cartoon, > with the glycosides *and* the side chains they're attached to shown in > sticks. How do I do that? > > I show the protein as cartoon: > > Load foo.pdb > Hide lines > As cartoon > > Then I select the glycosides > > Select gluco, resn NDG > Show sticks, gluco > > This only shows me the glycoside, but NOT the side chain it's attached to. > > I tried > > Select gluco, bound_to resn NDG > Show sticks, gluco > > But that doesn't work, shows no side chains. > > Any help much appreciated! > > Thanks and Cheers > Markus > > -Original Message- > From: David Hall [mailto:li...@cowsandmilk.net] > Sent: Monday, October 06, 2014 4:40 PM > To: Markus Heller > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] CONECT table > > http://www.pymolwiki.org/index.php/Connect_mode > > -David > > > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: > > > > Hello, > > > > How can I get PYMOL to use the CONECT table from a PDB file? My protein > is glycosylated, and I'd like to properly and automatically display the > glycosides including their linkage to the protein. > > > > Thanks and Cheers > > Markus > > > > -- > > Markus Heller, Ph.D. > > NMR Scientist > > CDRD - The Centre for Drug Research and Development > > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: > > (604) 827-1147 > > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | > > www.cdrd.ca > > > > > > > > > > > > > > Follow us: > > > > This email and any files transmitted with it are confidential and > intended solely for the addressee. If you are not the named addressee you > should not disseminate, distribute, copy, or alter this email. > > > > > > > > > > -- > > Slashdot TV. Videos for Nerds. Stuff that Matters. > > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. > > clktrk ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: > > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > -- > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] CONECT table
Oh, and it should be glucoasn, of course. :-P On Oct 8, 2014 1:26 AM, "Andreas Warnecke" <4ndreas.warne...@gmail.com> wrote: > Hi, > > It appears that the following: > Select gluco, bound_to resn NDG > Show sticks, gluco > > does not work. I'm not sure if the glycosylation is handled as a separate > residue, but you could try: > select glucoasp, byres (neighbor (resn NDG)) > show sticks, glucoasp > > FYI: There are pages on selection algebra on the Pymol wiki that may give > more inspiration. > > Hope this gets you started, > > /Andreas > On Oct 7, 2014 10:02 PM, "Markus Heller" wrote: > >> D'uh. Thanks for pointing this out. >> >> Follow-up question: I want to show my glycosylated protein as cartoon, >> with the glycosides *and* the side chains they're attached to shown in >> sticks. How do I do that? >> >> I show the protein as cartoon: >> >> Load foo.pdb >> Hide lines >> As cartoon >> >> Then I select the glycosides >> >> Select gluco, resn NDG >> Show sticks, gluco >> >> This only shows me the glycoside, but NOT the side chain it's attached to. >> >> I tried >> >> Select gluco, bound_to resn NDG >> Show sticks, gluco >> >> But that doesn't work, shows no side chains. >> >> Any help much appreciated! >> >> Thanks and Cheers >> Markus >> >> -Original Message- >> From: David Hall [mailto:li...@cowsandmilk.net] >> Sent: Monday, October 06, 2014 4:40 PM >> To: Markus Heller >> Cc: pymol-users@lists.sourceforge.net >> Subject: Re: [PyMOL] CONECT table >> >> http://www.pymolwiki.org/index.php/Connect_mode >> >> -David >> >> > On Oct 6, 2014, at 6:35 PM, Markus Heller wrote: >> > >> > Hello, >> > >> > How can I get PYMOL to use the CONECT table from a PDB file? My >> protein is glycosylated, and I'd like to properly and automatically display >> the glycosides including their linkage to the protein. >> > >> > Thanks and Cheers >> > Markus >> > >> > -- >> > Markus Heller, Ph.D. >> > NMR Scientist >> > CDRD - The Centre for Drug Research and Development >> > 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >> > (604) 827-1147 >> > Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | >> > www.cdrd.ca >> > >> > >> > >> > >> > >> > >> > Follow us: >> > >> > This email and any files transmitted with it are confidential and >> intended solely for the addressee. If you are not the named addressee you >> should not disseminate, distribute, copy, or alter this email. >> > >> > >> > >> > >> > -- >> > Slashdot TV. Videos for Nerds. Stuff that Matters. >> > http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. >> > clktrk ___ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: >> > http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> -- >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper >> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer >> >> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] set size nb_spheres
Hi Erica, I prefer to leave the vdw value untouched, as this may affect operations that rely on this value. Instead you can alter the sphere scale: set sphere_scale, , e.g.: set sphere_scale, 1.5, hetatm show_as spheres will increase the sphere scale of heteroatoms (i.e. non-bonded) to 1.5 Cheers, Andreas On Thu, Nov 20, 2014 at 3:41 PM, Matthew Baumgartner wrote: > Hi, > Just to chime in, you might need to call 'sort' and/or 'rebuild' after > using the alter command to see the changes. > Matt Baumgartner > > > On 11/20/2014 08:20 AM, Osvaldo Martin wrote: > > Hi Erica, > > I think something like: > > alter name ca, vdw=10 > > should help. Change "10" for the value you want. > > > Best Regards, > Osvaldo. > > On Wed, Nov 19, 2014 at 11:16 AM, Erica Valentini > wrote: > >> Dear all, >> >> I would like to change the size of nonbonded spheres. >> They are nonbonded c-alpha atoms not heteroatoms therefore I don't >> know how to specifically select them in order to change them. >> >> Thanks a lot in advance, >> >> Erica >> >> -- >> Erica Valentini >> >> EMBL-Hamburg >> Notkestrasse 85, >> +49 040 899 02 182 >> >> >> >> >> >> >> >> -- >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> >> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, > FREEhttp://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to build imedazole by using builder
Hi Surya, Using the interactive builder is usually the way to go. To get you started you may need a starting atom, which you could create using the pseudoatom command: http://www.pymolwiki.org/index.php/Pseudoatom Note that the builder has some templates, e.g. the cyclopendadiene that you can use and then replace carbons by nitogens. Another alternative is to make use of pre-existing structres, e.g. frag HIS will give you a histidine that you can edit using the "remove" command to work on the ring. You may want to rename some of the atoms though. This page has some general hints for structure editing: http://www.pymolwiki.org/index.php/Modeling_and_Editing_Structures Note that when you save non amino acid structures, PyMOL may not interpret them as intended if you save your imidazole in .pdb format. I recommend using .pkl format, as this will preserve information concerning double bonds etc. Cheers, Andreas On Sat, Nov 15, 2014 at 2:32 PM, Osvaldo Martin wrote: > Hi Surya, > > I don't know exactly what problem are you experiencing (I tried to do > something similar without any problem). I guess that maybe the problem is > that when you are rebuilding the ring, you are positioning the atoms in a > not very good position and maybe PyMOL is having trouble to figure-out the > connectivity. > > I think one possible solution is to optimize the geometry of the molecule > (before saving the pdb file) using the optimize plugin > http://www.pymolwiki.org/index.php/Optimize. This will give you the > correct bond angles and bond lenght and also will (hopefully) write the > correct connectivity to the pdb file. > > Best regards, > Osvaldo. > > > > On Sat, Nov 15, 2014 at 10:08 AM, Seera Suryanarayana > wrote: > >> Dear pymol users >> >> I have been trying to build imidazol ring to one incomplete His of my pdb >> file by using builder in pymol. After finishing this ring I saved and >> opened once again by pymol. I have seen some thing like mess formation with >> in the residues. I request you to tell me what could be the reason and how >> do I overcome it. >> >> Thanks in advance >> >> Surya >> Graduate student >> India. >> >> >> -- >> Comprehensive Server Monitoring with Site24x7. >> Monitor 10 servers for $9/Month. >> Get alerted through email, SMS, voice calls or mobile push notifications. >> Take corrective actions from your mobile device. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Goodsell colouring
Hi Jacob, I'm not familiar with "goodsell", but some selection algebra should be a solution: Try something like: util.cbaw # color by atom (white carbons) color grey80, chain B and elem C color grey70, chain C and elem C #... etc. There are also pymol wiki pages for coloring and selection algebra for reference. Hope this helps, Andreas On Dec 5, 2014 3:00 PM, "Jacob Lewis" wrote: > Hi, > > I am trying to colour a protein which is a hexamer using the “goodsell” > colouring method where by carbons are a light shade and all other atoms are > a darker shade, however I want to colour alternating subunits of the > hexamer for clarity. Is there a way of selecting two different carbon > colours on 2 separate chains? As well as colouring N, O and S in the same > way too? > > Any help would be greatly appreciated. > > Cheers, > > Jacob > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selection of a set of amino acids
Hi, There is a script available on the pymol wiki called "zero_residues". This will allow you to easily renumber any AA sequence. As far as other heteroatoms are concerned you could consider removing them (remove hetatm), or extract them into a second object. Another alternative is to simply adjust the coloring command according to the pdb. Hope that helps, Andreas On Dec 13, 2014 4:41 PM, "Alireza Kashani" wrote: > Dear All, > > I would like to colour different regions of a protein in different colour; > say region one, amino acid number 1 to 100 and region two amino acid 101 to > 150; However, when I look into a pdb file using pymol; by displaying the > residuals, I see the residue number 1, does not correspond to the first > amino acid; I assume, because of other atoms (metals, ions and etc). > > I was wondering if I should filter the pdb file, beforehand to be free > from these metals, or is there any command that I can put them away and > make a selection based on set of amino acids ? > > I appreciate your help, > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ray trace mode 1 playing up pymol 1.7.4?
Hi, This may also be related to the setting: ray_trace_mode Try: set ray_trace_mode, 0 This will deactivate outlines (ray_trace_color) during ray tracing. The wiki page has some examples. Cheers, Andreas On Dec 16, 2014 6:05 PM, "H. Adam Steinberg" wrote: > The thickness, or weight of the black outline is related to the size of > the viewport or the ray command. > > If you ray the image larger, the thickness of the black outline will be > greatly reduced. This will improve the clarity of colored sphere surface by > reducing the amount of black in those areas. > > I would try using surface instead of spheres to make the black outline > work in a more cleaner style. If you want to stick with spheres, remove the > black outline and use ambient occlusion lighting: > > set light_count,8set spec_count,1set shininess, 10set specular, 0.25set > ambient,0set direct,0set reflect,1.5set ray_shadow_decay_factor, 0.1set > ray_shadow_decay_range, 2 > unset depth_cue > > > > On Dec 15, 2014, at 4:33 AM, Jacob Lewis wrote: > > Hi, > > I have a very complicated image to render in pymol and everytime I go to > render it in colour with a black outline in spheres I get the render below > whereby all the spheres have messing black lines in them? How do I > circumvent this? > > > Cheers, > > Jacob > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Phosphoserine
Hi Monica, You can check out the plugin PyTMs, which allows you to introduce PTMs into protein models within PyMOL: http://www.pymolwiki.org/index.php/Pytms Let me know should you need any assistance with this plugin. Cheers, Andreas On Fri, Jan 30, 2015 at 4:59 PM, Monica Mittal wrote: > Hi, > > Does any one know if there is a simple way to mutate a serine to a > phosphoserine using pymol? Or what would be the best way to achieve this? > > Thanks > > Monica > > > > -- > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol wiki search is not working
Hej, While its not perfect I usually end up using google search and adding 'pymol wiki' to the search terms. Works for me. Cheers, Andreas On Feb 4, 2015 2:50 PM, "Matthew Baumgartner" wrote: > Yes, I've been having this problem for a while. > I contacted Jason Vertrees about it a while ago, but never heard back from > him. > > However, when I search "color" (an exact article title) I actually do go > to the page. > > In addition, if you search for a something that doesn't have a page in the > search bar at the top, like "colors" no hits are returned like Justin > mentioned. This brings up another search box in the middle of the page. I > do not get any results when searching for any term in this box, even exact > article titles. > > > Matt > > On 02/04/2015 04:08 AM, Justin Lecher wrote: > > Hi everyone, > > is it just me or is the pymol wiki search broken? > > Simple search for e.g. "color" doesn't yield anything. Only if there is a page > with exactly the search term as name, you will get a hit. > > In other wikis you will get also hit for search term inside the article as it > was before also in the Pymol wiki. > > Could this be fixed? > > thanks, > > Justin > > > > > -- > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > > > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > -- > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Printing Protein Surface residues
Hej,
depends on what you want, single atoms or residues. You can output the
available surface are for every atom and then decide which ones are
accessible based on your cutoff stringency.
Here is some code that will print the info in PyMOL, alternatively you
could modify it to print to a file instead, but copy-paste to EXCEL works
fine.
# Object list
objectlist=cmd.get_object_list()
# Calculate area:
python
cmd.set('dot_solvent',1)
for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
# this writes the area into the b-factor field
python end
# print info
print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
Then, in EXCEL you can use the data (sort/filter) to figure out which atoms
are most exposed, or above a set threshold.
Hope this is useful,
Andreas
On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
vinod.devar...@schrodinger.com> wrote:
> Hi All
>
> I have a task in hand where need your suggestions and comments
>
> Task is to print list of solvent exposed surface amino acids or protein
> surface amino acids .
>
> By searching I had found this script
> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>
> which select the residues on the surface but I dont know
>
> how to print the residues names as an output ?
>
> Thanks in advance ...
>
> --
> Please feel free to call me or mail me
>
> Thanks and Regards
>
> Vinod.D M.Pharm.
> Jr. Applications Scientist
> Mobile no:+91-9900090044
>
> http://www.schrodinger.com/
>
>
>
> --
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>
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Re: [PyMOL] Printing Protein Surface residues
Hej,
Just a minor amendment:
the line
for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
will treat heteroatoms etc. as part of the area calculation and may thus
affect the calculation of available surface area.
To ignore heteroatams, remove them before, or change the line to:
for obj in objectlist: cmd.get_area(selection='%s and not hetatm'%obj,
load_b=1)
In the latter case the area will not be calculated for the heteroatoms (b
will be b-factor still), but also they will not be considered when
calculating area for the other atoms.
It is also possible to run both lines sequentually, but usually one doesn't
care for the heteroatoms.
This is just to avoid potential influences by surrounding waters, or other
stuff.
Cheers,
Andreas
On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke <
4ndreas.warne...@gmail.com> wrote:
> Hej,
>
> depends on what you want, single atoms or residues. You can output the
> available surface are for every atom and then decide which ones are
> accessible based on your cutoff stringency.
> Here is some code that will print the info in PyMOL, alternatively you
> could modify it to print to a file instead, but copy-paste to EXCEL works
> fine.
>
> # Object list
> objectlist=cmd.get_object_list()
>
> # Calculate area:
> python
> cmd.set('dot_solvent',1)
> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
> # this writes the area into the b-factor field
> python end
>
> # print info
> print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
> cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
>
> Then, in EXCEL you can use the data (sort/filter) to figure out which
> atoms are most exposed, or above a set threshold.
>
> Hope this is useful,
>
> Andreas
>
>
> On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
> vinod.devar...@schrodinger.com> wrote:
>
>> Hi All
>>
>> I have a task in hand where need your suggestions and comments
>>
>> Task is to print list of solvent exposed surface amino acids or protein
>> surface amino acids .
>>
>> By searching I had found this script
>> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>>
>> which select the residues on the surface but I dont know
>>
>> how to print the residues names as an output ?
>>
>> Thanks in advance ...
>>
>> --
>> Please feel free to call me or mail me
>>
>> Thanks and Regards
>>
>> Vinod.D M.Pharm.
>> Jr. Applications Scientist
>> Mobile no:+91-9900090044
>>
>> http://www.schrodinger.com/
>>
>>
>>
>> --
>> One dashboard for servers and applications across Physical-Virtual-Cloud
>> Widest out-of-the-box monitoring support with 50+ applications
>> Performance metrics, stats and reports that give you Actionable Insights
>> Deep dive visibility with transaction tracing using APM Insight.
>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
--
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Re: [PyMOL] Viewing Electrostatic Potential maps for multimeric complexes
You could try to split the states and subunits in PyMOL, then save them as individual .pdb's and then use those to generate multuple .dx files. On Jun 8, 2015 2:38 AM, "Rahul Sheth" wrote: > Hello, > > I am new to using PyMol. I wanted to see the electrostatic potential map > for a multimeric protein complex (Viral particle). The problem is that when > I generate the .dx file from pdb2pqr server and open it in PyMol, only one > unit (monomer) gets colored by the electrostatic potentials and the other > units do not. I can see the entire complex using split_states command but > the EP maps color only one unit. Is there a way to generate electrostatic > potentials for the entire complex? > Would appreciate any help on this! > > Thanks! > > > -- > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Pymol for inorganic chemists - dealing with bonds
Hej Henrique, not an inorganic chemist here, but some suggestions anyway: Metallic centers should be displayable as spheres using the *show*, or *show_as spheres* commands. The radius can be altered using: *set sphere_scale, value, selection* The bonds are more problematic. Pymol has some options for editing bonds, but a display as dotted line doesn't exist as such to my knowledge (maybe something to expand on in future PyMOL versions?). What you could try is to use distance objects instead, but depending on the complexity of the model this may be applicable, or not. Note that you may have to unbond the metallic center to remove any existing PyMOL bonds for the display. http://pymolwiki.org/index.php/Distance The distance objects can be colored and there are several settings related to dashes, e.g. radius, shapes, gaps etc. etc (use the settings-->edit all--> and filter by "dash"). Hope this may help, otherwise there may be other approaches, Cheers, Andreas On Thu, Nov 19, 2015 at 3:54 PM, Henrique C. S. Junior < henrique...@gmail.com> wrote: > Dear Pymol users, > As an inorganic chemist, to represent metallic centers and ligands in a > comprehensive way is very important. I've tried to select my metallic > centers and the atoms bonded directly to them, change this selection to > ball and stick and keep all the rest as wireframe. Some bonds changed to > sticks, some others not (and they are not changing, even if I try again). > What I want to do is this: > * Represent my metallic centers as spheres (maybe tweaking the radius a > little) > * Change bonds directly connected to my metallic centers to dashes or dots > (and change the colors of this dashes/dots if possible). > Any help is much appreciated. > > -- > *Henrique C. S. Junior* > Químico Industrial - UFRRJ > Mestrando em Química Inorgânica - UFRRJ > Centro de Processamento de Dados - PMP > > > -- > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Electrostatic Map for a molecule containing a citrulline
Dear all, a colleague is interested in generating an electrostatic map of a protein containing a citrulline. Does anybody have any experience with this and could recommend any approach? Cheers, Andreas -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Selective valency on bond
The easiest way to deal with this is setting the valence or valence_mode individually for the object. set valence, 0, object1 set valence, 1, object2 Cheers, Andreas On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick wrote: > Dear PyMol users, > > I have a crystal structure of my protein with an unnatural amino acid > present. This amino acid has a double bond within it, which I would like to > display as such. However I would like the surrounding protein side chains > to not show double bond character. Is this possible at all? > > So far, I can either keep valence mode set to '0' and see no double bonds > across the whole protein, or set to '1' and see all of the double bonds, > which I don't want. > > My question is, is it possible to selectively 'set valency' onto a single > bond, or is it a global command which is not capable of this fine-tuning? I > am using MacPyMol if this makes a difference at all? > > Thanks for your help, > Patrick > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Detecting holes/cavities in surface
I haven't used it before, but I there is a PyMOL plugin called KVfinder that detects cavities. Potentially this offers an approach for you. On Jul 20, 2016 12:05 AM, "Daniel James" wrote: > Hi all, > > I haven't used this list before but can't find an answer to my question > elsewhere. I am selecting the antibody binding site automatically to > calculate the surface area of the binding sites. > > However, some of the binding sites have holes/cavities in the surface - I > would like to be able to detect if a surface has a hole in it on PyMol (to > make a note that it needs to be looked at manually). > > I create an object of the antigen binding site, show surface and then use > get_area to get SASA. > > Any help will be appreciated. > > Thanks, > Daniel > > > -- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Coordinates of an atom
Hej,
try this command and specify the atom selection:
cmd.get_atom_coords('atom selection')
see also:
https://pymolwiki.org/index.php/Get_Coordinates_I
Cheers,
Andreas
On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:
> Hi all,
>
>
>
> Can anyone please help me in how to get coordinates of a selected atom or
> residue?
>
>
>
> Thank you
>
>
>
> Mohsen
>
>
> --
>
> ___
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Re: [PyMOL] PyTMs
Hej Raag,
my name is Andreas and I wrote PyTMs back for my PhD. It essentially uses
PyMOLs basic editing functions to build PTMs onto protein models.
PyTMs is a simple tool and has its clear restrictions, but generally it is
nice to play around with and explore hypotheses with.
The challenge is that drawing conclusions about the impact of PTM on
tertiary structure is very limited and that there will be increasing
uncertainty about positioning of atoms the larger the PTM is. Also charge
effects are an issue and overall one will increasingly be confronted
with questions regarding Molecular Dynamics.
As far as your project is concerned you can rather easily add a Tyrosine
(or custom fragments) using the builder in PyMOL:
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures
In editing mode, you can select an atom to extend on and manually select:
*build-->residue *from the menu
Additionally I'd also point out the API command to experiment with:
editor.attach_amino_acid("pk1","tyr")
If you have any questions about the editing or PyTMs feel free to PM me.
Unfortunately, I can't promise to update the plugin unless I find the spare
time to invest.
Cheers,
Andreas
On Wed, Apr 12, 2017 at 9:36 AM, Raag Saluja wrote:
> Hi!
>
> PyTMs is wonderful and permits me to really play around with a lot of
> different PTMs!
>
> In PyTMs, I can find some of the PTMs that I need to work on (acetylation
> and phosphorylation) for my PhD. However, there are some PTMs that I need
> to work on for my PhD, but I can't find those features in PyTMs. I need to
> study (1) tyrosination/detyrosination, polyglutamylation and
> polyglycylation and (2) PTMs on the C-termini. How do I go about those?
>
> This might sound like I'm asking too much, but can you please include
> these in PyTMs as well? PyTMs is really user friendly. It would be
> wonderful if you can please do that!
>
> Regards,
> Raag
>
>
> --
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Re: [PyMOL] Enable selected atoms of disabled object
Hej, a disabled object will not show any display, but you can easily work with selections, provided that a selection is defined. Try something like: hide everything object show sticks selection Cheers, Andreas On Jun 19, 2017 6:00 AM, "Vijay Masand" wrote: > Dear All, > With the help of internal GUI, we can disable the appearance of an > object,however we can still operate on the representations of objects > that are disabled, even with the commands show and hide. The results > are apparent only when we subsequently enable the object. > Is there any way to enable selected atoms of disabled object? I mean > is there is method to visualize selected atoms even when the the > object is not visible in PyMOL's viewer area. > Cheers > Vijay > > -- > Assistant Professor > Department of Chemistry, > Vidya Bharati College, Amravati, 444 602 > Maharashtra, India. > Phone number- +91-9403312628 > https://sites.google.com/site/vijaymasand/ > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
