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
he 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 o
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
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 ca
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,
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 t
-- 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
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.
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
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 m
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/in
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
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
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".
Ei
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
gt; > 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, A
0) 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 th
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
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
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
Che
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
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 algebr
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 adjus
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 bl
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:
>
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,
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 inst
le 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,
&g
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 pro
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 option
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 In
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 wit
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 selec
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
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 t
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 inte
36 matches
Mail list logo
