Re: [PyMOL] Display coordinate vectors

[Hongbo Zhu]

Hi, Martin,

how about this:
http://www.pymolwiki.org/index.php/Symmetry_Axis

also check out the script drawing X, Y, and Z reference axes by Robert:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py

hope it helps,
hongbo

On 04/08/2011 04:29 PM, Martin Hediger wrote:
> Dear all
> I'm sure this question was answered before, but I could not find
> anything related to it in neither the mail list nor on the Wiki.
> Is it possible to display something like coordinate vectors in PyMOL?
> I.e. arrows in the 3d view space pointing towards [1,0,0], [0,1,0] and
> [0,0,1]?
>
> I would like to illustrate the alignment of the principal axes of a
> protein with the coordinate system.
>
> Kind regards and thank you for answers.
> Martin Hediger
>
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Re: [PyMOL] How to color in a different way different helix types?

[Hongbo Zhu]

Hi, if anybody is still interested in the topic, I have made a DSSP 
plugin for running DSSP and coloring proteins according to the DSSP 
secondary structure assignment. Please have a look at:

http://www.pymolwiki.org/index.php/DSSP

This plugin invokes DSSP (presuming you already have DSSP binary on your 
hard drive) and reads the output using BioPython. It then makes several 
selections, each for a kind of secondary structure elements (SSE) if 
there is at least one residue in the input selection is assigned with 
the SSE.

regards,
hongbo

On 04/06/2011 04:34 PM, H. Adam Steinberg wrote:
> Hi Ramiro,
>
> Like you, I would love to see secondary structure colored by helix type.
> Jmol however does not show this as a default. Do you know what steps you
> took to get Jmol to show secondary structure colored by helix type?
>
> I can't seem to find that setting in any of the menu options.
>
> style/scheme/cartoon
> color/structure/cartoon/By Scheme/Secondary Structure
>
> This shows all of the helices in the same color.
>
> Adam
>
>
> On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote:
>
>> Hi and thanks for reading this.
>>
>> I have googled for a way to achieve what I want and have gone through
>> the wiki, to no avail.
>>
>> I would like to color in a different way the different helix types:
>> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>> distinct colors for each type by default. But if the same pdb file is
>> open with PyMOL all helices are treated the same way. Can't PyMOL
>> distinguish helix types?
>>
>> Thanks in advance,
>> Ramiro Téllez Sanz
>> Dept. Physical Chemistry
>> University of Almeria
>> Spain
>>
>> --
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Re: [PyMOL] How to color in a different way different helix types?

[Hongbo Zhu]

Hi, Jason and Thomas,

Thank you for your interest and suggestions!

The plugin has been updated s.t. it now also recognizes objects. The 
support for single-word selectors ('polymer', 'all', etc) is also added. 
Thanks again for the feedback!

best regards,
hongbo

On 04/12/2011 05:16 PM, Thomas Holder wrote:
> Hi Hongbo,
>
> very nice!
>
> Your plugin only accepts named selections, predefined selections like
> (all), (polymer) or object names do not work. Could you change this?
>
> Cheers,
>    Thomas
>
> On Tue, Apr 12, 2011 at 4:22 PM, Hongbo Zhu
>   wrote:
>> Hi, if anybody is still interested in the topic, I have made a DSSP
>> plugin for running DSSP and coloring proteins according to the DSSP
>> secondary structure assignment. Please have a look at:
>>
>> http://www.pymolwiki.org/index.php/DSSP
>>
>> This plugin invokes DSSP (presuming you already have DSSP binary on your
>> hard drive) and reads the output using BioPython. It then makes several
>> selections, each for a kind of secondary structure elements (SSE) if
>> there is at least one residue in the input selection is assigned with
>> the SSE.
>>
>> regards,
>> hongbo
>

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Re: [PyMOL] How to color in a different way different helix types?

[Hongbo Zhu]

Hi,

just for your information, the "DSSP plugin for PyMOL" has been updated 
to "DSSP & Stride plugin for PyMOL" :-)

The plugin generates a selection for each SSE type assigned by DSSP or 
Stride. Using the brilliant "copy to object" function of PyMOL, you can 
make two copies of protein fragments of the same SSE defined by DSSP and 
Stride respectively and compare them visually !

The plugin also accepts (correct) PyMOL selection expressions as input 
beside selection/object names. Thanks for Thomas Holder for the suggestion!

Your feedback and suggestions are always welcome!
cheers,hongbo

On 04/12/2011 04:22 PM, Hongbo Zhu wrote:
> Hi, if anybody is still interested in the topic, I have made a DSSP
> plugin for running DSSP and coloring proteins according to the DSSP
> secondary structure assignment. Please have a look at:
>
> http://www.pymolwiki.org/index.php/DSSP
>
> This plugin invokes DSSP (presuming you already have DSSP binary on your
> hard drive) and reads the output using BioPython. It then makes several
> selections, each for a kind of secondary structure elements (SSE) if
> there is at least one residue in the input selection is assigned with
> the SSE.
>
> regards,
> hongbo
>
> On 04/06/2011 04:34 PM, H. Adam Steinberg wrote:
>> Hi Ramiro,
>>
>> Like you, I would love to see secondary structure colored by helix type.
>> Jmol however does not show this as a default. Do you know what steps you
>> took to get Jmol to show secondary structure colored by helix type?
>>
>> I can't seem to find that setting in any of the menu options.
>>
>> style/scheme/cartoon
>> color/structure/cartoon/By Scheme/Secondary Structure
>>
>> This shows all of the helices in the same color.
>>
>> Adam
>>
-- 
Hongbo ZHU
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
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Re: [PyMOL] Get Protein Dimension

[Hongbo Zhu]

you can write your own loop in python to implement the function.

fh = open(pdbfilename)
coords = 
numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])] 
for line in fh.readlines() if line.startswith('ATOM  ') or 
line.startswith('HETATM')])
fh.close()
extent = (numpy.min(coords,axis=0), numpy.max(coords,axis=0))

or course the code needs to be tuned if you need only the first MODEL or 
only the first alternate position etc.

cheers,hongbo

On 04/26/2011 01:40 PM, Martin Hediger wrote:
> Dear all
>
> I found that PyMOL offer the cmd.get_extent('protein') function, which
> returns the dimensions of the selection.
> Is it complicated to make this function available from within an
> ordinary Pythonscript?
>
> Thanks for hints.
> Martin
>
>
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Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

[Hongbo Zhu]

Hi, Harry,

I am curious. How do you merge objects resulting from >>distance<< ? Do 
you mean to "group" them? If so, you can use ungroup command to, well, 
ungroup them. But if the merged object is generated using a CGO, I doubt 
you can unmerge the CGO object. But I don't know dash CGOs, either. 
(Unless you make dashes using small line fragments :)

So do you have dashes or solid lines? Do you see a plus sign before the 
object in PyMOL?

hongbo

On 04/26/2011 11:47 AM, Harry Jubb wrote:
> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL 
> session files  which show inter-molecular interactions using PyMOL distance 
> objects. These were created using a script which colours each distance object 
> and merges them according to type of interaction. The problem I'm having is 
> that I would prefer to visualise the interactions on a per-residue basis, 
> i.e. showing all the interactions for one or more residues but not the 
> others, but as the dashes are merged by interaction type I can only hide by 
> that category. Extensive Googling has not led me to a solution to select and 
> hide individual dashes that are merged into one UI object, so I'd like to ask 
> if it is possible to do this? I'm unfortunately no longer able to run the 
> script again (I am at the end of a time limited project and am preparing 
> figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to 
> select and/or hide individual distance objects in a pymol session after they 
> have been merged into one object. Un-merging them would also be an attractive 
> solution.
>
> Thanks,
>
> Harry
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Re: [PyMOL] Downloading the biological assembly from the PDB

[Hongbo Zhu]

Yes, great trick:

fetch 1avd, type=pdb1

On 05/03/2011 10:22 PM, li...@cowsandmilk.net wrote:
> http://www.rcsb.org/pdb/files/1avd.pdb1
>
> The key is adding 1 to the suffix.  Sometimes there is more than one 
> biological unit, in which case, there is a pdb2, pdb3, etc.
>
> -David
>
> On May 3, 2011, at 4:00 PM, Martin Hediger  wrote:
>
>> Dear all
>> I would like to ask how it is possible to download the coordinate file
>> for the biological assembly of a protein structure from the PDB.
>> Naturally, this is not a question directly related to PyMOL, but I
>> thought I'll be reaching at least a couple of
>> Biochemists/Chrystallographers who know how to do this.
>> As an example, when downloading the PDB file of "1AVD", I get a file
>> with two chains. The biological assembly would be a tetramer, so I
>> wonder what URL I would require to write into a script that does the
>> downloading.
>>
>> Thanks for help on this.
>> Martin
>>
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Structural Bioinformatics

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Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
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Re: [PyMOL] glycan surface

[Hongbo Zhu]

other people recently asked about the ligand surface, and Jason gave the 
following answer on 02 Apr. Hope it is also helpful to your glycan case.

-

Hi Peter,

In order to do this you either need to extract the ligand to its own
object or unset the ignore flag on "rep surface".  That is,

# fetch the protein

fetch 1rg7, async=0

# show surface
show surface, resn MTX

# do not ignore surfacing of ligands

flag ignore, not rep surface

# force PyMOL to rebuild the surface

rebuild

Cheers,

-- Jason

On 05.05.2011 9:22, Yamei Yu wrote:

Hi all,

  I want to display the surface of my structure with pymol. The 
problem is that it automatically excludes all the glycans. Does 
anybody know the method to solve this problem?

Thank you very much!
yamei


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Re: [PyMOL] how to load two separate pdb files simultaneously

[Hongbo Zhu]

In one PyMOL instance you can load many structures. They can be load 
into different objects, or different states of the same object.

If you mean using one command line to load multiple structures, since 
its grammar is very similar to python, I think you can always use 
semicolon to separate two commands:

fetch 1A00; fetch 1A07

this command will load both 1A00 and 1A07, but one after the other, not 
simultaneously.

On 06/29/2011 03:07 PM, leila karami wrote:
> Daer users
>
> I want to know how to load two separate pdb files simultaneously.
>
> any help will highly appreciated.
>
>
> --
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>
>
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
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Re: [PyMOL] how to load two separate pdb files simultaneously

[Hongbo Zhu]

this also works:

fetch 1A00 or 1A07 or 1A08

but not:
load 1A00 or 1A07 or 1A08


On 06/29/2011 03:07 PM, leila karami wrote:
> Daer users
>
> I want to know how to load two separate pdb files simultaneously.
>
> any help will highly appreciated.
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
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-- 
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
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01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
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Re: [PyMOL] how to load two separate pdb files simultaneously

[Hongbo Zhu]

would python module multiprocessing meet your need?
is that simultaneity the kind of simultaneity you want?

On 06/29/2011 03:36 PM, leila karami wrote:
> Dear Hongbo
>
> very thanks for your attention.
>
> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not
> help me.
> I need to load two separate pdb files simultaneously.
>
>
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
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-- 
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Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

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Re: [PyMOL] how to load two separate pdb files simultaneously

[Hongbo Zhu]

for local files, apart from using load:

load pdb1; load pdb2; load pdb3; load pdbN

there is another shortcut: you put all the PDB files you need to load in 
the fetch_path of pymol. To find out the current fetch_path, use command:

get fetch_path

Then you can simply load all pdb at once using:

fetch pdb1 pdb2 pdb3 pdb4 pdbN



On 06/29/2011 03:56 PM, Hongbo Zhu wrote:
> would python module multiprocessing meet your need?
> is that simultaneity the kind of simultaneity you want?
>
> On 06/29/2011 03:36 PM, leila karami wrote:
>> Dear Hongbo
>>
>> very thanks for your attention.
>>
>> None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not
>> help me.
>> I need to load two separate pdb files simultaneously.
>>
>>
>>
>>
>> --
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
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>>
>>
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Re: [PyMOL] Help for surface coloring

[Hongbo Zhu]

I have a slightly different answer using (almost:) only PyMOL commands:

# take 1acb as example
fetch 1acb, async=0
import numpy
# center is [x0,y0,z0]
x0,y0,z0=[1,2,3]
alldist = []
iterate_state 1,  1acb, 
alldist.append(numpy.sqrt(numpy.sum([(x-x0)**2,(y-y0)**2,(z-z0)**2])))

# assign dist to b-factors!
di = iter(alldist)
alter 1acb, b=di.next()
spectrum b, rainbow, 1acb

The distance computation line is awkward. I thought of using distance() 
command to replace it. It is also much faster to use distance(). But I 
failed to dig distance values out of the object generated by distance(). 
Anybody knows how to do that?


cheers,hongbo

On 28.07.2011 5:06, Thomas Holder wrote:

Hi Robert,

you can set the distance between each atom and the center as b-factor, 
and then use spectrum (or spectrumany [1]) for coloring.


I wrote a small python script that will do that, see attachment.

Example (in PyMOL command line):

run distancecoloring.py
centerdistance2b (all)
spectrum b, blue_white_red, (all)

Cheers,
  Thomas

[1] http://pymolwiki.org/index.php/Spectrumany

On 07/28/2011 04:29 PM, Muench, Robert wrote:

Dear community,

I was searching the internet for several days now to find out how to
perform a distance dependent coloring in pymol.

The idea is to color the surface of a viral (spherical) structure. I
would like to define the xyz-coordinates of the center of the viral
structure an color all residues with a gradient depending on the
distance from these xyz coordinates.

Can anyone please help me out?

All the best

Robert

*Robert Münch***

-

Dipl. Biologist / PhD-Student

*Paul-Ehrlich-Institut*

Federal Institute for Vaccines and Biomedicines

Division of Medical Biotechnology

Section 6/5 - Viral Gene Transfer Medicinal Products

63225 Langen, Germany

Phone: +49-6103-77-4222

Fax: +49-6103-77-1255



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Re: [PyMOL] regarding the dssp plugins

[Hongbo Zhu]

I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In 
my case, secondary structures are calculated for all the 10 states of 
2LE0. The plugin can also update color and secondary structures for all 
the 10 states of the NMR structure. I did not have to choose one state 
and run, and the next state.

I tested the plugin under both Ubuntu and Windows 7.
Maybe I misunderstood your question?
regards,
hongbo

On 16.09.2011 5:45, lina wrote:

Hi,

a quick question,

how can update the ss for all states, not check one by one,

and run dssp and update ...

Thanks for any advice,

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Re: [PyMOL] regarding the dssp plugins

[Hongbo Zhu]

Hi, Lina,

I did not understand your question correctly. Now it is fixed. Try the 
new version on my page. It works for me for 2LE0 and your try.pse.

You still have to use "split_state"  to split your structure into 
different objects. Then you can specify these objects using wildcard to 
the DSSP plugin. The plugin will invoke DSSP to assign secondary 
structures for each object in your specified input.

hongbo zhu

On 19.10.2011 4:15, lina wrote:
> On Wed, Oct 19, 2011 at 6:43 PM, Hongbo Zhu
>   wrote:
>> I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In my
>> case, secondary structures are calculated for all the 10 states of 2LE0. The
>> plugin can also update color and secondary structures for all the 10 states
>> of the NMR structure. I did not have to choose one state and run, and the
>> next state.
> might my pdb file reason?
>
> you may try:
>
> https://docs.google.com/leaf?id=0B93SVRfpVVg3NGY4MzkwZTQtNmIzMC00ZjkzLTkxMzEtZWIyMmNlYmE0OWQ0&hl=en_GB
>
>> I tested the plugin under both Ubuntu and Windows 7.
>> Maybe I misunderstood your question?
>> regards,
> Thanks,
>> hongbo
>>
>> On 16.09.2011 5:45, lina wrote:
>>
>> Hi,
>>
>> a quick question,
>>
>> how can update the ss for all states, not check one by one,
>>
>> and run dssp and update ...
>>
>> Thanks for any advice,
>>
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>>
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>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
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>>
> --
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> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] msms_pymol.py

[Hongbo Zhu]

Hi, sujuan,

Robert provides a rich collection of pymol plugins. I myself benefit a 
lot from the collection.

For using msms, you can have a try of my alternative to Robert's 
msms_pymol.py at:
http://www.biotec.tu-dresden.de/~hongboz/pymol_script/msms_pymol.py

It has a graphical user interface. You can install it from PyMOL menu 
Plugin-->Manage Plugins-->Install. You can use the plugin to invoke MSMS 
for either a pdb file or a selection in PyMOL. It has been tested on 
PyMOL 0.98 and 1.20.

best regards,
Hongbo Zhu



Hi Sujuan, Given that this is my script, I'll answer. :) On Tue, 11 May 
2010 14:38:52 +0800 sujuan wang  wrote:
 > > Hi All,
 > > When i run the script download from
 > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/, I issue the 
commond:
 > > calc_msms_area 2mlt-melittin, there are always something wrong as 
follows:
 > >
 > > CmdLoad: "D:/singapore-NTU/HU/modelling/2MLT-melittin.pdb" loaded as
 > > "2MLT-melittin".
 > > PyMOL>run C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py
 > > PyMOL>calc_msms_area 2MLT-melittin
 > > Traceback (most recent call last):
 > >   File "C:\Program Files\DeLano 
Scientific\PyMOL/modules\pymol\parser.py",
 > > line 250, in parse
 > > self.result=apply(layer.kw[0],layer.args,layer.kw_args)
 > >   File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", 
line 281,
 > > in calc_msms_area
 > > volume,area_dict,tmp_msms_vert_file,tmp_msms_face_file =
 > > calc_msms(object_name,probe,density,keep,debug)
 > >   File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", 
line 131,
 > > in calc_msms
 > > convert_pdb_to_xyzrn(tmp_pdb_file,tmp_xyzrn_file,atmnumbers_file)
 > >   File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", 
line 21, in
 > > convert_pdb_to_xyzrn
 > > lines = open(numfile).readlines()
 > > IOError: [Errno 2] No such file or directory: ''
 > >
 > > who can give me an example of this command? or something needed to 
change
 > > the option of script?
It appears that the program is unable to find the file containing the atom
type numbers.  This should be a file called "atmtypenumbers" that comes with
the msms program -- they are all in the one .zip file. My script attempts to
find this file wherever your msms.exe program is installed.

If you need further assistance, let me know.

Cheers,
Rob

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Re: [PyMOL] PyMOL-users Digest, Vol 48, Issue 6

[Hongbo Zhu]

or, you can simply write the coordinates to a file in PDB format and 
load it in PyMOL.

According to my experience, this way is more flexible and you can 
manipulate the cloud easily. For example, you can change the color of 
the cloud, or show it as spheres of different radii. But for a cgo, you 
can not change its color on the fly.

best,
Hongbo Zhu

On 05/11/2010 04:49 PM, pymol-users-requ...@lists.sourceforge.net wrote:
> Message: 3
> Date: Tue, 11 May 2010 09:04:51 -0400
> From: Jason Vertrees
> Subject: Re: [PyMOL] drawing a cloud of points?
> To: Jose Borreguero
> Cc: pymol mailing list
> Message-ID:
>   
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jose,
>
> Depending on the number of points you could (1) create CGO objects for
> each; (2) use the pseudoatom command supplying the "pos" parameter for
> each particle.  For more info check out
> http://www.pymolwiki.org/index.php/Pseudoatom  and
> http://pymol.sourceforge.net/newman/user/S0500cgo.html  for starters.
>
> Cheers,
>
> -- Jason

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Re: [PyMOL] msms_pymol.py

[Hongbo Zhu]

You can solve it by adding the following line in the msms_pymol.py you 
downloaded from Robert's page to line 133, right before msms_cmd is defined.


if msms_path.startswith('C:/'): msms_path = '\"%s\"' % (msms_path,)

Basically, your problem was caused by the whitespace in the path to the 
MSMS executable file in Windows systems. By adding quotes to the full 
path solves the problem.


regards,
hongbo

On 5/12/2010 1:00 PM, sujuan wang wrote:

Dear Robert,
I downloaded the msms  2.6.1 from 
http://mgltools.scripps.edu/downloads#msms and installed into 
C:\Program Files\MSMS. But there are still something wrong after 
running the script:

There seems to be a problem with the msms output

Traceback (most recent call last):
  File "C:\Program Files\DeLano 
Scientific\PyMOL/modules\pymol\parser.py", line 250, in parse
self.result=apply(layer.kw 
[0],layer.args,layer.kw_args)
  File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", line 
282, in calc_msms_area
volume,area_dict,tmp_msms_vert_file,tmp_msms_face_file = 
calc_msms(object_name,probe,density,keep,debug)
  File "C:/Program Files/DeLano Scientific/PyMOL/msms_pymol.py", line 
159, in calc_msms

sys.exit(1)
SystemExit: 1
My pymol version is 1.1r1 with python 2.4.2 (#67, Sep 28 2005, 
12:41:11) [MSC v.1310 32 bit (Intel)]

As a beginner of pymol, thank you for your kindly help.
regards
Sujuan


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Re: [PyMOL] Fwd: What is the difference between Atom ID and Index

[Hongbo Zhu]

ID is the >>external-index-number<<, which is parsed from columns 7-11 
of the PDB file (Atom serial number).
Try pymol command:
select id 110

RANK is the order of the atoms as they are listed in the PDB file 
(0-based). Therefore, the nitrogen is at rank 11 (line 12).
Try pymol command:
select rank 11

INDEX is the >>internal-index-number<< of the atom. Obviously, the atoms 
get their internal indices based on their names as atoms of the same 
name are grouped together.
Try pymol command:
select index 1

PyMOL suggests that
" Atom indices are fragile and will change as atoms are added
   or deleted.  Whenever possible, use integral atom identifiers
   instead of indices. "


I suppose you should use >>RANK<<, if you like to "find a way to get the 
'linenumber-dependent' index of an atom".

cheers,
Hongbo Zhu


On 11/01/2010 10:02 AM, Martin Hediger wrote:
> Hi Tsjerk,
> I am still wondering about how the numbering is done.
> Given a PDB file looking like this (some random molecule):
>
> HETATM 1 C LIG 1 -4.242 2.555 -0.814 1.00 0.00 C
> HETATM 2 C LIG 1 -2.736 2.361 -0.665 1.00 0.00 C
> HETATM 3 H LIG 1 -4.461 3.588 -1.106 1.00 0.00 H
> HETATM 4 C LIG 1 -4.961 2.214 0.487 1.00 0.00 C
> HETATM 5 H LIG 1 -4.615 1.908 -1.617 1.00 0.00 H
> HETATM 6 H LIG 1 -2.333 3.133 0.004 1.00 0.00 H
> HETATM 7 H LIG 1 -2.247 2.493 -1.637 1.00 0.00 H
> HETATM 8 C LIG 1 -2.409 0.977 -0.105 1.00 0.00 C
> HETATM 9 H LIG 1 -4.728 2.975 1.243 1.00 0.00 H
> HETATM 10 C LIG 1 -4.549 0.837 1.003 1.00 0.00 C
> HETATM 11 H LIG 1 -6.045 2.243 0.329 1.00 0.00 H
> HETATM 110 N LIG 1 -3.097 0.727 1.164 1.00 0.00 N
> HETATM 13 H LIG 1 -4.907 0.053 0.324 1.00 0.00 H
> HETATM 14 H LIG 1 -5.027 0.653 1.972 1.00 0.00 H
> HETATM 15 H LIG 1 -1.329 0.896 0.057 1.00 0.00 H
> HETATM 16 H LIG 1 -2.677 0.200 -0.831 1.00 0.00 H
> HETATM 17 H LIG 1 -2.789 1.419 1.847 1.00 0.00 H
>
> What PyMOL-function returns me the 'physical' index in the array of
> atoms? So for atom '12' (nitrogen), (with label '110') I would like '12'
> displayed in the PyMOL viewer. Right now, 'ID' displayes '110', 'RANK'
> displays '11' and 'INDEX' displayes '1'.
>
> After deleting row 4, again for atom labeled '110' nitrogen, 'ID'
> displayes '110', 'RANK' displayes '10' and index displayes '1'.
>
> I'm not sure now if this is in agreement with what we have said so far.
> What I dont like too much about relying on 'ID' is the fact that if the
> labels get changed (or none are present), its not possible to tell
> anymore which atom has which index. Thats why i was hoping to find a way
> to get the 'linenumber-dependent' index of an atom.
>
> Thanks for your help so far.
>
> Martin
>
>
>

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Re: [PyMOL] High Resolution Interface

[Hongbo Zhu]

If you mean the GUI of PyMOL, I guess you can change your screen 
resolution and then make a screenshot.

hongbo
On 11/23/2010 02:52 PM, David Hall wrote:
> Dear all,
>
> I want to take high resolution screenshots of the PyMol interface for
> figures in a methods paper where PyMol is used for some steps.  Is
> there a way to make the elements of the interface display 4 times as
> large so I can get ~300 dpi images instead of 72 dpi?  I have access
> to Linux, OS X, and Windows, so answers on any of these systems will
> be useful.
>
> Thanks,
> David
>
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Re: [PyMOL] negative image of binding cavity

[Hongbo Zhu]

Hi, Tom,
have a look at MSPocket:
http://appserver.biotec.tu-dresden.de/MSPocket/
It uses MSMS to generate protein solvent excluded surface (SES) and then 
detects pockets on the SES. It also calculates the volume for cavities 
(internal pockets buried in proteins) based on the SES.
cheers,
hongbo

On 12/03/2010 06:15 PM, Thomas Evangelidis wrote:
> Dear Pymol users,
>
> I want to display clearly the volume of a buried cavity inside my
> protein. Does anybody know how to do this? I've tried CastP and Caver
> plugins already, but they do not produce exactly the volume I want to
> display. I would greatly appreciate any advice.
>
> thanks,
> Tom
>
>
>
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Re: [PyMOL] A selection function supporting math expression

[Hongbo Zhu]

Hi Cun Zhuang,

I think what you need to do is adding one line in the end of mathexpr.py:

cmd.extend("SelectByExpr",Select)

then you can type in command line
SelectByExpr x>5

see the following page for more explanation:
http://www.pymolwiki.org/index.php/Simple_Scripting


hongbo

On 12/13/2010 11:00 AM, Tsjerk Wassenaar wrote:
> Ni Hao Cun Zhang
>
> The real 'problem' is that Pymol does not allow selection based on
> coordinates. Probably this should be on the wish list (and easy to
> implement). Expressions are allowed, for instance selecting based on
> b-factor or occupancy.
>
> In your script, you can use some shortcuts. Maybe something like:
>
> def cselect(selection="all",expression=lambda (x,y,z): True):
>  return [i.id for i in cmd.get_model(selection).atom if 
> expression(i.coord)]
>
> The expression can be a predefined function, or a lambda function,
> like here. You could then say:
>
> ids = cselect("n. ca",lambda (x,y,z): x<10 and y>5)
> cmd.show("spheres","id %s"%",".join([str(i) for i in ids]))
>
> Hope it helps :)
>
> Cheers,
>
> Tsjerk
>
>
>
> On Mon, Dec 13, 2010 at 9:44 AM, Cun Zhang  wrote:
>> Hi,all
>>
>> I haven't found any pymol script supports using math expression to select
>> atoms,
>> so I spend several hours to write one function to do it.
>>
>> I write a script(mathexpr.py) containing this function, then run
>> mathexpr.py,
>> function 'Select' now can be called. Can anybody tell me how to combine this
>> function into pymol,
>> or 'select' command,  so it can be called like 'select x>5'.
>> Hope it useful for you.
>>
>> Thank you!
>>
>> Yours,
>> Cun Zhang
>>
>>
>> def Select(expr='x>5',sel='all'):
>> """
>>A function which supports selection by math expressions.
>> example:
>>   x=Select('x>5 and y<2','name C')
>> """
>>  ATOMS=cmd.get_model(sel)
>>  vec,index=ATOMS.get_coord_list(),cmd.identify(sel)
>>  command='[index[vec.index([x,y,z])] for x,y,z in vec if '+expr+']'
>>  ID=eval(command) #list type
>>  return ID
>>
>> --
>> 
>> Cun Zhang
>> Ph.D. Candidate
>> LNM,Institute of Mechanics
>> Chinese Academy of Sciences
>> Beijing, 100190, China
>> Tel:86-10-82544204
>> http://www.edwardpku.com/cun
>> 
>>
>> --
>> Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL,
>> new data types, scalar functions, improved concurrency, built-in packages,
>> OCI, SQL*Plus, data movement tools, best practices and more.
>> http://p.sf.net/sfu/oracle-sfdev2dev
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>>
>
>
>

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Re: [PyMOL] installing_running vasco

[Hongbo Zhu]

Hi, Yarrow,

It says MSMS calculation error.

*Possible reason*

MSMS is a brilliant program for computing protein solvent excluded 
surfaces. It is a 3rd-party program (see 
http://mgltools.scripps.edu/downloads ) and its binary is included in 
VASCo. The version shipped with VASCo by default is for Linux 
(msms255i86Linux.5 and msms261x86_64Linux). Since you are using a mac (I 
suppose it is not running Linux), the binary MSMS will not execute 
successfully.


*Possible solution*

Solution 1. Try using VASCo on Linux (e.g. remove your mac OS X and 
install Linux on your mac :)

Solution 2. replace the linux version of MSMS by the mac OsX version 
(again, see http://mgltools.scripps.edu/downloads).
Then, you either have to look for where MSMS is invoked in the python 
source code of VASCo and replace all the names of the MSMS program, or, 
cheat VASCo by renaming the mac version of MSMS to the linux version 
MSMS (this is a easier way, but I do not have a mac at hand and can not 
tell you whether this trick will work).

hope that helps,
hongbo

On 02/24/2011 05:18 PM, Yarrow Madrona wrote:
>
> Hello pymol users,
>
> I apologize if this posting is not appropriate for the pymol user list.
> If there is a better place to direct these questions please let me know.
>
> I have installed the vasco plugin into pymol on my mac by:
>
> "python setup_vasco_x.py install" in the Vasco modules directory. I have
> also installed the plugin into pymol.
>
>
> "python VASCo.py -testrun
>
> 1.  However instead of making a test_out directory it makes an input.ppix
> to use on the next run.
>
> 2.  When I add my pdb and run I get an error message.  Here is the log file:
> (Is this a problem with PDB format?)
>
> Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc)
> Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc)
> 
> Run MSMS...
> -no_header
> -probe_radius 1.4
> -density 1
> -all_components
> Delete Inner MSMS Surface files...
> MSMS Warnings:   0
> ERROR: msms calculation error
> MSMS surface calculating error, try to skip file and continue run.
> CODE  ;TIME SEC  ;DATE;RUN_ID;STATUS
> ;REASON;PROPERTIES;CHAINS;UNITS ;ATOMS
> ;SURFPNT   ;  PATCHPNT
> CIN4sfA   ;0.000 ;Wed Feb 23 20:57:24 2011;0 ;ERROR
> ;MSMS:ERROR: msms calculation error;  ;1
>   ;1 ;3152  ;  ;
> 
> 
> Finish: time:16 sec
> 
> ++++++++
>
>
> Thank you for your help.
>
> -Yarrow
>
>
>
>
>

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hongbo@biotec.tu-dresden
Webpage: www.biotec.tu-dresden.de

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Re: [PyMOL] installing_running vasco

[Hongbo Zhu]

I forgot to mention that the msms shipped with your VASCo (v1.0.2) is 
installed at:

VASCo_1.0.2/unix/VASCo-Modules-1.0.2/ppix_modules/cprogr/unix/msms

cheers,
hongbo

On 02/24/2011 05:18 PM, Yarrow Madrona wrote:
>
> Hello pymol users,
>
> I apologize if this posting is not appropriate for the pymol user list.
> If there is a better place to direct these questions please let me know.
>
> I have installed the vasco plugin into pymol on my mac by:
>
> "python setup_vasco_x.py install" in the Vasco modules directory. I have
> also installed the plugin into pymol.
>
>
> "python VASCo.py -testrun
>
> 1.  However instead of making a test_out directory it makes an input.ppix
> to use on the next run.
>
> 2.  When I add my pdb and run I get an error message.  Here is the log file:
> (Is this a problem with PDB format?)
>
> Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc)
> Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc)
> 
> Run MSMS...
> -no_header
> -probe_radius 1.4
> -density 1
> -all_components
> Delete Inner MSMS Surface files...
> MSMS Warnings:   0
> ERROR: msms calculation error
> MSMS surface calculating error, try to skip file and continue run.
> CODE  ;TIME SEC  ;DATE;RUN_ID;STATUS
> ;REASON;PROPERTIES;CHAINS;UNITS ;ATOMS
> ;SURFPNT   ;  PATCHPNT
> CIN4sfA   ;0.000 ;Wed Feb 23 20:57:24 2011;0 ;ERROR
> ;MSMS:ERROR: msms calculation error;  ;1
>   ;1 ;3152  ;  ;
> 
> 
> Finish: time:16 sec
> 
> ++++++++
>
>
> Thank you for your help.
>
> -Yarrow
>
>
>
>
>

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hongbo@biotec.tu-dresden
Webpage: www.biotec.tu-dresden.de

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Re: [PyMOL] rotation of protein

[Hongbo Zhu]

Hi, Kanika,

are you looking for biological units of proteins when you say stable 
dimer? If this is the case, I recommend the page:

http://pdbwiki.org/index.php/Biological_unit
at the bottom of the page you can find four very useful servers for the 
determination of biological units of proteins (PQS is not updated anymore):
 The Protein Quaternary Structure Server (PQS) [2] or [3]
 The Macro-Molecular Structure Database (MSD) [4] or [5]
 The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
 Protein quaternary structure investigation (PiQSi) [7]

As a matter of fact, the PDB also provides the biological assembly of 
each PDB entry for download. More information can be found at:
http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html

If your protein is not from the PDB, you can still try pisa ( 
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts 
protein coordinate files uploaded by the users and determines the 
"stable dimer" or else-mer of your protein.

hope these help!
hongbo

On 02/25/2011 01:46 PM, kanika sharma wrote:
> Hi,
> i am working to generate a dimer of my protein..I have made a duplicate
> of my proteinCan any one tell me how to rotate my molecule to get
> maximum stability..???
>
>
> Regards..
> Kanika
>
>
>
> --
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-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
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Re: [PyMOL] Selecting ASP and GLU

[Hongbo Zhu]

I believe the confusion is caused by the simplified selection expression 
in PyMOL (and some other visualization tools as well). I remember that 
one of my colleagues once questioned strongly the reason of using OR 
instead of AND in such situation.

The expression:

select resn GLU or resn ASP

actually means

select (resn == GLU) or (resn == ASP)

The reason of using Boolean operator *or* is very clean when the two 
operands are stated completely. But when the operands are simplified, 
our first reaction is to use *and* because it is very natural to say

"I want GLU *and* ASP"

if you want both GLU and ASP.

And it is even more confusing in Jmol :

select 110 or 112 (select resno==110 or resn==112)

if want you really want is 110 *and* 112 :)

hongbo

On 03/01/2011 05:43 PM, Jason Vertrees wrote:
> Hi Martin,
>
> To select all ASPs and GLUs just type,
>
> select resn GLU+ASP
>
> or
>
> select resn GLU or resn ASP
>
> or, if you need parentheses,
>
> select ((resn GLU) or (resn ASP))
>
>
> Maybe this will help:
>
> # fetch a test protein
>
> fetch 1rsy, async=0
>
> # color all ASPs and GLUs red
>
> color tv_red, (resn ASP or resn GLU)
>
>
> While the boolean 'and' works, the following will fail to select and
> color any atoms:
>
> color tv_red, (resn ASP and resn GLU)
>
> because there will be no _single atom_ in both an ASP and a GLU.  The
> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in
> any ASP _and_ in any GLU--which is impossible.
>
> Cheers,
>
> -- Jason
>
>
>
> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger  wrote:
>> Dear all
>> What is the selection syntax to select all GLU and ASP residues within an
>> object?
>>
>> I'm trying it the way its written on the wiki:
>>
>> remove resn hoh# remove water
>> h_add  # add hydrogens
>>
>> as surface
>> color grey90
>>
>> color slate, resn lys   # lysines in light blue
>> color paleyellow, resn cys  # cysteines in light yellow
>> color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in light
>> red
>>
>> but, the selection kind of does not work for me (I'm assuming the operator
>> for the logical AND is 'and').
>> What is it that I need to do differently?
>>
>> Kind regards
>> Martin
>>
>> --
>> Free Software Download: Index, Search&  Analyze Logs and other IT data in
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>>
>
>
>

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
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Re: [PyMOL] Selecting ASP and GLU

[Hongbo Zhu]

On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote:
> Hey :)
>
> It's good to note that programs are written by programmers, using
> programmer's logic.

First of all, I was not complaining about the logic of the PyMOL 
programmers. I tried to help find out the reason that might cause 
Martin's script to break based on the similar complains I had received.

It is true that programs are written by programmers. But I guess many 
users actually hate that fact so much because they see again and again 
that some programmers just presume that all users will think the same 
way as they think. (Of course after these users become programmers they 
start to do the same ;)

The confusion is not so much caused by the
> simplified expression, but by users with little background in
> mathematics/logic assessing 'and' and 'or' from a linguistic
> background.In computer science and mathematics OR := union, AND :=
> intersection. It's covered quite well in
> http://www.pymolwiki.org/index.php/Selection_Algebra
I disagree. I think it is caused by the simplified expression to the 
users who think intuitively instead of immediately mathematically when 
they try to write down the first line of selection script, no matter how 
much mathematics/logic they have (the colleague I mentioned is a 
computer scientist). After staring at the unexpected outcome for a 
while, they will try to think mathematically or google-ly ;).

I can not think of a good way to address this small issue for new users. 
Maybe a more informative hint to the users is helpful rather than just 
print "0 atoms selected". For example, PyMOL can print the selection 
result of each operand, or print the complete selection expression 
translated from the the simplified selection expression.

>
> Cheers,
>
> Tsjerk
>
> On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu
>   wrote:
>> I believe the confusion is caused by the simplified selection expression
>> in PyMOL (and some other visualization tools as well). I remember that
>> one of my colleagues once questioned strongly the reason of using OR
>> instead of AND in such situation.
>>
>> The expression:
>>
>> select resn GLU or resn ASP
>>
>> actually means
>>
>> select (resn == GLU) or (resn == ASP)
>>
>> The reason of using Boolean operator *or* is very clean when the two
>> operands are stated completely. But when the operands are simplified,
>> our first reaction is to use *and* because it is very natural to say
>>
>> "I want GLU *and* ASP"
>>
>> if you want both GLU and ASP.
>>
>> And it is even more confusing in Jmol :
>>
>> select 110 or 112 (select resno==110 or resn==112)
>>
>> if want you really want is 110 *and* 112 :)
>>
>> hongbo
>>
>> On 03/01/2011 05:43 PM, Jason Vertrees wrote:
>>> Hi Martin,
>>>
>>> To select all ASPs and GLUs just type,
>>>
>>> select resn GLU+ASP
>>>
>>> or
>>>
>>> select resn GLU or resn ASP
>>>
>>> or, if you need parentheses,
>>>
>>> select ((resn GLU) or (resn ASP))
>>>
>>>
>>> Maybe this will help:
>>>
>>> # fetch a test protein
>>>
>>> fetch 1rsy, async=0
>>>
>>> # color all ASPs and GLUs red
>>>
>>> color tv_red, (resn ASP or resn GLU)
>>>
>>>
>>> While the boolean 'and' works, the following will fail to select and
>>> color any atoms:
>>>
>>> color tv_red, (resn ASP and resn GLU)
>>>
>>> because there will be no _single atom_ in both an ASP and a GLU.  The
>>> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in
>>> any ASP _and_ in any GLU--which is impossible.
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>>
>>>
>>> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hedigerwrote:
>>>> Dear all
>>>> What is the selection syntax to select all GLU and ASP residues within an
>>>> object?
>>>>
>>>> I'm trying it the way its written on the wiki:
>>>>
>>>> remove resn hoh# remove water
>>>> h_add  # add hydrogens
>>>>
>>>> as surface
>>>> color grey90
>>>>
>>>> color slate, resn lys   # lysines in light blue
>>>> color paleyellow, resn cys  # cysteines in light yellow
>>>> color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in 
>>>> light
>>>> red
>>>

Re: [PyMOL] Different color on each side of strand

[Hongbo Zhu]

how do you define "front" and "back" sides of sheets in general?

On 03/07/2011 01:32 AM, Keitaro Yamashita wrote:
> Dear all,
>
> Sorry for my unclear explanation.
>
> I made a picture explaining what I'd like to do.
> I want to color the front and back of sheets separately.
>
> Jason said it should be possible, could anyone tell me how to do it?
>
> Cheers,
>
> Keitaro
>
>
>
> 2011/3/7 Jason Vertrees:
>> Hi Keitaro,
>>
>> Use the "cartoon_highlight_color" setting.  For example:
>>
>> set cartoon_highlight_color, red
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita
>>   wrote:
>>> Dear all,
>>>
>>> Can PyMOL set different colors on each side of cartoon strand?
>>>
>>> I tried cartoon_discrete_colors but it was not for this purpose.
>>> (I mean the sides from which sidechains are protruded.)
>>>
>>> Thanks in advance,
>>>
>>> Keitaro
>>>
>>> --
>>> What You Don't Know About Data Connectivity CAN Hurt You
>>> This paper provides an overview of data connectivity, details
>>> its effect on application quality, and explores various alternative
>>> solutions. http://p.sf.net/sfu/progress-d2d
>>> ___
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>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>>
>>
>> --
>> What You Don't Know About Data Connectivity CAN Hurt You
>> This paper provides an overview of data connectivity, details
>> its effect on application quality, and explores various alternative
>> solutions. http://p.sf.net/sfu/progress-d2d
>>
>>
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Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

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Fax: +49 (0) 351 463-40087
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Re: [PyMOL] Different color on each side of strand

[Hongbo Zhu]

Hi, Keitaro,

On 03/08/2011 03:11 AM, Keitaro Yamashita wrote:
> Dear Hongbo,
>
> For example, user can put something like light source and "front" is
> defined as the side light hits.
> (though it would be undefined If sheet plane is placed parallel to the ray..)
and even the same strand can have half of it facing the light source and 
the other half turned opposite to the source.
>
> But I think any definition is ok if front and back could be alternated
> easily by user operation.
sounds like an interesting operation, though.
>
>
> Cheers,
>
> Keitaro
>
> 2011/3/8 Hongbo Zhu:
>> how do you define "front" and "back" sides of sheets in general?
>>
>
> --
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
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Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de

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Re: [PyMOL] Different color on each side of strand

[Hongbo Zhu]

I like the idea about coloring tim-barrels.

At the moment the secondary structures can be selected in PyMOL using 
selector "ss". I wonder whether it makes sense to label each strand with 
an index so we can select each strand individually, e.g.

select ss s5 # select the 5th strand from the N-term

and then one can flip the colors of the two "sides" of the strand in 
case it is not colored properly according to the user.

hongbo

On 03/08/2011 10:16 AM, Keitaro Yamashita wrote:
> Dear Hongbo,
>
>>> For example, user can put something like light source and "front" is
>>> defined as the side light hits.
>>> (though it would be undefined If sheet plane is placed parallel to the 
>>> ray..)
>> and even the same strand can have half of it facing the light source and
>> the other half turned opposite to the source.
>
> I think this definition is useful when color e.g. beta-barrel, but
> definitely includes ambiguity.
> Then, how about defining front side as the C-beta direction of
> starting residue of sheet?
>
>
> Cheers,
>
> Keitaro
>
> 2011年3月8日火曜日 Hongbo Zhu hongbo@biotec.tu-dresden.de:
>> Hi, Keitaro,
>>
>> On 03/08/2011 03:11 AM, Keitaro Yamashita wrote:
>>> Dear Hongbo,
>>>
>>> For example, user can put something like light source and "front" is
>>> defined as the side light hits.
>>> (though it would be undefined If sheet plane is placed parallel to the 
>>> ray..)
>> and even the same strand can have half of it facing the light source and
>> the other half turned opposite to the source.
>>>
>>> But I think any definition is ok if front and back could be alternated
>>> easily by user operation.
>> sounds like an interesting operation, though.
>>>
>>>
>>> Cheers,
>>>
>>> Keitaro
>>>
>>> 2011/3/8 Hongbo Zhu:
>>>> how do you define "front" and "back" sides of sheets in general?
>>>>
>>>
>>> --
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>>
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>>
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>
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Re: [PyMOL] Different color on each side of strand

[Hongbo Zhu]

I was also thinking along that line :) But that is pretty trick for a 
structure like beta-barrel, since you have to actually shrink the barrel 
toward the center.

here is another hack that might work:

1. render only the black outline of the cartoon representation of your 
protein:
set ray_trace_mode,2  # see http://www.pymolwiki.org/index.php/Ray

2. fill the cartoon, especially the beta strands using different colors 
using some image manipulation program (a great example is GIMP). This is 
fairly easy as most of such programs provide a "Fill Tool" (in GIMP it 
is the bucket button). Using such a tool you have the picture in a few 
clicks. I have actually made an example of a beta barrel (1opfA):

http://www.biotec.tu-dresden.de/~hongboz/pymol_example/1opfA.html

(In this quick example, I have oriented the protein such that both sides 
of some strands can be seen.)

hongbo


On 03/09/2011 04:03 PM, Tsjerk Wassenaar wrote:
> Hi Keitaro,
>
> You can try to create a copy from the piece containing the sheet,
> colour it differently, and change the coordinates slightly. It's a bit
> tricky maybe, especially if you've got quite a bit of curvature.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Mar 9, 211 at 3:22 PM, Keitaro Yamashita
>   wrote:
>> Hi,
>>
>> Yes, there're definitely a few (?) exceptional cases.
>> But maybe people don't use this feature in such case.
>>
>> Anyway, this feature is not included in current PyMOL, right?
>> Then, is it hard to implement this feature (many changes in code required)?
>>
>> Keitaro
>>
>> 2011/3/8 gilleain torrance:
>>> Hi,
>>>
>>> Although most of the time the strands in a sheet have clear 'sides',
>>> this won't always be true. Keitaro already mentioned the possibility
>>> of twisted strands, but you can also get two sheets that share the
>>> 'same' long strand - well, depending on the SSE assignment algorithm,
>>> I suppose.
>>>
>>> Jellyrolls (http://www.cathdb.info/cathnode/2.60.120) are an example
>>> of this, I seem to remember, as they have long strands that cross from
>>> one sheet to another. As the sheets are in a sandwich, the strand will
>>> change side halfway through.
>>>
>>> This coloring scheme still sounds like it would be useful, but there
>>> might be some odd visual effects, or an algorithm to take care of
>>> corner cases.
>>>
>>> gilleain
>>>
>>> On Tue, Mar 8, 2011 at 10:12 AM, Hongbo Zhu
>>>   wrote:
>>>> I like the idea about coloring tim-barrels.
>>>>
>>>> At the moment the secondary structures can be selected in PyMOL using
>>>> selector "ss". I wonder whether it makes sense to label each strand with
>>>> an index so we can select each strand individually, e.g.
>>>>
>>>> select ss s5 # select the 5th strand from the N-term
>>>>
>>>> and then one can flip the colors of the two "sides" of the strand in
>>>> case it is not colored properly according to the user.
>>>>
>>>> hongbo
>>>>
>>>> On 03/08/2011 10:16 AM, Keitaro Yamashita wrote:
>>>>> Dear Hongbo,
>>>>>
>>>>>>> For example, user can put something like light source and "front" is
>>>>>>> defined as the side light hits.
>>>>>>> (though it would be undefined If sheet plane is placed parallel to the 
>>>>>>> ray..)
>>>>>> and even the same strand can have half of it facing the light source and
>>>>>> the other half turned opposite to the source.
>>>>>
>>>>> I think this definition is useful when color e.g. beta-barrel, but
>>>>> definitely includes ambiguity.
>>>>> Then, how about defining front side as the C-beta direction of
>>>>> starting residue of sheet?
>>>>>
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Keitaro
>>>>>
>>>>> 2011年3月8日火曜日 Hongbo Zhu hongbo@biotec.tu-dresden.de:
>>>>>> Hi, Keitaro,
>>>>>>
>>>>>> On 03/08/2011 03:11 AM, Keitaro Yamashita wrote:
>>>>>>> Dear Hongbo,
>>>>>>>
>>>>>>> For example, user can put something like light source and "front" is
>>>>>>> defined as the side light hits.
>>>>>>> (though it would be undefined If sheet plane is placed parallel 

Re: [PyMOL] plugin dependencies

[Hongbo Zhu]

Just another reminder:

If the version of the "external" python and the python shipped with 
PyMOL are different enough on the user's computer, the package might 
still fail to work in PyMOL even if the user has installed the package 
using the external python and edited the PYTHONPATH.


So, how about ship all the BioPython packages you need in your python 
code together with your plugin? Of course all dependencies should be 
included.

On 03/10/2011 06:17 AM, rv...@libero.it wrote:
> Hello everyone,
>
> my plugin needs Biopython.
> I wish check the Biopython installation by
>
> try:
>  from Bio import AlignIO   # or similar
> except ImportError:
>  .. prompt the user with a msg ..
>
> The problem is:
> what the msg to the user?
>
> Downloading and installing Biopython is not enough:
> If the user downloads and installs Biopython in the external python
> interpreter still Biopython continues to be unavailable for the internal 
> python
> interpreter in pyMOL.
>
> Of course the user could edit the PYTHONPATH environment variable and so all
> the python interpreters can read Biopython but  working with environment
> variables could be too difficult for a not experienced user.
>
> Is there a simpler way?
>
> Cheers,
>roberto
>
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
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[PyMOL] New plugin: MSMS plugin for PyMOL

[Hongbo Zhu]

Dear PyMOLers,

As many of you might be aware of, MSMS is an excellent program developed 
by Michel Sanner for computing protein surface, especially solvent 
excluded surface (SES). (see http://mgltools.scripps.edu/packages/MSMS/ 
). Due to its outstanding usability, Robert Campbell had already 
provided several very helpful PyMOL scripts about MSMS (see 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ ).

I have also been using the MSMS program heavily in my work and developed 
a MSMS plugin for PyMOL with a graphical user interface (GUI). If you 
have interest, please take a look at the plugin at:
---
http://www.pymolwiki.org/index.php/MSMS
---
Features:
MSMS can be configured and invoked in the GUI.
The triangulated protein SES can be rendered as mesh or/and vertices 
plus normal vectors.
The color of surface mesh or vertices can also be configured.

Your feedback and suggestions are particularly welcome!

Best regards,
Hongbo

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Re: [PyMOL] symexp

[Hongbo Zhu]

Hi, Kanika,

The source code can be found at function
ExecutiveSymExp()
in the file
./trunk/pymol/layer3/Executive.c

Normally, a PDB is equivalent to an ASU (except for some cases like 
capsid). "Symexp is used to reconstruct neighboring ASUs."
( http://pymolwiki.org/index.php/Symexp )
It seems REMARK 290 that contains crystallographic symmetry 
transformations is used for computing the positions of neighboring ASUs.

But be careful with some of the capsid cases (e.g. 3p0s). The symexp 
will not generate any neighboring molecules as they are not related by 
crystallographic symmetry, but non-crystallographic symmetry.

BTW, it seems symexp has a bug when running on 3p0s. It does not return 
after displaying the message:
"ExecutiveSymExp: Generating symmetry mates..."

regards,
hongbo

On 03/22/2011 06:44 AM, kanika sharma wrote:
> I used symexp command for 3QK9 using distance of 2.75 to generate
> ASU(asymmetric unit). Does symexp generate these symmetry mates from the
> remark290 of PDB file? I couldnot find the code for symexp in pymolwiki.
> Can anyone help out?
>
>
>
>
> Regards,
> Kanika
>
>
>
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
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Re: [PyMOL] CASTp plugin

[Hongbo Zhu]

Hi, Tomas,
Usually, the "Bad magic number" is caused by wrong python version when 
running .pyc file (the .pyc must have been compiled using a different 
version of python than the one in PyMOL 1.3, which is python 2.5.4). 
Maybe you have also noticed on the first line of the CASTpyMOL webpage :

"To use CASTpyMOL version 2, you must be using PyMOL version 0.99 "

pymol 0.99 and pymol 1.3 uses different versions of python.

Maybe you should contact the CASTpyMOL people to get a .py file so you 
can try them with your pymol 1.3, or ask them to compile a .pyc using 
python 2.5.4 for you. Or install pymol 0.99 in parallel to you pymol 1.3.

good luck!
hongbo

On 03/22/2011 11:03 AM, Tomáš Kučera wrote:
> Hello pymol users,
>
> I try to install this castp plugin:
> http://sts.bioengr.uic.edu/castp/pymol.php
> ->  http://sts.bioengr.uic.edu/castp/infoPages/CASTpyMOL_v2.pyc
>
> I have pymol 1.3 (windows7 64bit)
>
> and I got:
>
> ImportError: Bad magic number in C:\Program Files
> (x86)\PyMOL\PyMOL/modules\pmg_tk\startup\CASTpyMOL_v2.pyc
> Error: unable to initialize plugin 'CASTpyMOL_v2'.
>
> Does anyone have any idea how to fix this issue?
>
> Thanks, Tomas
>

-- 
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Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
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Re: [PyMOL] symexp

[Hongbo Zhu]

You are right, Thomas! The information is redundant in REMARK 290.

I just performed a small test which confirms your conclusion:
remove CRYST1 will make symexp to complain "ExecutiveSymExp-Error: No 
symmetry loaded!" even if REMARK 290 is present, while removing REMARK 
290 does not have any effect on symexp.

don't know whether it make sense to monitor both cryst1 and remark 290...

On 03/22/2011 10:19 AM, Thomas Holder wrote:
>> It seems REMARK 290 that contains crystallographic symmetry
>> transformations is used for computing the positions of neighboring ASUs.
>
> the CRYST1 record is sufficient for generating symmetry mates, so
> pymol most likely does not read REMARK 290.
>
> Cheers,
>Thomas
>

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[PyMOL] Residue selection problem in PyMOL 1.6

[Hongbo Zhu 朱宏博]

Hi,

I have downloaded PyMOL v1.6.0.0 from sourceforge and installed it on my
Ubuntu 12.04. It works very well. Recently I noticed there is a problem
when selecting residues from the sequence panel (Display -> Sequence). If I
select multiple residues using mouse in the sequence panel, only the first
selected residue is highlighted in the corresponding structure. Then rest
selected residues are not highlighted. But if I disable my selection and
enable it again (e.g. by clicking on the selection name in the control
panel), all the selected residues will be highlighted. This is different
from PyMOL 1.5 or older version, and I don't think it is a feature (I read
what's new for 1.6 :). There is no any warning or error message output on
the terminal. Has anyone had similar problem?

Hongbo
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Re: [PyMOL] Residue selection problem in PyMOL 1.6

[Hongbo Zhu 朱宏博]

I found a previous report on the same issue and it is fixed in the svn:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11581.html

I guess I will try the updated version.

Hongbo
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[PyMOL] option pdb_conect_nodup unavailable in OpenSource version 1.7

[Hongbo Zhu 朱宏博]

Hi,

I am using PyMOL 1.7 open source version in Ubuntu 14.04.
I wanted to try a new setting  pdb_conect_nodup in pymol 1.7.
It is listed as new features available for both "Open Source and Incentive"
at:
http://pymol.org/features#v1.7

when I set it to on, I got:

"Setting-Warning: not supported in open-source version of PyMOL"

though the setting could be successfully set (get pdb_conect_nodup).

After saving a test PDB files, I still see duplicate CONECT lines in the
PDB file generated by PyMOL. So I guess the feature is indeed missing in
open source version.

Should the feature be made available to open source version users?
cheers,
Hongbo
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Re: [PyMOL] option pdb_conect_nodup unavailable in OpenSource version 1.7

[Hongbo Zhu 朱宏博]

Hi, Thomas,

thanks for checking that and responding quickly. I also found out the
meaning of the option myself. At the moment, I write
some post-processing scripts to cope with that issue.

best,
Hongbo


On Tue, Aug 19, 2014 at 4:05 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:

> Hi Hongbo,
>
> you are right that the website and the implementation don't match, thanks
> for pointing that out. This was a feature request from a paying PyMOL
> sponsor, which often means that we put the feature only (or first) in
> Incentive PyMOL. But thinking about it, this is a rather small change and
> probably not worth to keep as a distinguishing feature. I'll port it to
> open-source today.
>
> To clarify the issue with duplicated connect record. This is an unofficial
> PDB feature to store the bond order and is supported by several
> applications that read PDB files, but may break PDB file loading in other
> applications which don't support it. PyMOL always wrote duplicated connect
> records and the new setting allows you to switch that off.
>
> Cheers,
>   Thomas
>
> On 18 Aug 2014, at 15:04, Hongbo Zhu 朱宏博  wrote:
> > Hi,
> >
> > I am using PyMOL 1.7 open source version in Ubuntu 14.04.
> > I wanted to try a new setting  pdb_conect_nodup in pymol 1.7.
> > It is listed as new features available for both "Open Source and
> Incentive" at:
> > http://pymol.org/features#v1.7
> >
> > when I set it to on, I got:
> >
> > "Setting-Warning: not supported in open-source version of PyMOL"
> >
> > though the setting could be successfully set (get pdb_conect_nodup).
> >
> > After saving a test PDB files, I still see duplicate CONECT lines in the
> PDB file generated by PyMOL. So I guess the feature is indeed missing in
> open source version.
> >
> > Should the feature be made available to open source version users?
> > cheers,
> > Hongbo
>
> --
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> PyMOL Developer
> Schrödinger, Inc.
>
>
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