pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all,
I am running pymol 1.6 on a Debian wheezy machine. I encountered a weird
conflict of sphere display and mouse selection. When I show the ion in
sphere, I cannot select residues by clicking it with mouse. Only after I
hide the sphere am I able to accomplish click selection. Does anybody have
some clues?
Thank you so much in advance!
Sincerely,
Chen

MacPymol 1.3r1 - just downloaded yesterday - does not launch under Mac Os 10.10 Yosemite beta 1 (but 
works fine on 10.9.4)

Hi James,
you can save multi-model PDBs with state=0:
PyMOL> save trajectory.pdb, state=0
There is also a "save_traj" function in PSICO which can write DCD format:
http://pymolwiki.org/index.php/Psico
The latter is based on the "save2traj" script by Sean Law:
http://pymolwiki.org/index.php/Save2traj
Cheers,
 Thomas
On 25 Jul 2014, at 04:24, James Starlight <jms...@gm...> wrote:
> Dear Pymol Users!
> 
> I wounder whether it will be possible to save big ensemble of the loaded into pymol Pdb's files as the trajectory output (like dcd format) what are actually can be performed by vmd (e.g by means of http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/). The problem in last case is that I don't know how to perform superimposition of my conformers agains refeence frame (alternatively what is easily performed in pymol). I'll be thankful for any suggestions.
> 
> Best wishes,
> 
> James
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Dear PyMOL users,
I'm in trouble in using APBS plugin to display the molecular surface.
The calculations of "set Grid" and "Run APBS" were successfully finished,
but showing the surface by the button of "show" in the Visualization (1) tab fails with the following message
 ObjectMapLoadDXFile: Loading from '/Users/yoshitaka/Desktop/pymol-generated.dx'.
 DXStrToMap: Dimensions: 97 129 129
 DXStrToMap: Origin -31.288 -19.104 -13.876
 DXStrToMap: Grid 0.484 0.497 0.462
 DXStrToMap: 1614177 data points.
<type 'exceptions.ValueError'> Exception in Tk callback
 Function: <bound method VisualizationGroup.showMolSurface of <pmg_tk.startup.apbsplugin.VisualizationGroup instance at 0x1077ca3f8>> (type: <type 'instancemethod'>)
 Args: ()
Traceback (innermost last):
 File "/usr/local/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__
 return apply(self.func, args)
 File "/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py", line 2433, in showMolSurface
 self.updateMolSurface()
 File "/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py", line 2471, in updateMolSurface
 self.updateRamp()
 File "/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py", line 2458, in updateRamp
 ramp_name = self.getRampName()
 File "/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py", line 2440, in getRampName
 idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i) == 'object:molecule'].index(self.molecule.getvalue())
<type 'exceptions.ValueError'>: '' is not in list
Please tell me how to solve this plobrem.
I describe my settings as follows:
machine: Mac OS X 10.9.4, Intel Core i7, 16GB.
Xquartz is installed. The versions of gcc and g++ compilers are 4.8.1.
I installed tcl/tk (ver. 8.5.15), python (ver. 2.7.8), pmw (ver. 1.3.3), and PyMOL (ver. 1.7.1.3) by using Homebrew.
 brew uninstall python tcl-tk pmw pymol
 brew tap homebrew/dupes
 brew tap homebrew/science
 brew install homebrew/dupes/tcl-tk --enable-threads --with-x11
 brew install python --with-brewed-tk
 brew install pymol
Next, I installed openmpi 1.8.1 in this way:
 brew install openmpi
 cd /usr/lib/
 sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libmpi.1.dylib libmpi.0.dylib
 sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-rte.7.dylib libopen-rte.0.dylib
 sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-pal.6.dylib libopen-pal.0.dylib
APBS and PDB2PQR binaries were employed from "APBS-1.4-osx.tar.gz" and "pdb2pqr-osx-bin-1.9.0.tar.gz", respectively.
The plugin "apbsplugin.py" was downloaded from "http://www.pymolwiki.org/index.php/Apbsplugin".
The environment variable "DYLD_FALLBACK_LIBRARY_PATH" was set as "/usr/local/Cellar/open-mpi/1.8.1/lib:/Users/yoshitaka/apps/APBS-1.4-osx/lib:$DYLD_FALLBACK_LIBRARY_PATH"
for the calculation.
Thank you for your help.
Yoshitaka
**********************************************************
Yoshitaka Moriwaki
Dept. of Biotechnology, Grad. Sch. of Agri. and Life Sci.,
The Univ. of Tokyo
**********************************************************

Hi, 
I was wondering if there is a work around to get the PyMOL app to launch in OS X 10.10 (Yosemite)? Currently, when trying to launch the app from /Applications folder it does nothing. I have the new XQuartz. 
When I try to launch it using terminal, I get this error:
$python launch_pymol.py 
Traceback (most recent call last):
 File "launch_pymol.py", line 27, in <module>
 modules_path = os.environ['PYMOL_PATH']+'/modules'
 File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/UserDict.py", line 23, in __getitem__
 raise KeyError(key)
KeyError: 'PYMOL_PATH'
If I try to launch from the MacPyMOL in the /Contents/MacOS folder, I get this error:
/Applications/MacPyMOLhybrid.app/Contents/MacOS/MacPyMOL ; exit;
'import site' failed; use -v for traceback
LookupError: no codec search functions registered: can't find encoding
Traceback (most recent call last):
 File "<string>", line 1, in <module>
ImportError: No module named os
Traceback (most recent call last):
 File "<string>", line 1, in <module>
NameError: name 'sys' is not defined
Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/Applications/MacPyMOLhybrid.app/pymol/modules/pymol/__init__.py", line 32, in <module>
 import copy
ImportError: No module named copy
Traceback (most recent call last):
 File "<string>", line 1, in <module>
NameError: name 'pymol' is not defined
PyMOL-ERROR: can't find module 'invocation'logout
Any ideas on how to fix this?
Thank you for your help!
Ryan

Dear Pymol Users!
I wounder whether it will be possible to save big ensemble of the loaded
into pymol Pdb's files as the trajectory output (like dcd format) what are
actually can be performed by vmd (e.g by means of
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/).
The problem in last case is that I don't know how to perform
superimposition of my conformers agains refeence frame (alternatively what
is easily performed in pymol). I'll be thankful for any suggestions.
Best wishes,
James

Hi Jared, thanks for your efford. Just to add more information, if you
have to do it many times, you'd better overlay the border by a script.
You can use ImageMagick or GraphicMagick to do that.
composite -gravity center overlay.png base.png base_with_border.png:
See http://www.imagemagick.org/script/composite.php
For how to erase the extra outline, see this thread I'm asking in the
ImageMagick forum:
http://www.imagemagick.org/discourse-server/viewtopic.php?f=1&t=25970&p=113686#p113686
It's quite complicate though.

Hi Pymolers
I have solved my problem. I am using surface cavity_mode, 3. I need to
change the ray_interior_color instead of the surface color. I guess this
is because pymol is visualizing the interior of the surface not the
exterior.
-Yarrow
On Thu, Jul 24, 2014 at 11:08 AM, Yarrow Madrona <ama...@uc...> wrote:
> I think the problem may have to do with the surface_cavity_mode being set
> to 3. I try to change the surface_cavity_mode but I still detect cavities
> instead of the surface. It seems like any option related to the surface is
> locked.
>
> -Yarrow
>

I think the problem may have to do with the surface_cavity_mode being set
to 3. I try to change the surface_cavity_mode but I still detect cavities
instead of the surface. It seems like any option related to the surface is
locked.
-Yarrow

Hello Pymol users,
As anyone experienced an instance where the surface transparency remained
stuck in one color? I changed it to pink a while back. However, now issuing
the comand:
set surface_color, green, object1
does nothing. Object1 is the object I want to color. Even if I try to
change the surface color globally it doesn't work (set surface_color,
green, all)
I would appreciate any help I can receive. Thank you.
-Yarrow

Hi Ooker -
As I understand it, you want to overlay a line to show which part of the surface belongs to which residue. There is currently no way to do this directly within PyMOL. However, is possible to achieve something similar using multiple layers in a composite image. See this previous thread: https://www.mail-archive.com/pym...@li.../msg12281.html
I’ve also just created a page on the PyMOL Wiki with an example: http://www.pymolwiki.org/index.php/Outline
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jul 24, 2014, at 10:15 AM, Ooker <gan...@gm...<mailto:gan...@gm...>> wrote:
I have a potential map of a protein and I would like to have a border
between a specific residue while the map keeps unchanged.
I have thought about making a new object of the residue and tried to
find a command similar to:
set label_outline_color, black
but I can't find one.
Do you have any ideas? Thank you so much.
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Seems to be working!
Thanks,
Matt
On 07/23/2014 02:33 PM, Thomas Holder wrote:
> Hi Matt,
>
> I pushed a fix to SVN rev 4084.
>
> Cheers,
> Thomas
>
> On 23 Jul 2014, at 14:06, Thomas Holder <tho...@sc...> wrote:
>
>> Hi Matt,
>>
>> thank you for the bug report. We will fix this as soon as possible.
>>
>> Cheers,
>> Thomas
>>
>> On 23 Jul 2014, at 13:06, Matthew Baumgartner <mp...@pi...> wrote:
>>> Hi, I am using pymol from the SVN, and I have run into a problem when
>>> using revision 4083.
>>> When loading an sdf file of small molecules, pymol segfaults with the
>>> following error:
>>>
>>> /usr/local/bin/pymol: line 3: 29872 Segmentation fault (core
>>> dumped) "/usr/bin/python"
>>> "/usr/local/lib/python2.7/dist-packages/pymol/__init__.py" "$@"
>>>
>>> I don't get the error when I revert to revision 4082.
>>> The diff indicates that the error is in the ObjectMoleculeSetDiscrete
>>> function in layer2/ObjectMolecule.c
>>>
>>> Thanks,
>>> Matt Baumgartner

I have a potential map of a protein and I would like to have a border
between a specific residue while the map keeps unchanged.
I have thought about making a new object of the residue and tried to
find a command similar to:
set label_outline_color, black
but I can't find one.
Do you have any ideas? Thank you so much.

Hi Jordan,
use the "pepseq" selection operator:
 select align_1, protein_1 and pepseq YYDFGHSFG
 select align_2, protein_2 and pepseq YYDFGHSFG
 align align_1, align_2
Cheers,
 Thomas
Jordan Willis wrote, On 07/23/14 21:58:
> Hi, 
> 
> I have a really just awful way of doing this and was wondering if there is a pymol solution that would make it easier.
> 
> Here is the problem.
> 
> Given two protein sequences, align their corresponding amino acids. The position of each of the strings is not known, just the sequence.
> 
> Ex.
> 
> Protein 1 - XXXXXXXXXXXXXXYYDFGHSFGXXXXXXXXXXX
> 
> Protein 2 - - XXXXXXYYDFGHSFGXXXXXXXXXXX
> 
> 
> What I would like is to select the sequences (pseudocode obviously).
> 
> 	select align_1 ,protein_1 and YYDFGHSFG
> 	select align_2, protein_2 and YYDFGHSFG
> 	align align_1, align_2
> 	RMSD is X.XX
> 
> Does this functionality exist?
> 
> Jordan
-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

Hi Justin,
before loading the map, do:
PyMOL> set normalize_ccp4_maps, off
Assuming you are loading from a ccp4 map file. There is also
normalize_grd_maps and normalize_o_maps.
Cheers,
 Thomas
Biel, Justin wrote, On 07/23/14 21:50:
> Is it currently possible to contour map representations (i.e. isomesh)
> by absolute values (electrons per cubic angstroms) rather than by the
> map's sigma value? For example, this is useful when making figures
> comparing maps from two different structures.
> 
> Sincerely,
> Justin T. Biel
> Graduate Student
> University of California San Francisco
> Integrative Program in Quantitative Biology
> Jus...@uc...
-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

Hi, 
I have a really just awful way of doing this and was wondering if there is a pymol solution that would make it easier.
Here is the problem.
Given two protein sequences, align their corresponding amino acids. The position of each of the strings is not known, just the sequence.
Ex.
Protein 1 - XXXXXXXXXXXXXXYYDFGHSFGXXXXXXXXXXX
Protein 2 - - XXXXXXYYDFGHSFGXXXXXXXXXXX
What I would like is to select the sequences (pseudocode obviously).
	select align_1 ,protein_1 and YYDFGHSFG
	select align_2, protein_2 and YYDFGHSFG
	align align_1, align_2
	RMSD is X.XX
Does this functionality exist?
Jordan
(apologize if you receive this in duplicate)

Is it currently possible to contour map representations (i.e. isomesh) by absolute values (electrons per cubic angstroms) rather than by the map's sigma value? For example, this is useful when making figures comparing maps from two different structures.
Sincerely,
Justin T. Biel
Graduate Student
University of California San Francisco
Integrative Program in Quantitative Biology
Jus...@uc...

Hi Matt,
I pushed a fix to SVN rev 4084.
Cheers,
 Thomas
On 23 Jul 2014, at 14:06, Thomas Holder <tho...@sc...> wrote:
> Hi Matt,
> 
> thank you for the bug report. We will fix this as soon as possible.
> 
> Cheers,
> Thomas
> 
> On 23 Jul 2014, at 13:06, Matthew Baumgartner <mp...@pi...> wrote:
>> Hi, I am using pymol from the SVN, and I have run into a problem when 
>> using revision 4083.
>> When loading an sdf file of small molecules, pymol segfaults with the 
>> following error:
>> 
>> /usr/local/bin/pymol: line 3: 29872 Segmentation fault (core 
>> dumped) "/usr/bin/python" 
>> "/usr/local/lib/python2.7/dist-packages/pymol/__init__.py" "$@"
>> 
>> I don't get the error when I revert to revision 4082.
>> The diff indicates that the error is in the ObjectMoleculeSetDiscrete 
>> function in layer2/ObjectMolecule.c
>> 
>> Thanks,
>> Matt Baumgartner
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Matt,
thank you for the bug report. We will fix this as soon as possible.
Cheers,
 Thomas
On 23 Jul 2014, at 13:06, Matthew Baumgartner <mp...@pi...> wrote:
> Hi, I am using pymol from the SVN, and I have run into a problem when 
> using revision 4083.
> When loading an sdf file of small molecules, pymol segfaults with the 
> following error:
> 
> /usr/local/bin/pymol: line 3: 29872 Segmentation fault (core 
> dumped) "/usr/bin/python" 
> "/usr/local/lib/python2.7/dist-packages/pymol/__init__.py" "$@"
> 
> I don't get the error when I revert to revision 4082.
> The diff indicates that the error is in the ObjectMoleculeSetDiscrete 
> function in layer2/ObjectMolecule.c
> 
> Thanks,
> Matt Baumgartner
-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi, I am using pymol from the SVN, and I have run into a problem when 
using revision 4083.
When loading an sdf file of small molecules, pymol segfaults with the 
following error:
/usr/local/bin/pymol: line 3: 29872 Segmentation fault (core 
dumped) "/usr/bin/python" 
"/usr/local/lib/python2.7/dist-packages/pymol/__init__.py" "$@"
I don't get the error when I revert to revision 4082.
The diff indicates that the error is in the ObjectMoleculeSetDiscrete 
function in layer2/ObjectMolecule.c
Thanks,
Matt Baumgartner
-- 

Hello Hidhi,
On Wed, 2014年07月23日 16:39 EDT, Nidhi Jatana <nid...@bi...>
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?
You should use the RMSF calculation as that takes into account all of the
structures. RMSD is a calculation that applies only to pairs of structures.
> I tried doing this using rmsf_states.py and color_b.py scripts:
As the author, I am somewhat familiar with these 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?
It sounds correct to me. Did it not produce the result you expected? By
setting byres=1, you are automatically only calculating the RMSF for the
C-alpha atoms of each residue, but that value is then used to modify the
B-values of all of the atoms in each residue. 
> 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?
Yes, as Andreas said to turn on the display of all states:
set all_states, 1
and to revert to just showing a single state:
set all_states, 0
Cheers,
Rob
-- 
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
<rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc

BS"D
Dear Andreas,
 Thanks very much for the help....
Harry
On Jul 23, 2014, at 2:34 PM, Andreas Warnecke wrote:
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
-------------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Weizmann Institute of Science Phone: 972-8-934-3625
234 Herzl St. Facsimile: 972-8-934-4159
Rehovot, 76100
Israel
Har...@we...<mailto:Har...@we...>

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 <nid...@bi...>
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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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 <
har...@we...> 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 Science Phone: 972-8-934-3625
> 234 Herzl St. Facsimile: 972-8-934-4159
>
> Rehovot, 76100
>
> Israel
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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.