pymol-users Mailing List for PyMOL Molecular Graphics System

Thank you Matt!
> On Feb 27, 2015, at 4:24 PM, Matthew Baumgartner <mp...@pi...> wrote:
> 
> Hi Adam,
> You can retrieve them using the iterate method.
> See: http://pymolwiki.org/index.php/Color#Getting_Atom_Colors <http://pymolwiki.org/index.php/Color#Getting_Atom_Colors>
> 
> HTH,
> Matt Baumgartner
> 
> 
> On 2/27/2015 4:28 PM, H. Adam Steinberg wrote:
>> I am creating a new PyMOL session and I have to match the colors that someone else used in a different PyMOL session. Is there any way to identify what colors they used for an obj or sele?
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
>> by Intel and developed in partnership with Slashdot Media, is your hub for all
>> things parallel software development, from weekly thought leadership blogs to
>> news, videos, case studies, tutorials and more. Take a look and join the 
>> conversation now. http://goparallel.sourceforge.net/ <http://goparallel.sourceforge.net/>
>> 
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users <https://lists.sourceforge.net/lists/listinfo/pymol-users>
>> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the 
> conversation now. http://goparallel.sourceforge.net/_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

much easier with ‘remove’
> reinitialize
> fetch 1Z92, type=pdb1
> as cartoon
> bg_color white
> 
> color red, ss h
> color yellow, ss s
> color green, ss l+"
> 
> remove /1Z92//A
On Feb 28, 2015, at 12:28 AM, Brenton Horne <bre...@ym...> wrote:
> Hi,
> 
> I've got this pml code:
> delete all
> fetch 1Z92, type=pdb1
> as cartoon
> bg_color white
> 
> color red, ss h
> color yellow, ss s
> color green, ss l+"
> 
> delete /1Z92//A
> But it doesn't delete chain A as I'd like it to. Any ideas of how I can delete chain A without removing any other parts of the structure? 
> 
> Thanks for your time,
> Brenton
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the 
> conversation now. http://goparallel.sourceforge.net/_______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi,
I've got this pml code:
 |delete all||
 ||fetch 1Z92, type=pdb1||
 ||as cartoon||
 ||bg_color white||
 ||
 ||color red, ss h||
 ||color yellow, ss s||
 ||color green, ss l+"||
 ||
 ||delete /1Z92//A|
But it doesn't delete chain A as I'd like it to. Any ideas of how I can 
delete chain A without removing any other parts of the structure?
Thanks for your time,
Brenton

Hi Adam,
You can retrieve them using the iterate method.
 See: http://pymolwiki.org/index.php/Color#Getting_Atom_Colors
HTH,
Matt Baumgartner
On 2/27/2015 4:28 PM, H. Adam Steinberg wrote:
> I am creating a new PyMOL session and I have to match the colors that 
> someone else used in a different PyMOL session. Is there any way to 
> identify what colors they used for an obj or sele?
>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

I am creating a new PyMOL session and I have to match the colors that someone else used in a different PyMOL session. Is there any way to identify what colors they used for an obj or sele?
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi all,
Incentive PyMOL 1.7.4.3 is up which fixes the wall-eye stereo bug.
Cheers,
 Thomas
On 22 Feb 2015, at 16:46, Thomas Holder <tho...@sc...> wrote:
> Hi Steve,
> 
> bug confirmed, thanks for reporting. We'll look into this ASAP.
> 
> I recommend to downgrade to 1.7.4.1.
> 
> Cheers,
> Thomas
> 
> On 22 Feb 2015, at 14:45, Hubbard, Stevan <Ste...@me...> wrote:
> 
>> I recently upgraded from PyMOL 1.3 to 1.7.4.2. Although it worked fine in 1.3, I cannot see side-by-stereo in 1.7.4.2. When I select Display>Stereo>Wall-Eye Stereo (or Cross-Eye Stereo), the screen splits into two halves, but the molecule is only shown in one half (right half for Wall-Eye, left half for Cross-Eye). Any suggestions?
>> 
>> Thanks,
>> Steve Hubbard
>> _______________________________________
>> Stevan Hubbard, Ph.D.
>> Professor
>> Skirball Institute &
>> Department of Biochemistry and Molecular Pharmacology
>> New York University School of Medicine 
>> 540 First Avenue 
>> New York, NY 10016
>> phone: 212-263-8938
>> fax: 212-263-8951
>> http://hubbard-lab.med.nyu.edu
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Good news for all those who are wondering about Adobe and the semantic web.
Larry Masinter (http://larry.masinter.net) will be with us at Sepublica. He
will be our keynote speaker with "Getting More Data Through the Publication
Pipeline". Larry will also participate in our round table, so if you want
to discuss the semantic web and document formats used for publication,this
is the right moment
Dont forget to submit your paper to Sepublica,
http://sepublica.mywikipaper.org/drupal/
-- 
-- 
Alexander Garcia
http://www.alexandergarcia.name/
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

Hi Pawel,
only "discrete" objects have per-state bonding. In discrete objects, states have independent atom sets, which comes down to similar memory consumption like individual objects (split_states).
PyMOL> load example.xyz, discrete=1
If you want to make a movie, instead of using one discrete object, I would create two objects. One for state 1-X, and one for X-N.
PyMOL> load example1to4.xyz, obj1
PyMOL> load example5to10.xyz, obj2, state=5
PyMOL> mset 1-10
Hope that helps.
Cheers,
 Thomas
On 01 Jan 2015, at 13:11, Pawe? Gniewek <gni...@gm...> wrote:
> Hi all,
> 
> I am having some troubles with the following problem:
> 
> I have a trajectory stored in a file having XYZ format - let's assume it has 10 states in total.
> 
> At the very beginning I have 5 atoms connected in a loop (like in cyclopentane):
> 
> ATOM1 - ATOM2
> ATOM2 - ATOM3
> ...
> ATOM5 - ATOM1
> 
> I create bonds by:
> "bond ATOM1, ATOM2"
> and so on.
> 
> However in my simulations at some point (let's say in state #4) a new element is introduced.
> If that happens I must break a bond ("unbond" command) between e.g. "ATOM1 - ATOM5" and then then create two new bonds:
> "ATOM1-ATOM6" 
> and 
> "ATOM5-ATOM6"
> 
> So what I want to obtain is a bond between atoms 1 and 5 up to the state #4, at the time of #4 I want to break a bond and create two new ones, and from that moment proceed with the new bonds' topology - so I can render every frame with a correct bonds network.
> 
> Moreover my trajectory files are usually too large to use "split_states".
> 
> Any ideas how to work this problem out?
> 
> Thanks,
> Pawel
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear everyone,
I have a MD simulation of coarse grain molecules, therefore not defined 
as typically for "normal" protein/ligands, but as beads.
I want to represent it using Pymol, and need to define bonds between the 
beads.
The problem is that I have 400 copies of my ligand, and all with the 
same name. I want to link bead1 with bead2, all having the name LIG.
How can I do it?
The CONECT record works only to define connections on a one-on-one 
basis, so it would be horrible for the whole file.
I tried the bond command in pymol with the following argument, but it 
doesn't work:
PyMOL>bond resi LIG and name B1, resi LIG and name B2
Editor-Warning: bonds cannot be created between objects, only within.
I guess this command line will create also bonds between B1 to all the 
399 other LIG B2...
(If "resi" would take into account the residue number, it would work?)
here is what the pdb file looks like:
ATOM6129B1LIG97740.880 105.97099.0901.000.00
ATOM6130B2LIG97741.700 105.20097.1801.000.00
ATOM6131B3LIG97741.880 104.86094.7501.000.00
...
ATOM6138B1LIG978116.680 127.990 105.9901.000.00
ATOM6139B2LIG978117.300 129.230 107.7201.000.00
ATOM6140B3LIG978119.340 130.290 108.5901.000.00
...
thank you for your help.
best
Vincent
-- 
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 07
http://www.ibcp.fr

Hi Steve,
bug confirmed, thanks for reporting. We'll look into this ASAP.
I recommend to downgrade to 1.7.4.1.
Cheers,
 Thomas
On 22 Feb 2015, at 14:45, Hubbard, Stevan <Ste...@me...> wrote:
> I recently upgraded from PyMOL 1.3 to 1.7.4.2. Although it worked fine in 1.3, I cannot see side-by-stereo in 1.7.4.2. When I select Display>Stereo>Wall-Eye Stereo (or Cross-Eye Stereo), the screen splits into two halves, but the molecule is only shown in one half (right half for Wall-Eye, left half for Cross-Eye). Any suggestions?
> 
> Thanks,
> Steve Hubbard
> _______________________________________
> Stevan Hubbard, Ph.D.
> Professor
> Skirball Institute &
> Department of Biochemistry and Molecular Pharmacology
> New York University School of Medicine 
> 540 First Avenue 
> New York, NY 10016
> phone: 212-263-8938
> fax: 212-263-8951
> http://hubbard-lab.med.nyu.edu
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I recently upgraded from PyMOL 1.3 to 1.7.4.2. Although it worked fine in 1.3, I cannot see side-by-stereo in 1.7.4.2. When I select Display>Stereo>Wall-Eye Stereo (or Cross-Eye Stereo), the screen splits into two halves, but the molecule is only shown in one half (right half for Wall-Eye, left half for Cross-Eye). Any suggestions?
Thanks,
Steve Hubbard
_______________________________________
Stevan Hubbard, Ph.D.
Professor
Skirball Institute &
Department of Biochemistry and Molecular Pharmacology
New York University School of Medicine
540 First Avenue
New York, NY 10016
phone: 212-263-8938
fax: 212-263-8951
http://hubbard-lab.med.nyu.edu

Hey :)
If I try to import scipy.linalg, Pymol quits abruptly. I could trace it to
a problem with the importing fblas, but can't work out what's wrong there.
I've checked my native implementation of Python 2.7 with SciPy, which works
without problem. Here's the log:
 PyMOL(TM) Incentive Product - PyMOL Executable Build
 Copyright (C) Schrodinger, LLC
 This PyMOL Executable Build is available only to PyMOL Power, Casual, and
 Developer Users who have a valid license to use this software product. Any
 other usage is specifically prohibited and may constitute a violation of
 United States and international copyright laws.
 This Executable Build integrates and extends Open-Source PyMOL 1.7.4.0.
 Detected OpenGL version 2.0 or greater. Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
 GL_VENDOR: NVIDIA Corporation
 GL_RENDERER: NVIDIA GeForce GT 750M OpenGL Engine
 GL_VERSION: 2.1 NVIDIA-8.26.28 310.40.55b01
 Detected 8 CPU cores. Enabled multithreaded rendering.
2015年02月19日 17:36:38.355 MacPyMOL[46379:507] HID: Apple Internal Keyboard /
Trackpad
2015年02月19日 17:36:38.356 MacPyMOL[46379:507] HID: Counted 1 buttons on this
device.
2015年02月19日 17:36:38.356 MacPyMOL[46379:507] HID: Tsjerk Wassenaar‚Äôs Mouse
2015年02月19日 17:36:38.356 MacPyMOL[46379:507] HID: Counted 2 buttons on this
device.
2015年02月19日 17:36:38.357 MacPyMOL[46379:507] HID: Apple Internal Keyboard /
Trackpad
2015年02月19日 17:36:38.357 MacPyMOL[46379:507] HID: Counted 3 buttons on this
device.
2015年02月19日 17:36:38.357 MacPyMOL[46379:507] HID: Max number of buttons
found: 3.
PyMOL>import scipy.linalg.fblas
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
If you need more info, let me know.
Cheers,
Tsjerk
-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Stephen,
I was missing libfreetype6 library and libxml2 needed to be updated.
Cheers,
Arnaud
On 31/01/15 19:09, Stephen P. Molnar wrote:
> Seeing as youa re using a Debian derivative try the following:
>
> sudo apt-get install subversion build-essential python-dev python-pmw 
> libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev
>
> cd /tmp
> svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
> cd pymol
>
> prefix=/home/computation/Apps/pymol
> modules=$prefix/modules
>
> python setup.py build install \
> --home=$prefix \
> --install-lib=$modules \
> --install-scripts=$prefix
>
> Of course, edit the file to suit your system.
>
>
> On 01/30/2015 04:13 AM, Arnaud Basle wrote:
>> Dear all,
>>
>> I am trying to compile pymol from source following the instructions
>> here: http://www.pymolwiki.org/index.php/Linux_Install
>>
>> It used to work for me a while ago but now the compilation hangs without
>> error. Pressing return give me back the terminal prompt. The compiling
>> process does not stop always at the same point.
>>
>> I am using Linux Mint 17 64 bits (based on Ubuntu).
>>
>> Anyone has seen such behaviour?
>>
>> Cheers,
>> Arnaud
>> PS: see below example of output
>>
>> layer3/Selector.cpp:11037:36: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++)
>> ^
>> layer3/Selector.cpp: In function ‘int* SelectorEvaluate(PyMOLGlobals*,
>> char (*)[1024], int, int)’:
>> layer3/Selector.cpp:11107:15: warning: variable ‘opFlag2’ set but not
>> used [-Wunused-but-set-variable]
>> int opFlag, opFlag2, maxLevel;
>> ^
>> layer3/Selector.cpp:11108:19: warning: variable ‘cc2’ set but not used
>> [-Wunused-but-set-variable]
>> char *q, *cc1, *cc2;
>> ^
>> layer3/Selector.cpp: In function ‘char (* SelectorParse(PyMOLGlobals*,
>> char*))[1024]’:
>> layer3/Selector.cpp:11562:51: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> if((q - q_base) >= sizeof(SelectorWordType)) {
>> ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> float, float*)’:
>> layer3/Selector.cpp:11845:32: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp:11859:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> int, int, float*, int*)’:
>> layer3/Selector.cpp:12102:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp:12118:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp:12146:36: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp: In function ‘DistSet*
>> SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int,
>> int, int, int, int, float*, int*)’:
>> layer3/Selector.cpp:12378:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp:12428:34: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp:12474:38: warning: comparison between signed and
>> unsigned integer expressions [-Wsign-compare]
>> for(a = cNDummyAtoms; a < I->NAtom; a++) {
>> ^
>> layer3/Selector.cpp: In function ‘int SelectorLoadCoords(PyMOLGlobals*,
>> PyObject*, int, int)’:
>> layer3/Selector.cpp:6705:9: warning: ‘itemsize’ may be used
>> uninitialized in this function [-Wmaybe-uninitialized]
>> switch(itemsize) {
>> ^
>>
>>
>> ... and then nothing
>>
>
-- 
Dr Arnaud Basle X-ray facilities manager
Newcastle Structural Biology Laboratory
University of Newcastle
Medical School
ICAMB
Framlington place
NE2 4HH Newcastle upon tyne
Phone 0191 208 8931
 

Hello Everyone,
Is it possible to open Jmol session file : ".spt" with Pymol? If so, then how?
Or is there a converter?
Would be a great help.
Thanks.
Regards,
Nicee Srivastava
Doctoral student
Dr. Dirk Fasshauer's lab
Department of Fundamental Neurosciences
University of Lausanne
CH-1005 Lausanne
+41 21 692 52 67
Nic...@un...

Hi Jared, Simon and all Edu PyMOL users,
I don't think Python 3.x is involved here, the interpreter does know about "reduce". However, inside list comprehension syntax, "reduce" is not known anymore (?). Edu MacPyMOL is linked against Python 2.5, which on OS X 10.10 is actually symlinked to Python 2.6.
So far Schrödinger had no plans to update the Edu builds. They "just worked" and provided enough functionality for educational purposes. Unfortunately, this is not true anymore for OS X 10.10. That being said, we don't want to provide software that doesn't work, and we also are committed to provide free and easy (precompiled) PyMOL access to people in education. We are now working on an updated Edu build, testing and approval in progress.
Cheers,
 Thomas
On 17 Feb 2015, at 09:43, Sampson, Jared <Jar...@ny...> wrote:
> Hi Simon - 
> 
> It looks like your default Python is now 3.x rather than 2.x. The built-in function reduce() was moved to functools.reduce() as of version 3.0. You can confirm whether this is the case via "python --version" on the command line.
> 
> One solution might be to make 2.7 the default again, perhaps via symlink to /usr/bin/python2.7 or adjusting your $PATH, although honestly I'm not sure about which Python is actually used by the precompiled Edu binaries. Maybe others can chime in on that.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
> 
> 
> 
> 
> 
> 
> On Feb 16, 2015, at 8:24 AM, Simon Fortier <sim...@um...> wrote:
> 
>> Hi,
>> I'm trying to select specific chains with the following command, which used to work.
>> 
>> select xxxx, /3J3A//D
>> 
>> However, under Yosemite 10.10.2 (latest update), I keep receiving the following error msg and can't select chains anymore...very annoying...any ideas?
>> 
>> Traceback (most recent call last):
>> File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/parser.py", line 254, in parse
>> self.result=apply(layer.kw[0],layer.args,layer.kw_args)
>> File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selecting.py", line 103, in select
>> selection = selector.process(selection)
>> File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selector.py", line 113, in process
>> st = reduce(lambda x,y:x+"&"+y,lst)
>> AttributeError: 'module' object has no attribute 'reduce'
>> 
>> Thanks
>> 
>> -- 
>> Simon Fortier
>> Ph.D Candidate
>> Institute of Research in Immunology and Cancer
>> Université de Montréal
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear pymol gurus,
I am using find_buried_waters.py (
http://www.pymolwiki.org/index.php/Find_buried_waters) which returns a list
of buried water atoms. I would like to discard from this selection those
waters with some, but not all, of their atoms buried. I can't figure out
how to do the selection. Can anyone help me out, please?
Best,
Jose Borreguero

Hi Simon -
It looks like your default Python is now 3.x rather than 2.x. The built-in function reduce() was moved to functools.reduce() as of version 3.0. You can confirm whether this is the case via "python --version" on the command line.
One solution might be to make 2.7 the default again, perhaps via symlink to /usr/bin/python2.7 or adjusting your $PATH, although honestly I'm not sure about which Python is actually used by the precompiled Edu binaries. Maybe others can chime in on that.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Feb 16, 2015, at 8:24 AM, Simon Fortier <sim...@um...<mailto:sim...@um...>> wrote:
Hi,
I'm trying to select specific chains with the following command, which used to work.
select xxxx, /3J3A//D
However, under Yosemite 10.10.2 (latest update), I keep receiving the following error msg and can't select chains anymore...very annoying...any ideas?
Traceback (most recent call last):
 File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/parser.py", line 254, in parse
 self.result=apply(layer.kw<http://layer.kw/>[0],layer.args,layer.kw_args)
 File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selecting.py", line 103, in select
 selection = selector.process(selection)
 File "/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selector.py", line 113, in process
 st = reduce(lambda x,y:x+"&"+y,lst)
AttributeError: 'module' object has no attribute 'reduce'
Thanks
--
Simon Fortier
Ph.D Candidate
Institute of Research in Immunology and Cancer
Université de Montréal
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Dear colleagues,
For a review, I'd like to re-create a picture of an ELF of a water molecule similar to the example at http://www.pymolwiki.org/index.php/Ramp_New in a different orientation and with different colours perhaps. I have no experience with the calculation of ELFs nor with TopMod, so I wonder if would be possible to just obtain the H2O_elf.cube and the H2O_esyn.cube files used in the example above (Schrödinger?)? Needless to say, this will be properly acknowledged in any publication.
Cheers,
Uli
---------------------------------------------------------------------------
dr ulrich gohlke
staff scientist - macromolecular structure and interaction
max-delbrück-center for molecular medicine (mdc)
+49 30 9406 - 2725<tel:+49%2030%209406%20-%202725> (w)
+49 30 9406 - 2548<tel:+49%2030%209406%20-%202548> (fax)
ulr...@md...<mailto:ulr...@md...>
http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/

Hi,
I'm trying to select specific chains with the following command, which used
to work.
select xxxx, /3J3A//D
However, under Yosemite 10.10.2 (latest update), I keep receiving the
following error msg and can't select chains anymore...very annoying...any
ideas?
Traceback (most recent call last):
 File
"/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/parser.py",
line 254, in parse
 self.result=apply(layer.kw[0],layer.args,layer.kw_args)
 File
"/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selecting.py",
line 103, in select
 selection = selector.process(selection)
 File
"/Users/Simon/Downloads/MacPyMOLEdu.app/pymol/modules/pymol/selector.py",
line 113, in process
 st = reduce(lambda x,y:x+"&"+y,lst)
AttributeError: 'module' object has no attribute 'reduce'
Thanks
-- 
Simon Fortier
Ph.D Candidate
Institute of Research in Immunology and Cancer
Université de Montréal

Hi Yuxing,
3j3y has no b-factors (they are all 0.0), but the map_new command takes b-factors into account. The solution is, before calling map_new:
PyMOL> set gaussian_b_floor, 50
Cheers,
 Thomas
On 12 Feb 2015, at 16:12, Yuxing Liao <Yux...@UT...> wrote:
> Hi all,
> 
> I was trying to show low resolution surface representation for very large structures following the example athttp://www.pymolwiki.org/index.php/Huge_surfaces. I was able to do it for the PDB 1AON using
> 
> PyMOL>fetch 1aon, type=cif
> PyMOL>set gaussian_resolution, 10
> PyMOL>map_new map, gaussian, 10, 1aon, 10
> ObjectMap: Map created.
> ObjectMap: Computing Gaussian map for 58870 atom positions.
> ObjectMap: Normalizing: mean = 1.537536 & stdev = 2.457675.
> Executive: object "map" created.
> PyMOL>isosurface surf, map, 1.0
> Executive: object "surf" created.
> Isosurface: created "surf", setting level to 1.000
> ObjectSurface: updating "surf".
> 
> But for some recent huge structures that are only available in mmCIF format, like 3J3Y, the isosurface command produces nothing.
> 
> PyMOL>fetch 3j3y, type=cif
> PyMOL>set gaussian_resolution, 10
> PyMOL>map_new map, gaussian, 10, 3j3y, 10
> ObjectMap: Map created.
> ObjectMap: Computing Gaussian map for 2116800 atom positions.
> Executive: object "map" created.
> PyMOL>isosurface surf, map, 1
> 
> Any ideas? It is run in Pymol 1.7.4.0 on a computer with Windows 7 and 4GB memory. Thanks.
> 
> Yuxing Liao
> 
> UT Southwestern
> 
> Medical Center
> 
> The future of medicine, today.
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi all,
I was trying to show low resolution surface representation for very large structures following the example at http://www.pymolwiki.org/index.php/Huge_surfaces. I was able to do it for the PDB 1AON using
PyMOL>fetch 1aon, type=cif
PyMOL>set gaussian_resolution, 10
PyMOL>map_new map, gaussian, 10, 1aon, 10
ObjectMap: Map created.
ObjectMap: Computing Gaussian map for 58870 atom positions.
ObjectMap: Normalizing: mean = 1.537536 & stdev = 2.457675.
Executive: object "map" created.
PyMOL>isosurface surf, map, 1.0
Executive: object "surf" created.
Isosurface: created "surf", setting level to 1.000
ObjectSurface: updating "surf".
But for some recent huge structures that are only available in mmCIF format, like 3J3Y, the isosurface command produces nothing.
PyMOL>fetch 3j3y, type=cif
PyMOL>set gaussian_resolution, 10
PyMOL>map_new map, gaussian, 10, 3j3y, 10
ObjectMap: Map created.
ObjectMap: Computing Gaussian map for 2116800 atom positions.
Executive: object "map" created.
PyMOL>isosurface surf, map, 1
Any ideas? It is run in Pymol 1.7.4.0 on a computer with Windows 7 and 4GB memory. Thanks.
Yuxing Liao
________________________________
UT Southwestern
Medical Center
The future of medicine, today.

Hi Jett,
We are currently working on better (multi-level) transparency for all representations, this will be a feature for the next PyMOL release.
In the current PyMOL version, you may see two artefacts for semi-transparent spheres in real-time rendering:
1) The "shading" that you describe comes from unsorted triangles. This affects the old non-shader rendering, where spheres are made from triangles. I assume you use an older PyMOL version or a graphics driver which does not support shaders.
2) New shader based sphere rendering (PyMOL 1.6+) looks much better, but for two intersecting semitransparent spheres, only one of them will be transparent with respect to the other one.
Ray tracing should show the correct transparency, so I wonder why it looks solid for you. PyMOL by default does single-layer transparency per representation (transparency_mode 2) Maybe you expect multi-layer, which would be transparency_mode 1:
PyMOL> set transparency_mode, 1
Hope that helps.
Cheers,
 Thomas
On 12 Feb 2015, at 12:45, SongJianHui <gi...@ho...> wrote:
> Hello, everyone,
> 
> I've been trying use pymol to generate an image based on C-alpha coordinates only. I tried to set the sphere to be transparency by the command "set sphere_transparency, 0.5". However, the surface of the sphere shows some shading which looks quite odd. If I ray trace the image, the surface looks nice but it is solid rather than transparent. Any suggestions? Thanks.
> 
> Best,
> Jett Song
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello, everyone,
I've been trying use pymol to generate an image based on C-alpha coordinates only. I tried to set the sphere to be transparency by the command "set sphere_transparency, 0.5". However, the surface of the sphere shows some shading which looks quite odd. If I ray trace the image, the surface looks nice but it is solid rather than transparent. Any suggestions? Thanks.
Best,
Jett Song
 		 	 		 

 Hi pymol community, 
How I can get the atomic list and coordinates involve in solvent accessible area from PDB structure using pymol. Any suggestion regarding program or script would be great. 
thank you Regards,Sajid

Hi Hugo,
unfortunately, "partial" loading of named selections is currently not supported. As a workaround, you could use the following function to write out a script which recreates all current selections.
from pymol import cmd
@cmd.extend
def dump_selections(filename):
 '''
DESCRIPTION
 Dump a script which recreates all current named selections
 '''
 handle = open(filename, 'w')
 for name in cmd.get_names('selections'):
 for (model, index) in cmd.index(name):
 print >> handle, 'cmd.select("%s", "(%s`%d)", merge=1)' % (
 name, model, index)
Hope that helps.
Cheers,
 Thomas
On 05 Feb 2015, at 06:44, Hugo Botelho <hug...@gm...> wrote:
> Dear all,
> 
> I wish to merge multiple PyMOL *.pse sessions. Each file contains multiple objects and named selections. The names of each object and selection are unique.
> 
> Is there a way to merge two pse files while preserving named selections?
> 
> I followed the advice of a previous thread ( https://sourceforge.net/p/pymol/mailman/message/28993953/ ) and tried the following commands:
> 
> load sessionA.pse
> load sessionB.pse, partial=1
> 
> These commands indeed merge the two sessions but ALL named selections in sessionB.pse are lost.
> 
> Thank you,
> Hugo
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.