Re: [PyMOL] Pymol Morph movie error

> mpeg_encode_in, mpeg_encode_out, mpeg_encode_err = > os.popen3(_mpeg_encode_exe) > > WindowsError: [Error 2] The system cannot find the file specified: 'Ex: > C\\Temp /c "C:\\Program Files\\PyMOLPyMOL\\ext\\bin\\mpeg_encode.exe"' > > produce: compression faile

Re: [PyMOL] Segmentation fault when I tried to load a pdb file

F pymol: line 3: 17889 Segmentation fault. Could you help me to fix > this please? Thanks. Beibei -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- ___ PyMOL-users

Re: [PyMOL] Atoms appears on cartoon at high resolution

when zooming in. Cheers, Thomas On 07 Oct 2015, at 09:48, Thomas Holder <thomas.hol...@schrodinger.com> wrote: > Hi Lucile, > > This picture looks unusual, can you give some details on how you created it? > E.g. is this a full-atom protein structure, or a CA-only or pseudo-atom >

Re: [PyMOL] Atoms appears on cartoon at high resolution

> when ray tracing at high resolution an helix cartoon? (see attached picture) > thanks in advance > Lucile > > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Full-scale, agent-less Infras

Re: [PyMOL] GROMACS trajectories

> outdated and defunct now. > pymolwiki.org/index.php/User:Speleo3/VMD_plugins -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Full-scale, agent-less Infrastructure Monitoring from a single d

Re: [PyMOL] Problems loading new mrc-format electron density files into pymol

t; > I can provide the .mrc files if someone would like to take a look at them. > They are too large to attach to this email (they bounced back from the pymol > mail server). > > > Thanks in advance for any help, > > > Mike > > Michael F

Re: [PyMOL] morphing with heteroatoms

I am trying to morph two structures using the commercial version of > Pymol. Pymol looses heteroatoms (zinc in my case) while morphing. Is > there any way around this? > > (I tried replacing zinc with water and linking it to the protein using > CONECT - didn't work) > &g

Re: [PyMOL] measuring wizard

ferent atom from object1 is being chosen. Is it a bug in > program or am I doing something wrong? > > > Regards, > > Vaheh Oganesyan > MedImmune, ADPE > www.medimmune.com -- Thomas H

Re: [PyMOL] measuring wizard

esy...@medimmune.com> wrote: > Thank you reply, Thomas. > > Invoking > > alter all, ID = index > > didn't help. > > Regards, > > Vaheh Oganesyan > www.medimmune.com > > > -Original Message- > From: Thomas Holder [mailto:thomas.hol...@sch

Re: [PyMOL] Pymol crash when deleting callback object

> As an aside, you can also crash many versions of pymol by making mistakes in > the callback, such as passing a different name for the callback and the cgo > object (yes, this is a silly thing to try, but it shouldn't crash). > > -Spencer -- Thomas Holder PyM

Re: [PyMOL] pdbml

useful we can include that in the next PyMOL release. Cheers, Thomas ''' Adds a "load_pdbml" command to PyMOL. (c) Thomas Holder, Schrodinger, LLC ''' import os from pymol import cmd @cmd.extend def load_pdbml(filename, object='', discrete=0, multiplex=1, zoom=-1, quiet=1, _self=c

Re: [PyMOL] Ploting coordinates

7278cc > 141.61303 115.28156 115.56962 0.448000.471680.8 > #7278cc > > Where the first three columns are the x, y and z coordinates, the next three > are the size of the object, and the last is the colour (which isn’t so > important - neither is the size, rea

Re: [PyMOL] label

y have any idea whether pymol could label the absolute > configuration (R/S) for a chiarity atom? > > Thank you very much. > > Albert -- Thomas Holder PyMOL Princi

Re: [PyMOL] how can we display properties?

logP, surface area and so on. I am just wondering is it > possible to display those properties in Pymol? > > Thank you very much > > Albert -- Thomas Holder PyMOL Pri

Re: [PyMOL] pymol fails to open (crash)`

program”. Same issue from the start menu. I can open the > program by double clicking on a pdb file and there are no issues. > > Current version is 1.7.6.2 > > Any idea how to fix this? Might be my hardware but just wondering if others > see this or there is a fix?

[PyMOL] PyMOL Open-Source Fellowship - Call for Applications

to develop free resources to help scientific progress and the community as a whole. Details and application instructions can be found on http://pymol.org/fellowship The application deadline is November 1st, 2015. We look forward to your submissions! Cheers, Thomas -- Thomas Holder PyMOL

Re: [PyMOL] XYZ format - max size of the name field

; defined with 0 atoms > > However, at the same time if I do: > select H_100, name H100 > I get: > selection "H100" defined with 2 atoms > what means that the last character has been omitted. > > Of course I can work it out by naming atoms like: HH01 instead of H1000

Re: [PyMOL] any hotkey?

tkey in Pymol so that we can center > in the Ligand automatically? For instance: > > If I press keyboard "L", Pymol zoom to ligand binding pocket > automatically > > Thanks a lot > > Albert -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ---

Re: [PyMOL] how to copy color?

...@gmail.com wrote: Hello: I've colored object1 in various color in different regions. I am just wondering how can we copy the color scheme for object1 to object2? Object 2 is the same protein with object1 but with different conformations. Thank you very much Albert -- Thomas Holder

Re: [PyMOL] python command to get b-factor and occupancy of a single atom?

Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Pymol crash when raytracing empty graphics

) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] How to name overfull chains in PDB file?

either because there is only one colum (colum 22) for the chain ID in PDB file format. So what is the proper way to name the chains for this circumstance? Thanks in advance. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Thomas Holder PyMOL Principal Developer

Re: [PyMOL] bonding nucleic acid bases

. Cheers, Thomas ''' (c) 2015, Thomas Holder, Schrodinger LLC License: BSD-2 ''' from pymol import cmd try: get_raw_distances except NameError: try: from psico.querying import get_raw_distances except ImportError: print 'please install psico or download and run

Re: [PyMOL] test message

blacklisted for some reason? Thanks, H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's

Re: [PyMOL] installing other libraries with pymol python

recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips. Jordan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Monitor 25 network devices or servers

Re: [PyMOL] installing other libraries with pymol python

2015, at 18:04, Jordan Willis jwillis0...@gmail.com wrote: Wow that is so cool. Is there any drawbacks I can expect? On Jun 23, 2015, at 1:44 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Jordan, if you want to use MacPyMOL with other libraries then I recommend to use

Re: [PyMOL] Difficulty running RNA coloring program

have attempted to run the attached program. I know the program works on older versions, but I get the following error: AttributeError: 'module' object has no attribute 'extend' Does anyone know how to fix this? RNA_coloring_pymol.py -- Thomas Holder PyMOL Principal Developer Schrödinger

Re: [PyMOL] Error: NameError: name 'callback' is not defined

to Thomas Holder this is now fixed in github. In the next weeks we are going to try to get out a new release of CMview that contains the patch. In the meantime you can try using an older PyMOL version, e.g. 1.7.2 (I've just tested it and it worked for me). Cheers Jose

Re: [PyMOL] Unusual error after distance measurement

Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] citing pymol script in thesis--copyright issues?

on the modified script make sure to note what modifications I did versus what was there originally? Thanks. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] SCWRL version with educational-use PyMOL?

, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello. Does anyone know which version of SCWRL (backbone-dependent rotamer library) is used in the educational-use-only version of PyMOL? Regards, Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] create bonds between selections within cutoff radius

with time and capability willing to take this up and maintain this resource or are we just letting this wither away? Cheers, Carsten -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Thursday, May 28, 2015 9:17 AM To: Osvaldo Martin Cc

Re: [PyMOL] MacPyMOL in command line mode

errors about connecting to WindowServer And I can tell it actually tried to launch the GUI very briefly, then returned to the command line to process the scripts. Is this right? Can I run it remotely on another computer just from pure command line. Thanks. CY -- Thomas Holder PyMOL

Re: [PyMOL] What legal license does PyMOL's logo available under?

Hi Justin, the logo that Brenton is referring to isn't included in the Open-Source repo or tarballs. It's only used with Mobile PyMOL and Incentive PyMOL. Cheers, Thomas On 28 May 2015, at 14:16, Justin Lecher j.lec...@fz-juelich.de wrote: On 28/05/15 19:26, Thomas Holder wrote: Hi

Re: [PyMOL] What legal license does PyMOL's logo available under?

of PyMOL's logo (i.e., this one), as I would like to upload it to Wikimedia Commons. Thanks for your time, Brenton -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] create bonds between selections within cutoff radius

atom like iterate (n. pd), bond id ID, (n. si) within 2.5 of (id ID) but get an syntax error. Is it possible to create bonds within an iteration? Best regards, tmartin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] white background

only after clicking inside the viewer window. I don’t think either of the mentioned are special features. Can it be fixed, please? Thank you. Regards, Vaheh Oganesyan MedImmune, ADPE www.medimmune.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Handling of scene specific global settings?

for different scenes. Right now I am using 1.7.3, but was wondering if anything has changed in 1.7.6 in that regard? The issue is not new, but it would be nice if there would be a feature like this implemented. Cheers, Carsten -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] regarding theseus wrapper

/pymol/modules/psico/fitting.py, line 648, in _run_theseus handle = open(os.path.join(tempdir, 'theseus_transf2.txt')) IOError: [Errno 2] No such file or directory: '/tmp/tmpwXC24Y/theseus_transf2.txt' -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] regarding theseus wrapper

Hi Priyan, I updated the wrapper, it now supports THESEUS 3.x: https://github.com/speleo3/pymol-psico Cheers, Thomas On 15 May 2015, at 07:26, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Priyan, the wrapper fails because THESEUS 3.0.0 changed the output. I suggest to use

Re: [PyMOL] Logging commands errors

the following error. Error: unknown setting '6'. The log.pml file: $ cat log.pml /cmd.set('6',1,'',0) It seems to not be getting the right name for the background setting and is just putting in '6' instead. Thanks for your help, Matt Baumgartner -- Thomas Holder PyMOL Principal

Re: [PyMOL] Someone interested in writing a DSSR plugin for PyMOL?

-5334 mesguerra.org mauricio.esgue...@icm.uu.se +++ -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard

[PyMOL] Someone interested in writing a DSSR plugin for PyMOL?

experience with Python and the PyMOL API for writing an extension or plugin. Please contact me if this sounds appealing to you. Get DSSR from http://x3dna.org/ See it hooked up with JSmol: http://chemapps.stolaf.edu/jmol/jsmol/dssr.htm Cheers, Thomas -- Thomas Holder PyMOL Principal Developer

Re: [PyMOL] Delete all but one object

: 858.646.3100 x 4216 Email: blechtenb...@sanfordburnham.org -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box

Re: [PyMOL] RMS over a MD trajectory.

Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical

Re: [PyMOL] Difficulty with Pymol segfault in CentOS 7 VM

movement. It may also be of interest to note that I have used opencascade without any problems as a 3d rendering and cad visualization software on this same VM. Thank you, Derek Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

[PyMOL] PyMOL 1.7.6 released

at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications

Re: [PyMOL] Raw map access

. electron density) at a particular coordinates? I would like to know sigma value for a particular atom. Is there any way, using python, to achieve that? Best regards, Filip -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

;http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html Thanks very much for your help again. Best wishes On 24/04/2015, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Wei-Bing, support to load topology files with the vmd plugins was added in PyMOL 1.7.4 (previous versions only

Re: [PyMOL] 3D mouse

parties without the express consent of the sender. If you believe you have received this email in error please inform the sender and remove it from your system. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] How to use vmd molfile_plugin in pymol?

-- -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50

Re: [PyMOL] Problem with How do I change the font in the Tck/Tk external GUI window?

=app.my_fw_font) What file I must modify and with which code ? What with ./python2.7/dist-packages/pmg_tk/skins/normal/__init__.pyc? Thanks in advance ( expecially from my eyes ) Saverio -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Interleaved atoms when creating from two objects

of the objects, but I haven't been able to find a workaround yet. Sort seems to operate on the resi and ignores the ID chain. Is this a bug or am I doing something wrong? Thanks, Spencer -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Beginning with PyMol

is perhaps broken. I will do an extensive testing and be back with information. Is there a self-sustaining package in your website that can run on its own, just like Geogebra independent package? Regards, Rajib Yuktimmana On 04/20/2015 06:48 PM, Thomas Holder wrote: Hi Rajib Yuktimmana

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

, 1.74 save session.pse There are limitations. For details, see: http://pymolwiki.org/index.php/pse_export_version Cheers, Thomas On 08 Apr 2015, at 15:12, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Matt, there might be room for improvement regarding our versioning scheme

Re: [PyMOL] Beginning with PyMol

On 04/19/2015 07:28 PM, Thomas Holder wrote: Hi Rajib Yuktimmana, you can interactively build molecules using the builder: http://pymolwiki.org/index.php/Builder Enjoy! Cheers, Thomas On 19 Apr 2015, at 08:03, bkpsusmitaa bkpsusmi...@gmail.com wrote: Dear Sir / Madam, My

Re: [PyMOL] Beginning with PyMol

? Eagerly awaiting your reply, Rajib Yuktimmana -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance

Re: [PyMOL] MacPyMol working dir

” file starting from the working directory with the fancy interface of MacPyMol, rather than the basic Unix interface. Thanks, gg-kawa -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free

Re: [PyMOL] working on mmCIF assembly support

. Cheers, Tsjerk On Thu, Apr 9, 2015 at 6:48 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi all, I'm working on reading biological assemblies from mmCIF files. The patch against the latest SVN code can be downloaded from http://pymol.org/tmp/pymol-assembly-svn-r4115.patch

Re: [PyMOL] Cartoon visualization of per-residue txt data

-- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best

Re: [PyMOL] when number of atoms changes, colors change in an uncontrolled manner

Braun -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

. ExectiveSetSession-Warning: restore may be incomplete. Any idea what is wrong, or do I need to downgrade back to 1.7.4? Thanks in advance, Matt Baumgartner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Backwards compatibility error: ExectiveSetSession-Error: after names .

inform my collaborators not to update past 1.7.4. On 4/8/15 2:38 PM, Thomas Holder wrote: Hi Matt, PyMOL session files are in general not forward compatible. See for example: https://sourceforge.net/p/pymol/mailman/message/31070268/ Cheers, Thomas On 08 Apr 2015, at 14:19

Re: [PyMOL] Zoom animation

on this mailing list. Thanks for your time, Brenton -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance

[PyMOL] Educational-Use-Only PyMOL Updated

/ This is not a full version of PyMOL and is not intended as a free replacement for academic PyMOL licenses. Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming

Re: [PyMOL] Compile Errors on SVN 4111

systems flawlessly. Justin -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership

Re: [PyMOL] green rings

Incentive PyMOL 1.7.4.4 fixes this problem. Cheers, Thomas On 13 Mar 2015, at 23:55, Thomas Holder thomas.hol...@schrodinger.com wrote: The latest update to SVN fixes the ring color problem. Cheers, Thomas H. Adam Steinberg wrote, On 03/10/15 10:39: Thank you! On Mar 10, 2015

Re: [PyMOL] Assign secondary structure on group

The latest update to SVN fixes this. Cheers, Thomas Thomas Holder wrote, On 03/06/15 15:35: Hi Matt, thanks for the bug report. If you use the command line instead, it works if you put the group name in parenthesis, which forces PyMOL to treat it as an atom selection: PyMOL dss

Re: [PyMOL] green rings

The latest update to SVN fixes the ring color problem. Cheers, Thomas H. Adam Steinberg wrote, On 03/10/15 10:39: Thank you! On Mar 10, 2015, at 9:07 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Quentin, Adam, David, Francis, I just looked at the code, color is hardcoded

[PyMOL] Recent changes to SVN

need: export CPPFLAGS=-std=c++0x Cheers, Thomas -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed

[PyMOL] Announcing Jared Sampson's fellowship renewal

Source Fellowship Program and the fellows here http://pymol.org/fellowship. Cheers, Thomas the PyMOL Team at Schrödinger -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel

Re: [PyMOL] epymol module error

, x86, 64 bit (PyMol v.1.7.2.4). Could anybody suggest the way to overcome, please? Sincerely, Niyaz -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go

Re: [PyMOL] Assign secondary structure on group

, I'm using pymol 1.7.4.0. The A assign sec. struct. command doesn't seem to work when you call it on a group. It works fine on the objects in the group individually, but it doesn't apply the command to the objects when called from a group. Thanks, Matt Baumgartner -- Thomas Holder PyMOL

Re: [PyMOL] PyMOL syntax .properties file for SciTE

a .properties file for the PyMOL syntax for use in SciTE. Currently I'm using python .properties for highlighting PyMOL code but as you's know PyMOL syntax isn't 100% consistent with python syntax. Thanks for your time, Brenton -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] scipy problem

: PyThreadState_Get: no current thread Abort trap: 6 If you need more info, let me know. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive

Re: [PyMOL] bonds in ligands for MD simulations?

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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Can't import pymol2 on Windows machines

-- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- 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

Re: [PyMOL] Wall-eye stereo problem in PyMOL 1.7.4.2

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 thomas.hol...@schrodinger.com wrote: Hi Steve, bug confirmed, thanks for reporting. We'll look into this ASAP. I recommend to downgrade to 1.7.4.1

Re: [PyMOL] XYZ trajectory file - unbond two atoms, insert a new one, and create new bonds.

too large to use split_states. Any ideas how to work this problem out? Thanks, Pawel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel

Re: [PyMOL] Wall-eye stereo problem in PyMOL 1.7.4.2

://hubbard-lab.med.nyu.edu -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports

Re: [PyMOL] Chain Selection doesn't work (MacPymolEdu)

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. -- Download BIRT iHub

Re: [PyMOL] shade on transparent spherical surface

-- Thomas Holder PyMOL Principal Developer Schr?0?2dinger, Inc. -- 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

Re: [PyMOL] Low resolution surface of large structures

, today. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub

Re: [PyMOL] merging pse sessions selections

but ALL named selections in sessionB.pse are lost. Thank you, Hugo -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored

Re: [PyMOL] cartoon_highlight_color for specific regions of structure?

with the command set cartoon_highlight_color, yellow, /Unwin_4Ang_2bg9//B What is the correct syntax for applying cartoon_highlight_color to specific selections of a protein? Thanks. Gregg -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Polar contact residues

are no longer automatically selected. Is there a setting that I need to change? Regards, Sze Yi -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming. The Go

Re: [PyMOL] Cannot compile svn source

Biology Laboratory University of Newcastle Medical School ICAMB Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 8931 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World

Re: [PyMOL] apbs error (Error in background function)

I manually set up the paths but they get lost when I exit pymol. Is there a way to permanently store this information? Kind regards, Matic On 28. 01. 2015 16:58, Thomas Holder wrote: Dear Matic, this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/ Please install

Re: [PyMOL] scripting: pymol.session

scripts from .pymolrc.py, load a session file *and* get the correct pymol.session object within the script? Or is there an alternative way to get custom data saved in session files that can be used in scripts? Best, Christian -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Phosphoserine

, Does any one know if there is a simple way to mutate a serine to a phosphoserine using pymol? Or what would be the best way to achieve this? Thanks Monica -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Bug in Save Molecule dialog box

4107 from the SVN built from source on Ubuntu 14.04. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed

Re: [PyMOL] apbs error (Error in background function)

savvy user here so this may be entirely my fault. Thank you! -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel

Re: [PyMOL] different colours for isomeshes in version 1.7.4.0

. Is this a bug, a feature or maybe just something specific to my system? Any ideas? Best regards, Gerhard -- Gerhard Fischer, PhD Postdoctoral Research Associate University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge United Kingdom -- Thomas Holder

Re: [PyMOL] MacPyMOL fink download

/pymol.py /Applications/Chimera.app/Contents/Resources/share/Molecule/copymolecule.py /sw/lib/cctbx/cctbx_sources/iotbx/pymol.py ... and many more ... -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- New Year

Re: [PyMOL] How to determine distance of matching atoms in aligned nonidentical structures?

to snoop around in the alignment object created by the align command, but did not make much inroads. Anyone have any experience with this? Thanks Carsten -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

-15 16:55, Sampson, Jared wrote: set spec_reflect, 0, all and not organic -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET

Re: [PyMOL] Lift PyMOL Viewer Window

doctorat || PhD student Laboratoire du Pr Rafael Najmanovich Faculté de Médecine et des Sciences de la Santé (FMSS) Université de Sherbrooke lmore...@me.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] Cel shading in PyMOL

the Goodsell-like representation from here? Cheers, Osvaldo. On Tue, Jan 13, 2015 at 7:29 AM, Jacob Lewis jl...@uowmail.edu.au wrote: Hi all, Has anyone figured out a good way to do Cel shading in pymol? Or even the sort of variables to play with? Cheers, Jacob -- Thomas

Re: [PyMOL] exporting maps

created a pseudo-low resolution electron density map from a PDB-file using the map_new command. Is it possible to export or save that map to a file? Any format should be fine. Daniel -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

Re: [PyMOL] The angle between two subunit of a protein

...@aliyun.com wrote: Dear all, I have a protein complex which contains two subunit. How can I measure the angle between these to subunit? Thanks Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc

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