Re: [PyMOL] pymol does not open from a terminal
Maia, you have to install libpng and/or libpng-devel. Andreas On Fri, Sep 11, 2009 at 3:04 AM, Maia Cherney ch...@ualberta.ca wrote: Hi, Could you please help me with a pymol problem. I have ubuntu linux and I have pymol in the /usr/bin (comes with ubuntu installation) and also one in the /programs/linux directory. But I can't open pymol in a terminal (both installations), only from applications/education menu. I get this error from /usr/bin/pymol: Traceback (most recent call last): File /var/lib/python-support/python2.5/pymol//__init__.py, line 167, in module import pymol File /var/lib/python-support/python2.5/pymol/__init__.py, line 412, in module from pymol import _cmd ImportError: /var/lib/python-support/python2.5/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding or this error from the programs/linux/pymol Traceback (most recent call last): File string, line 1, in ? File /raid/programs/linux/pymol-0.99rc1/modules/pymol/__init__.py, line 353, in ? import _cmd ImportError: libpng.so.3: cannot open shared object file: No such file or directory Could anybody ,please, advise me how to fix it. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Alignment Objects
Hi David On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com wrote: Is there any documentation on getting information out of alignment objects into scripts? I tried looking around the wiki, but I didn't see anything. I'm just wondering things like if I have a residue in one object, finding the residue in another object that has been aligned. If you create an alignment object when you do the alignment: align proteinA, proteinB, object=A_on_B then you can save a clustal formatted alignment file by typing: save A_aligned_with_B.aln, A_on_B (same applies if you use the super command instead of align). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Morph Movies
Hi, Anyone know how I can include a morph in the middle of a more complex movie? I have generated the morph (refine_rigimol.pdb) but cant figure how to include this set of frames into the middle of my movie. Im using Macpymol 1.2 ( generated the rigimol morph in ipymol). Many thanks Colin -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Alignment Objects
Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Morph Movies
Colin, Can you describe what you are trying to accomplish (overall) in more detail? There are different approaches one could take depending on the objective... The simplest, but limited approach is to use the mset and madd commands with variable numbers of frames: # show the initial state (1) for 60 frames mset 1 x60 # morph through to the final state (30) madd 1 -30 # play the final state 60 times madd 30 x60 # morph back to the initial state (1) madd 30 -1 And so on... Cheers, Warren -Original Message- From: Colin Levy [mailto:c.l...@manchester.ac.uk] Sent: Friday, September 11, 2009 11:40 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Morph Movies Hi, Anyone know how I can include a morph in the middle of a more complex movie? I have generated the morph (refine_rigimol.pdb) but cant figure how to include this set of frames into the middle of my movie. Im using Macpymol 1.2 ( generated the rigimol morph in ipymol). Many thanks Colin -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Alignment Objects
Maia, select all_arg_lys, resn arn+lys Cheers, Warren -Original Message- From: Maia Cherney [mailto:ch...@ualberta.ca] Sent: Friday, September 11, 2009 2:03 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Alignment Objects Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Alignment Objects
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney ch...@ualberta.ca wrote: Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? select resnam arg select chain A and (resnam lys or resnam arg) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] RMS
Carlos, David, etc., From the open-source code: http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/layer4/Cmd.c The returned rms values are as follows (in order): return Py_BuildValue((fiififi), rms_info.final_rms, rms_info.final_n_atom, rms_info.n_cycles_run, rms_info.initial_rms, rms_info.initial_n_atom, rms_info.raw_alignment_score, rms_info.n_residues_aligned); Cheers, Warren From: Carlos Ríos Vera [mailto:crosv...@gmail.com] Sent: Saturday, August 29, 2009 4:08 PM To: David Hall Cc: Warren DeLano; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RMS 2009/8/29 David Hall dwash59_2...@yahoo.com pymol.cmd.align(%s % name_struct1, %s % name_struct2) oh, thanks =) should return a list, the first element of which is the rms, if I remember correctly. Warren can probably say what the rest of the elements are. On this note, maybe we could start documenting on the wiki what exactly all these commands return. It would be very useful for scripting. Yeah, it would be great get that information. -David -- http://crosvera.blogspot.com Carlos Ríos V. Estudiante de Ing. (E) en Computación e Informática. Universidad del Bío-Bío VIII Región, Chile Linux user number 425502 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
