Re: [PyMOL] Spectrumany bug?
To wrap up and summarize, a new version of the script is available in the wiki that circumvents the minor python trouble, and this works well with 1.2r2 and I guess later Pymol versions, and it works really well! My favorite 'indian summer' gradients for now: spectrumany count, paleyellow yelloworange brightorange, chain A spectrumany count, olive deepolive splitpea, chain B spectrumany count, orange ruby firebrick , chain C Thanks - Tassos On Apr 6, 2011, at 8:54, Thomas Holder wrote: Hi Tassos, as Folmer already suggested your PyMOL version, or rather your python version could be the problem. The line that throws the error uses generator syntax, which was introduced in python 2.4. This can easily be backported so you don't need another python version. I updated the script in the wiki so it should work with older python now. Can you download again and try? Cheers, Thomas On Tue, Apr 5, 2011 at 8:49 PM, Anastassis Perrakis wrote: Hi - I am trying to use the script by Thomas Holder, Spectrumany http://www.pymolwiki.org/index.php/Spectrumany When I import the script (run) I get: PyMOL>run sp.pml Traceback (most recent call last): File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse parsing .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names) File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in run_file execfile(file,global_ns,local_ns) File "sp.pml", line 81 col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list) ^ SyntaxError: invalid syntax == any help? Tassos -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ 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] Spectrumany bug?
Hi - I am trying to use the script by Thomas Holder, Spectrumany http://www.pymolwiki.org/index.php/Spectrumany When I import the script (run) I get: PyMOL>run sp.pml Traceback (most recent call last): File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 332, in parse parsing .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names) File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 455, in run_file execfile(file,global_ns,local_ns) File "sp.pml", line 81 col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list) ^ SyntaxError: invalid syntax == any help? Tassos -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev ___ 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] disconnected loop in pymol
Dear all, I have a small domain which is mostly loops, its a Cys-knot. All residues are in the preferred Rama regions, and all atoms are present in the PDB, but Pymol decides to 'break' my cartoon! Would anyone have a solution to force pymol draw a nice loop where the break is? (see small image attached) Thanks in advance, Tassos <> -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] Smooth fading of surface in movie?
A silly but working solution is to embed the pymol script in a csh script which changes the value for the transparency in small steps. Not ellegant but if you know csh/sh/bash it's easy. A. Sent from my iPhone On 1 Sep 2009, at 16:23, "Schubert, Carsten [PRDUS]" > wrote: That would require execution of a python program within a specific scene, which is not supported as far as I know. Scenes are intended to be static representations of display states, for lack of a better word. You would need to manually run the fade script before transitioning the scene. Not sure if this is what you want. Looks as if you may be better off plunging into movies if you really need the effect. Mark Lutz, David Asher , Learning Python, o’Reilly Great book i f you want to dive into python. Cheers, Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 9:56 AM To: PyMOLBB Subject: Re: [PyMOL] Smooth fading of surface in movie? Dear Carsten, yes, thanks. However, for a smooth fading, that would require a lot of scenes. Is there a simple python loop, that would create scenes with smooth transparency fading-in from 0 to 1 and that I could use in my pymol-scripts? Unfortunately, I'm not familiar with python, yet ... Best regards, Dirk. Am 01.09.2009 um 15:39 schrieb Schubert, Carsten [PRDUS]: Dirk, you could try playing around with different transparency settings in subsequent scenes to emulate the effect. HTH Carsten From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de] Sent: Tuesday, September 01, 2009 8:57 AM To: PyMOLBB Subject: [PyMOL] Smooth fading of surface in movie? Dear Warren, using PyMOL without any additional "plug-ins", like slerpy or eMovie, is it possible to fade in or out a surface of, say, a ligand, between scenes? Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail:kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** --- --- --- - 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- us...@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
[PyMOL] 1-2 October: What is a Macromolecular Complex ? meeting at the NKI, Amsterdam
Dear all, This is a reminder and some news for the meeting: "What is a macromolecular Complex? Shades of Meaning Across Cellular, Systems, and Structural Biology" http://xtal.nki.nl/Oct2009 - Registration closes on Monday 7th September at 12:00 noon. No exceptions after the deadline. - There will be eight (8) fellowships for attending the meeting, 500 Euro (max) each (*) Best regards on behalf of the organizers, Tassos (*) Only available if your lab is NOT part of the EU programs that support the meeting (SPINE-2-Complexes, TEACH-SG, 3D-Repertoire) and you really wanted to attend but could not for financial reasons, but 500 Euro will make it possible for you to join us, please email a.perrakis.AT.nki.nl with a short motivation and research interests, 10-15 lines max (no attachments please, simple text). Preference will be given to people not yet registered, since we might well assume that people that already registered had the money already sorted. The amount is the MAXimum available per person for ALL expenses, and it will be reimbursed after the meeting, *** based on receipts ***! -- 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] mapping sequence conservation metrics on the B factor column ...
Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. Thanks in advance, Tassos
[PyMOL] pymol and EM 'models'
hi all - could one use pymol to read in EM/Tomography images in one the formats below: stacked images from IMOD .rec format. conversion of this stack of images to meta, patch, rib, or vrml ? Thanks, Tassos
[PyMOL] between views
Dear pymolers - One can store 'Scenes' and then switch between them; the algorithm that goes from one scene to each other is very nice. Can one ask Pymol to write frames going from one scene to another to png files to make a movie ? or does anyone have python code that can render the transitions between views/scenes in a different way ? best - tassos
[PyMOL] APBS and Pymol
Hi - I installed apbs and tools (0.4.0) in a Linux box. I then specified the location of psize.py and apbs executable. when i load a protein and click on 'set grid' according to instructions I get on a new window a rather cryptic response: Error: 6 ValueError Exception in Tk callback Function: at 0x414cfbc4> (type: ) Args: () Traceback (innermost last): File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwDialog.py", line 153, in command=lambda self=self, name=name: self._doCommand(name)) File "/Xsoftware/pymol/ext/lib/python2.3/Pmw/Pmw_1_2/lib/ PmwDialog.py", line 132, in _doCommand return command(name) File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1055, in execute self.runPsize() File "/Xsoftware/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1096, in runPsize size.runPsize(pdb_filename) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 267, in runPsize self.parseInput(filename) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 102, in parseInput self.parseLines(file.readlines()) File "/usr/local/apbs-0.4.0/tools/manip/psize.py", line 116, in parseLines self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00119.63 Any clues ? A.
[PyMOL] Last chance for Como !
Dear all, 11 April is the closing date for registering for the Como School if you want your abstract to be considered for an oral presentation ! http://www.crystallographyschool.org/ There's only a few places left ...! We are looking forward to see you all there for what we hope it will be a great meeting. Tassos, Andrea, Stefania, Marjolein and Derek.
[PyMOL] Como School: 21-25 May 2006
Dear all, On behalf of the organizing committee I would like to draw your attention to the 8th International School on the Crystallography of Biological Macromolecules For more information please visit: http://www.crystallographyschool.org The 'Como meeting' as it is commonly known, is unique in combining a series of methods talks that cover all aspect of crystallographic structure determination, with talks about exciting research in Structural Biology and lively and well-attended poster sessions - some of which are selected for oral presentations' and all these in the unique atmosphere and great hospitality offered in the lake-side city of Como. Don't miss the opportunity to register - we hope to see as many of you as possible to what we hope will be an excellent meeting, worthy of the history of the series ! Tassos
[PyMOL] Re: [ccp4bb]: Current Stereo 3D Display Info
Hi all - While on the subject and after thanking Warren for providing the excellent resource ...: We have some nice 3D monitors and Nvidia cards in Linux PC's we do stereo with. Warren correctly points out that you need: 1280x960 @ 120 Hz requires H-sync of 123 kHz 1344x1008 @ 120 Hz requires H-sync of 130 kHz 1400x1050 @ 120 Hz requires H-sync of 136 kHz (In fact you need your monitor to switch to these refresh rates only when in stereo, but thats a detail) However, I am totally unable to convince the NVidia drivers we have for Linux to operate at the sync rates I want them to and Warren advices! Thus, we have noticeable flicker at stereo mode (in the non-stereo windows only) which is a shame, given our excellent monitors. Is that expected or can be corrected ? Could anyone please advice me how to set the Nvidia Linux drivers to operate at the proper sync rates then ? Tassos PS - Iiyama Vision Master Pro 514 / HM204DT (H-sync: 142 kHz) is still available by some European vendors new and is great, we have two, plus an old trusty EIZO T966 which is also cool. (Warren, I could not find that on your list,its a good machine, does 136 and you might be able to find one still) On Jan 28, 2006, at 20:59, Warren DeLano wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Folks, Whether you favor Macintosh, Linux, or Windows for stereo 3D visualization, you're going to need some specific (and increasingly rare) hardware. To help you find it, we've just updated our information page on stereo-3D-capable displays, cards, emitters, and glasses: http://pymol.sf.net/stereo3d.html Remarkably, we can now only find one company selling a brand new CRT monitor suitable for stereo 3D. If you find any others, please do let us know! Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com
Re: [PyMOL] PyMOL author??
I am s impressed by Apple on that one: The page with Warren's name was corrected 'as we speak'...! Apple guys, since you are watching, why not add other Structural Biology software ? CCP4, ARP/wARP, Coot all run in OSX ... (and ARP/wARP modules ARE optimized for G5, in one instance outperforming the Linux version by being 20+ faster - lots of EXPs and smart programming from Serge Cohen ...) Happy that tomorrow we place the order for our new Xserve cluster ! Apologies for the non-Pymol interferences !!! Tassos On 27 Apr 2005, at 21:41, Anastassis Perrakis wrote: ... and furthermore, HKL2000 was not a graphics and visualization software last time I checked ...! Tassos On 27 Apr 2005, at 21:14, Jim Nettles wrote: Michael Love did some early Darwin ports. Thanks MIchael, and we do need to make sure Warren gets the appropriate limelight. Thanks Warren! Jim N. P.S. I'll send a note to my Apple person On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote: Seems like Apple thinks that PyMOL was written by Michael Love!? Go to http://www.apple.com/science/software/lifescience.html towards end of page. _ Mark A. Saper, Ph.D. sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --- SF.Net email is sponsored by: Tell us your software development plans! Take this survey and enter to win a one-year sub to SourceForge.net Plus IDC's 2005 look-ahead and a copy of this survey Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tell us your software development plans! Take this survey and enter to win a one-year sub to SourceForge.net Plus IDC's 2005 look-ahead and a copy of this survey Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tell us your software development plans! Take this survey and enter to win a one-year sub to SourceForge.net Plus IDC's 2005 look-ahead and a copy of this survey Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] PyMOL author??
... and furthermore, HKL2000 was not a graphics and visualization software last time I checked ...! Tassos On 27 Apr 2005, at 21:14, Jim Nettles wrote: Michael Love did some early Darwin ports. Thanks MIchael, and we do need to make sure Warren gets the appropriate limelight. Thanks Warren! Jim N. P.S. I'll send a note to my Apple person On Apr 27, 2005, at 2:37 PM, Mark A Saper wrote: Seems like Apple thinks that PyMOL was written by Michael Love!? Go to http://www.apple.com/science/software/lifescience.html towards end of page. _ Mark A. Saper, Ph.D. sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --- SF.Net email is sponsored by: Tell us your software development plans! Take this survey and enter to win a one-year sub to SourceForge.net Plus IDC's 2005 look-ahead and a copy of this survey Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tell us your software development plans! Take this survey and enter to win a one-year sub to SourceForge.net Plus IDC's 2005 look-ahead and a copy of this survey Click here to start! http://www.idcswdc.com/cgi-bin/survey?id=105hix ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
