From: Sona V. <vas...@nc...> - 2001-11-22 19:35:25
|
Hi! Just wondering if there is a way to save a pymol session like in Insight and setor if I want to get back to it. Thanks. sona ---------------------------------------------------------------- Sona Vasudevan National Center for Biotechnology Information National Library of Medicine National Institutes of Health,Bldg. 38A, Rm. B2N21I, 8600 Rockville pike, Bethesda, MD 20894, USA Voice: (301)594-3154; Home: (703)-893-8424 Email: vas...@nc... or son...@ni... ----------------------------------------------------------------- |
From: Sona V. <vas...@nc...> - 2002-06-07 17:53:32
|
Hello All, Need your help: I would like to overlay a cartoon representation onto a surface representation and would like to color certain residues that show up on the surface representation. This is what I did and recall doing awhile ago but it isn't working now. I would appreciate knowing what i am doing wrong. Step 1: load temp.pdb step 2: create cpy=temp show surf, cpy set transparency=0.5, cpy Then I go on to color individual residues: select t1=(resi 42) Now I want residue 42 to be coloured say red on the surface 1.e object cpy. Ofcourse overlaying is not the problem. Thanks much, sona |
From: Craig S. <boi...@ma...> - 2002-10-09 22:19:20
|
Hello, On the advice of a friend, I recently downloaded the OSX beta version of PyMOL. So far I'm very,very impressed. I have two questions: 1. How do you display a simple CA trace. I saw the selection for a backbone trace. 2. I want to rms-fit two structural homologs. How is this done in PyMOL? I tried using the fit command and kept getting errors. Thanks for you help Craig L. Smith, Ph. D. Molecular Microbiology Washington University School of Medicine 660 South Euclid Box 8230 Voice: (314) 362-9054 Fax: (314) 362-1232 e-mail: sm...@bo... |
From: <wg...@ch...> - 2002-10-31 21:21:59
|
Hi Lieven: I don't have windows pymol or access currently to a windows machine, so I will have to tell you how I did it on the Mac version and then hope it is essentially identical with windows. I did this about 6 months ago in order to hyperlink quicktime to Powerpoint in XP. I am assuming hyperlinking to Pymol would work the same way, since it works the same way on a Mac. But you never know with Windows since 90% of the operating system seems to be dedicated to preventing you from using your computer. Open up powerpoint and create a new slide. In it put a word or picture or something. Then select that word or picture or whatever it is. Go to insert > hyperlink and then put in the full file hierarchy path to your pymol application Then when you are in presentation mode, you click on this and it starts pymol. On XP it seemed to embed it in situ (at least when I was using quicktime). In OS X it changes over to the pymol display. That's the basis for my claim that it works better in XP. I apologize if this doesn't. HTH, Bill Scott William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) |
From: mkienetz <mki...@ua...> - 2003-05-28 23:12:31
|
Dear All, How do I show the unit cell using pymol? Martin Martin Kienetz 429 MSB Department of Biochemistry University of Alberta Edmonton AB T6G 2H7 (780) 492-2422 |
From: Cameron M. <cm...@uc...> - 2003-05-28 23:50:17
|
Hi Martin, Visit Robert Campbell's repository of PyMOL scripts (http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find Python scripts to import into PyMOL for drawing unit cell edges (draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff... Cameron mkienetz wrote: >Dear All, > >How do I show the unit cell using pymol? > >Martin > >Martin Kienetz >429 MSB >Department of Biochemistry >University of Alberta >Edmonton AB >T6G 2H7 >(780) 492-2422 > > > >------------------------------------------------------- >This SF.net email is sponsored by: eBay >Get office equipment for less on eBay! >http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 >_______________________________________________ >PyMOL-users mailing list >PyM...@li... >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
From: Tolbert, B. <Blanton_Tolbert@URMC.Rochester.edu> - 2003-08-20 07:59:54
|
I was attempting to install pymol 0.9 using fink and got the following error message, Failed: Can't resolve dependency "numeric-py22" for package "pymol-0.90-2" (no matching packages/versions found) Can anyone advise me on what to do to get around this? Thanks in advance. Blanton |
From: Matt S. <mat...@ma...> - 2003-08-20 10:41:20
|
Hi Blanton, Are you running the unstable tree, or have you just copied the pymol-0.90-2 package to stable, you either have to enable the unstable tree, or copy the numeric-py22 package from the unstable to stable, it can be found at '/sw/fink/dists/unstable/main/finkinfo/sci' see here; http://fink.sourceforge.net/faq/usage-fink.php#unstable Matt On Wednesday, Aug 20, 2003, at 12:01 Australia/Canberra, Tolbert, Blanton wrote: > I was attempting to install pymol 0.9 using fink and got the following > error > message, > > Failed: Can't resolve dependency "numeric-py22" for package > "pymol-0.90-2" > (no matching packages/versions found) > > Can anyone advise me on what to do to get around this? Thanks in > advance. > > > Blanton > > > ------------------------------------------------------- > This SF.net email is sponsored by Dice.com. > Did you know that Dice has over 25,000 tech jobs available today? From > careers in IT to Engineering to Tech Sales, Dice has tech jobs from the > best hiring companies. http://www.dice.com/index.epl?rel_code=104 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Mohammad W. B. <mb...@ho...> - 2004-04-05 12:52:53
|
Dear pymol usres I want to increase the resolution of the figure but how? Save file is png and resolution is very poor and print quality is not good. I also make CA model by xfit and save file is rasted3d and it is opened by pymol and save as png but figure is not good quality for its low resolution. png file save as windows resolution. Could you suggest me how to increse windows resolution I mean png resolution. Thanks in advance Wadud _________________________________________________________________ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 |
From: Warren D. <wa...@de...> - 2004-04-05 17:54:30
|
Mohammed, ray width, height png filename.png for example, for a 5x4 figure at 300 dpi: ray 1600,1200 png hires.png (or use Save image... from the File menu after the ray command) Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Mohammad Wadud Bhuiya > Sent: Monday, April 05, 2004 5:53 AM > To: pym...@li... > Subject: [PyMOL] (no subject) > > Dear pymol usres > > I want to increase the resolution of the figure but how? Save > file is png and resolution is very poor and print quality is > not good. I also make CA model by xfit and save file is > rasted3d and it is opened by pymol and save as png but figure > is not good quality for its low resolution. png file save as > windows resolution. Could you suggest me how to increse > windows resolution I mean png resolution. > > Thanks in advance > Wadud > > _________________________________________________________________ > Protect your PC - get McAfee.com VirusScan Online > http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: xiaofeng q. <xia...@ho...> - 2004-04-07 04:02:04
|
Hi,everybody: Is there someway so that I can generate several asymmetry molecules from one asymmetry unit in pymol? Thank you. Xiaofeng _________________________________________________________________ Check out MSN PC Safety & Security to help ensure your PC is protected and safe. http://specials.msn.com/msn/security.asp |
From: Christian R. <c....@gm...> - 2004-04-22 09:35:31
|
hi ppl, is there a way to sort the list of objects/selections in the panel on the right side other than loading/selecting stuff in a specific order? simple example: I compare several ligands in a specific site, and save the data as pymol sessions; after adding new ligands//site conformations I'd like to sort the sites 1st, then the ligands. any hints? thanks a lot, christian -- NEU : GMX Internet.FreeDSL Ab sofort DSL-Tarif ohne Grundgebühr: http://www.gmx.net/dsl |
From: Warren D. <wa...@de...> - 2004-04-22 15:28:30
|
Christian, This isn't implemented yet, but it is on the to do list. Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Christian Rummey > Sent: Thursday, April 22, 2004 2:35 AM > To: pym...@li... > Subject: [PyMOL] (no subject) > > > hi ppl, > > is there a way to sort the list of objects/selections in the > panel on the right side other than loading/selecting stuff in > a specific order? > > simple example: I compare several ligands in a specific site, > and save the data as pymol sessions; after adding new > ligands//site conformations I'd like to sort the sites 1st, > then the ligands. > > any hints? > > thanks a lot, > christian > > -- > NEU : GMX Internet.FreeDSL > Ab sofort DSL-Tarif ohne Grundgeb|hr: http://www.gmx.net/dsl > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IBM Linux Tutorials > Free Linux tutorial presented by Daniel Robbins, President and CEO of > GenToo technologies. Learn everything from fundamentals to system > administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: ELHAM M. <el...@jh...> - 2004-04-26 20:52:51
|
Hello! I have 2 questions: 1) What is the correct/common email address to send your questions on PyMOL? 2) I have downloaded PyMOL on a PC(microsoft windows XP)using the instructions posted on the PyMOL site. But I am not able to get input files form the Internet--I simply wanted to go to the PUBMED and get the structure of a protein from PUBMED/web directly into the PyMOL. SO going to the external GUI of PyMOL , then File, then Open did not give me the option of opening the internet eventhough it is on our desktop. I could open other files such as :my computer, my files, my network places, just not the Internet!!! Does anybody know how to do it? Thank you for your time and consideration, ELham |
From: James S. <jst...@sc...> - 2004-06-16 23:06:38
|
Hi, The lab I am part of now has the licensed MacPymol incentive product. In response to the brilliant crystallography on OS X website maintained by Bill Scott, he recommends using a Powermate dial (Griffin Technology). I would like to follow in his footsteps, however the instructions he provides for configuring the system (http://chemistry.ucsc.edu/%7Ewgscott/xtal/powermate_pymol_osx.html) requires me to edit my .pymolrc file. As far as I can tell, I have no need for a .pymolrc file with this version and if I create one, all I seem to get is syntax errors. If anyone can help me as I have little to no experience with python scripting. Many thanks in advance James |
From: Alexey V P. <lx...@gn...> - 2005-02-16 08:50:53
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Hi, I have a problem with PyMOl 0.97 viewing pdb file with several models (MODEL 1...ENDMDL) I can upload somewhere (or attach?) the screenshot + pdb file to show it (~1.3 Mb). |
From: Kolli, M. <Mad...@um...> - 2005-07-20 17:40:54
|
Hi, I've just started using PyMol for making some figures. I'm very happy that it is so easy to use. However the resolution of my pictures is very bad even after rendering them. When I print them they are very pixellated. I'm sure there is something I'm not doing right. Any help, suggestions will be appreciated. Thanks. Regards, Madhavi Kolli Graduate Student UMass Medical School Worcester |
From: Joel T. <joe...@ot...> - 2005-07-20 21:03:34
|
Check out the post on "High end graphics". This will solve the problem.=20 Basically you can ray-trace your molecule at a resolution bigger tahn=20 teh screen size and then cut it down afterwards effectively generating a = high resolution graphic from a 72 dpi starting point Cheers J Kolli, Madhavi wrote: > Hi, > > I=92ve just started using PyMol for making some figures. I=92m very hap= py=20 > that it is so easy to use. However the resolution of my pictures is=20 > very bad even after rendering them. When I print them they are very=20 > pixellated. I=92m sure there is something I=92m not doing right. Any he= lp,=20 > suggestions will be appreciated. > > Thanks. > > Regards, > > Madhavi Kolli > > Graduate Student > > UMass Medical School Worcester > --=20 Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand =20 Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti Aotearoa Ph / Waea +64 3 4797293=20 Fax / Waeawhakaahua +64 3 4797034 |
From: yi z. <zha...@ya...> - 2005-07-24 03:43:24
|
Hi, everyone, I used symexp command in pymol to generate symmetry-related molecule, something like: cmd.symexp('sym', 'obj', 'obj',10 ) of course, I can manually save each symmetry-related molecule to *.pdb file by clicking save molecule button, but how can I write a script to save all of them or part of them? the symmetry-related objects are not appendable. thanks! yi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
From: <li...@ul...> - 2005-07-25 11:14:33
|
On Sunday 24 July 2005 05:42, yi zhang wrote: > cmd.symexp('sym', 'obj', 'obj',10 ) > > of course, I can manually save each symmetry-related > molecule to *.pdb file by clicking save molecule > button, but how can I write a script to save all of > them or part of them? the symmetry-related objects > are not appendable. I have used something like this in the past: #-------------- # get symmetry mates objs = [ n for n in cmd.get_names() if n[0:3]=="sym" ] for obj in objs: if cmd.get_type(obj)!="object:molecule": print "Something's wrong!" else: cmd.save(obj+".pdb",obj) #-------------- Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel |
From: Joseph F. <joe...@ya...> - 2005-09-25 18:15:09
|
There is a very useful functionality in Sybyl, whereby the user can "merge" a residue from one molecular area, into another molecular area. The residue then becomes a part of the latter moleculear area, without deleting it. I wonder whether there is such a functionality in PyMol. As an example, I have created a new object, consisting of several residues that I have extracted from the active site of a protein (using the create command). I then deleted these residues from the original object (active site of protein). I now want to merge an additional residue from the active site into the ligand object, and delete the residue from the active site, but without deleting the ligand object. Any assistance on this matter would be appreciated. Joe ______________________________________________________ Yahoo! for Good Donate to the Hurricane Katrina relief effort. http://store.yahoo.com/redcross-donate3/ |
From: D. B. P. <bp...@ch...> - 2005-11-02 18:06:22
|
To all: I am new to PyMol, and to structure programs in general. I am trying to build a beta sheet from a peptide molecule in the pdb. I can't seem to load more than one molecule at a time, and I do not see any instructions related to it in the manual. I am running version 0.98 beta 32 on a Mac G5 with the OS X (10.3.9) operating system. Any help would be greatly appreciated. Many thanks, Bryan Prince |
From: <Sri...@ju...> - 2006-03-03 12:18:49
|
<FONT face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size= =3D2><DIV>dear all </DIV><DIV>can we superimpose structures in pymol<BR></D= IV><DIV>Thanks & Regards<BR>srilatha potlapelly<BR>MSc&n= bsp;Biotechnology<BR>Drug discovery, <BR>#450,4th D Mai= n, 12th cross, <BR>Mahalakshmipuram - 560086 = <BR>Bangalore <BR>Office: +9180-23495461-64 Extn.-1029= <BR></DIV></FONT>= |
From: Andrea S. <and...@gm...> - 2006-03-03 12:20:18
|
Hi try align or fit regards andrea 2006/3/3, Sri...@ju... <Sri...@ju...>: > dear all > can we superimpose structures in pymol > Thanks & Regards > srilatha potlapelly > MSc Biotechnology > Drug discovery, > #450,4th D Main, 12th cross, > Mahalakshmipuram - 560086 > Bangalore > Office: +9180-23495461-64 Extn.-1029 > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live webc= ast > and join the prime developer group breaking into this new coding territor= y! > http://sel.as-us.falkag.net/sel?cmdlnk&kid=110944&bid$1720&dat=121642 > _______________________________________________ PyMOL-users > mailing list PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- "La conoscenza libera il genere umano dalla superstizione" J. Watson |
From: Blanton T. <bla...@ur...> - 2006-03-04 13:59:27
|
Hi pymol community I would like to recapitulate the crystal packing arrangement of a protein structure to look for neighbor interactions. Is it possible to do this in pymol? If so, please provide me some insight. Thanks, Blanton Tolbert Graduate Student University of Rochester Biophysics and Structural Biology 585-275-5189 bla...@ur... |