[PyMOL] mset, cmd or objects, cut-off distance for interactions in a morph
Dear all, is there a way to specifically enable or disable objects during a movie? The command mv_cmd (rTools?) seems not work (e.g. mv_cmd 37,enable measure01). As you might guess I would like to disable or enable bonding distances in a morphing video. Does someone knows are more elegant way to show distances in certain frames during a morph depending on a cut-off distance (e.g <3.5A)? Thank you! Best regards, Bart -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] No module Error in running pymol
Dear friends I am having Ubuntu 10.04 and want to use pymol. There is no error in installation but it is giving following error during running pymol "r...@ritu-laptop:~$ pymol Traceback (most recent call last): File "", line 1, in ImportError: No module named pymol /usr/local/bin/python2.6: No module named pymol" Kindly help me in this situation. regards rituraj -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] python
Hello, How can I find out what version of python my current installation of pymol is using ? -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] No module Error in running pymol
Hi Rituraj, On Mon, 12 Jul 2010 17:43:02 +0530 rituraj purohit wrote: > Dear friends > > I am having Ubuntu 10.04 and want to use pymol. > There is no error in installation but it is giving following error > during running pymol > > "r...@ritu-laptop:~$ pymol > Traceback (most recent call last): > File "", line 1, in > ImportError: No module named pymol > /usr/local/bin/python2.6: No module named pymol" You seem to be running a python from the /usr/local/bin directory which is probably not what you want. The ubuntu 10.04 python is also python version 2.6, so you have no need to install another version in /usr/local/bin. Did you install PyMOL from the Ubuntu software repository (as opposed to getting from the PyMOL web site? It should work fine with the python in /usr/bin. 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 http://pldserver1.biochem.queensu.ca/~rlc -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] python
import sys print sys.version > -Original Message- > From: Vivek Ranjan [mailto:vran...@gmail.com] > Sent: Monday, July 12, 2010 10:37 AM > To: Pymol > Subject: [PyMOL] python > > Hello, > > How can I find out what version of python my current installation of > pymol is using ? > > -- > Thank you and Regards, > > Vivek Ranjan > > --- > --- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > 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 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] python
On Mon, 12 Jul 2010 10:37:07 -0400 Vivek Ranjan wrote: > Hello, > > How can I find out what version of python my current installation of > pymol is using ? One way is simply to type "python" in a terminal window and you should see something like: Python 2.6.5+ (release26-maint, Jul 1 2010, 00:47:18) [GCC 4.4.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> Or type "python -V" to see just the version. So I'm running version 2.6.5. 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 http://pldserver1.biochem.queensu.ca/~rlc -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] how to run a python script
Hi, Your assumptions are correct, as I've copied and tested your code, which works fine from the current working directory where I ran the pymol start script. It's probably a quirk w/ your installation? Otherwise, you can just specify the full path to your script or "cd" into the folder... either way. Goodluck, Paul On Fri, Jul 9, 2010 at 11:01 AM, Robert Campbell wrote: > On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan wrote: > > > Hello, > > > > I am trying to run a simple python script from Pymol and cannot run it: > > > > > I saved the above in a file named "axes.py" and put it in the same > > directory from where I type "pymol" (on ubuntu linux). Then I type > > "run axes.py" in pymol command bar. I get the following error message: > > > > * > > Traceback (most recent call last): > > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line > > 334, in parse > > parsing.run_file(path,self.pymol_names,self.pymol_names) > > File "/usr/local/lib/python2.6/dist-packages/pymol/parsing.py", line > > 455, in run_file > > execfile(file,global_ns,local_ns) > > IOError: [Errno 2] No such file or directory: 'axes.py' > > *** > > > > Any help ? > > Try typing the command "pwd" within PyMOL to see if it reports that you are > in the directory that you think you are. Also try typing "ls axes.py" to > see > if it can see it. Are you sure you haven't made a typo in the name of the > file? Otherwise I don't see why what you have done shouldn't work. > > 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 > http://pldserver1.biochem.queensu.ca/~rlc > > > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > 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 > -- Paul Rigor http://www.ics.uci.edu/~prigor -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ 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] pymol fetch
Hello, There is a script supercell at "http://pymolwiki.org/index.php/Supercell";. It uses the following example: run supercell.py fetch 2x19, async=0 Where is "2x19"... I mean the pdb file for this example is in which directory under pymol ? -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] pymol fetch
On 12/07/10 20:24, Vivek Ranjan wrote: > Hello, > > There is a script supercell at > "http://pymolwiki.org/index.php/Supercell";. It uses the following > example: > > run supercell.py > fetch 2x19, async=0 > > Where is "2x19"... I mean the pdb file for this example is in which > directory under pymol ? > > The fetch command directly fetches the pdb file from the online database. -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 signature.asc Description: OpenPGP digital signature -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ 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] Question on how to identify residue number on protein surface
Hi Jay Song, Why not use code that's already available? Check out http://pymolwiki.org/index.php/FindSurfaceResidues. Cheers, -- Jason 2010/7/12 SongJianHui : > Hi all, > > I am trying using PyMol to identify the residue numbers on a protein > surface. I have been thinking use a low efficient way to do this, i.e., > color each residues in surface display mode. I wonder if there is a better > way to fulfill this mission. > > Thanks in advance, > > Jay Song > > > 使用Messenger保护盾V2，支持多账号登录！ 现在就下载！ > -- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ___ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
