Re: [PyMOL] PYMOL MOVIE

ll of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/

Re: [PyMOL] movie enhancement feature request...

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 > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computation

Re: [PyMOL] Rotation of a Protein

ves: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University --

Re: [PyMOL] missing residues

OL-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 > -- Michae

[PyMOL] number of h-bonds

Dear PyMOL users, I was using Action -> find -> polar interactions within selection to get an idea about the hydrogen bonds and other polar interactions in some molecules. I would like to compare different conformations of a certain molecule and one metric could be the number of pair returned by

Re: [PyMOL] make morph with rigimol

one option would be to make intermediates based on linear interpolation and then make a movie of the "morph." Gerstein's group has done some work at this. http://www2.molmovdb.org/wiki/info/index.php/Morph_Server If you just want to visualize them together my suggestion would be to: show one of t

Re: [PyMOL] difficulties with pymol’s fuse command .

I have no experience with fuse, but my guess would be Mariana might want to just use 'bond' and translate one termini as needed. If she doesn't want to "manually" translate, there is always energy minimization to correct bond lengths. Take Care. On Tue, Dec 8, 2009 at 12:59 AM, Nir London wrote:

Re: [PyMOL] superimpose option

Dr. Vertrees, thank you for the thorough reply to Saeid's question. I just wanted to note that you don't have to install all of PyMol from source to use CE. You can set up CE and just run it when you want it, like other python add-ons. That might not be the case for the most recent version thoug

[PyMOL] select atoms near electron density

atoms in an object that are near to these density levels? Alternatively, can you turn a map into an object that can be used in this way (fill it with dummy atoms)? Thank you, Michael Zimmermann -- This SF.Net email is

Re: [PyMOL] Preserving sec. structure in states for animation

Another idea would be to use enable/disable. Load all the structures and then only have one enabled at a time load frame1.pdb, morph_frame1 . . . load frame20.pdb, morph_frame20 disable *frame* enable *frame1 take a picture disable *frame1 enable *frame2 take a picture repeat A bit tedio

Re: [PyMOL] Whitespacing?

If you have a lot of files to do this to, I would suggest learning at least a little bit of perl. It might not be as nice an option as a python tab manager (depending on your point of view), though. Perl uses regular expressions. In case you'd like to see how to do your tab-space replacement, th

[PyMOL] alignment algorithms

Dear PyMOL users, I have browsed the wiki and the first 300 mailing list messages in the archive (the sourceforge archive does not seem to have a search set up for the archive... arg!), but did not find any details about the algorithms behind 'fit' and 'super.' I understand how align works, and i

Re: [PyMOL] CEalign - PyMOL Build

ion > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > ___

Re: [PyMOL] draw the axes

ros just a phone call away. > http://p.sf.net/sfu/theplanet-com > ___ > 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] pml script execution speed

ot;png" then it runs considerably slower than if I open the GUI and run the script. I'm doing this to automate frame generation for movie making. Any idea why this would be and how to make the system call at least as fast as running the GUI? I use: Windows XP 64-bit SP2 PyMOL v. 1.2r

Re: [PyMOL] Rigimol morph using only part of protein

L 35487-0336 > > Phone: 205.348.8349 > FAX: 205.348.9104 > > E-mail: pfran...@bama.ua.edu > > > > > -- > > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourcefo

Re: [PyMOL] ellipsoidal particle

--- > ___ > 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] scripts with fetch

UME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb, prot Save: wrote "C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb". PyMOL>delete all -

Re: [PyMOL] scripts with fetch

; > On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann > wrote: > >> Dear PyMOL users, >> >> I was just making a script to selectively download sections of PDB files >> using fetch. When I run the pml from the GUI I see that all of the commands >> are execut

Re: [PyMOL] Atom selection based on Hydrogen Bonding Partners

rge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Departm

Re: [PyMOL] Moveable Camera

else fails. > > Thanks for your time, > > Tom > > -- > > ___ > 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

Re: [PyMOL] drawing of objects for illustration

s.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Zimmermann Ph.D. student in Bioinformatics and Co

Re: [PyMOL] stick transparency

it, contains privileged and > confidential information intended only for the use of the individual(s) or > entity named on the e-mail. If the reader of this e-mail is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient, you a

Re: [PyMOL] stick transparency

t to it, contains privileged and > confidential information intended only for the use of the individual(s) or > entity named on the e-mail. If the reader of this e-mail is not the intended > recipient, or the employee or agent responsible for delivering it to the > intended recipient,

Re: [PyMOL] coloring residues

Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State Unive

Re: [PyMOL] "Model" pdb section support

instills the confidence they need to proceed with transactions. > http://p.sf.net/sfu/oracle-sfdevnl > _______ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-use

Re: [PyMOL] APBS values

://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State Univer