Re: [PyMOL] missing residues

@lists.sourceforge.net -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- All the data continuously

Re: [PyMOL] Rotation of a Protein

://p.sf.net/sfu/splunk-d2dcopy2 ___ 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 -- Michael

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

/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 University

Re: [PyMOL] PYMOL MOVIE

: 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] APBS values

-users@lists.sourceforge.net -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- Colocation vs. Managed

Re: [PyMOL] Model pdb section support

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 University

Re: [PyMOL] stick transparency

. -- ___ 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 -- Michael Zimmermann

Re: [PyMOL] drawing of objects for illustration

@lists.sourceforge.net -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University

[PyMOL] scripts with fetch

- -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University

Re: [PyMOL] scripts with fetch

Marius On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann micha...@iastate.eduwrote: 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 executed and then the structure

Re: [PyMOL] ellipsoidal particle

-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 Computational Biology Department of Biochemistry, Biophysics

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

-- ___ 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 -- Michael Zimmermann Ph.D. student

[PyMOL] pml script execution speed

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. 1.2r1 -- Michael Zimmermann Ph.D

Re: [PyMOL] draw the axes

___ 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 -- Michael Zimmermann Ph.D. student

Re: [PyMOL] CEalign - PyMOL Build

://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 University

[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

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,

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

[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

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

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

[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