[PyMOL] NAMD/dcd

2006-02-09 Thread zie...@ecr6.ohio-state.edu
HI ! I new one with PyMol and found it very promising for my works. However, I need analyze MD trajectories DCD from NAMD. Is there any clue to load DCD's, as manual talks only abaout Amber format ? Best Arturas Z.

[PyMOL] dash transparency

2006-02-09 Thread Desiree Fong
Is it possible to adjust the dash transparency? I would like to incorporate it into a movie so that the bond would fade in and out with the cartoon/stick of the protein. Thanks. Desiree Fong

Re: [PyMOL] What residues have I selected?

2006-02-09 Thread Robert Campbell
Hi Aaron, * Aaron New [2006-02-09 09:36] wrote: > I have selected atoms near an object of interest, and extended this via > byres to a selection of the other atoms that are part of the same residue. > Is there any way to output a file that would have the coordinates of the > atoms I have selected

Re: [PyMOL] output formats

2006-02-09 Thread Jerome PANSANEL
Hi, I think this software could be used: http://www.tb-software.com/products3.html http://www.tb-software.com/download/3dto3dsrc.zip It's free (as in beer ideology). Jerome Pansanel Le Mercredi 08 Février 2006 19:29, scott_lu...@med.unc.edu a écrit : > Thank you Jerome. > > Do you know of any w

RE: [PyMOL] Resize window problem

2006-02-09 Thread Warren DeLano
Martin, I would suggest updating or reinstalling the latest graphics drivers for your graphics card. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA

[PyMOL] What residues have I selected?

2006-02-09 Thread Aaron New
I have selected atoms near an object of interest, and extended this via byres to a selection of the other atoms that are part of the same residue. Is there any way to output a file that would have the coordinates of the atoms I have selected and the residues they comprise? Any tips appreciated. Ch

[PyMOL] PYMOL saving coordinates of docked molecule

2006-02-09 Thread Brian J Goodfellow
Marylin, try saving using the command line instead of the pull down menu i.e "save newfilename.pdb" This should save everything in one file. Brian -- *** Brian J Goodfellow Departamento de Química Universidade de Aveiro 3810-193 Aveiro, Portugal Tel: