[PyMOL] labels not displaying

2006-04-05 Thread Yoder, Marilyn
This is an unusual and annoying problem. I'm running the latest version of Pymol on two PC machines, one in my office and one at home. I cart my session file on a jump drive back and forth. On my PC at home, the session file displays the labels just fine and dandy. But using the same session f

[PyMOL] disulfide bonds

2006-03-16 Thread Yoder, Marilyn
Hi, I apologize because I suspect this question has been asked before, but I don't see it in the FAQ, Wiki, and can't figure how to efficiently search the maillist archive. How does one draw a disulfide bond? My preference is the classical 'thunderbolt', from CA-S-S-CA atoms. Thanks, Marilyn

[PyMOL] ball-and-sticks, controlling bond color

2006-02-15 Thread Yoder, Marilyn
Hi all, There is a beautiful ball-and-stick image on pymol-wiki that I am trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). The wiki image has grey bonds and light blue balls for carbon, dark blue for nitrogen, and red balls for oxygen. My problem is that all my bonds an

[PyMOL] saving coordinates of docked molecules in new orientation

2006-02-08 Thread Yoder, Marilyn
Hi all, After manually docking a molecule to another molecule (from a different .pdb file), is it possible to write out the coordinates of the moved and docked molecule with it's 'new' coordinates relative to the .pdb to which it was docked? Marilyn Marilyn D. Yoder Division of Cell Biology a

[PyMOL] displaying electrostatic maps

2004-08-05 Thread Yoder, Marilyn
I'm am a very new PYMOL user. I'm trying to calculate and display and electrostatic map, similar to what I used to get in GRASP. My version of PYMOL I downloaded (yesterday) has the APBS plugin already installed. It's the subtleties of displaying the surface that has me confused. I displayed my