[PyMOL] Simulating electron density

Hey everyone, I remember at some point there was a command you could issue to pymol to generate a simulated electron density map around a structure. I'm trying to do this for a cover figure. Does anyone remember what the command (and syntax) is and if you can set the resolution (I actually wa

[PyMOL] Secondary Structure assignments and Molscript compatability

Hello All, I am a long-time Molscript user and devotee and am trying to make the move to PyMol for various reasons. A lot of the structures I work with are at moderate-low resolution making automated secondary-structure prediction difficult and most of them don't contain SS flags in the origin

[PyMOL] Series of general questions

Dear PyMol users, I realize the following may be somewhat basic questions, but after fiddling with the program a while and trying out example scripts from the web, I cannot seem to get things to work properly. The last question is kind of advanced and would have cool effects if someone knows h

[PyMOL] Ball and stick

I've noticed that 'stick_ball' was an added feature to PyMol in a recent version, however I can't seem to get it to work. I can change the stick_ball_ratio, but MacPyMol 0.95 doesn't recognize stick_ball in any format. Does anyone know how to create ball-and-stick representations in this version?

Re: [PyMOL] Motion Blur

Waren's example for a torsion looks pretty cool. If you're trying to make it look like a molecule is translating in some direction, you can actually pull this off quite nicely in photoshop. Select the thing you want create the action shot for and copy it. Before deselecting it use the motion blu

[PyMOL] Creating cell surface

Hey Fellow PyMolers, I should be able to figure this out but I simply haven't after much fiddling and googling. I'm trying to create a cell surface for a cover figure and in Molscript I usually did this by making a PDF file with a single atom, rendering it in CPK, and then blowing its atom_rad

Re: [PyMOL] Creating cell surface

.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > >> -Original Message- >> From: pymol-users-ad...@lists.sourceforge.net >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of >> Tony Giann

[PyMOL] Moving Objects

Hey fellow PyMoler's, If you have multiple objects loaded and on screen at once, is it possible to rotate one without rotating the others? I've had success using rotate and translate commands with selections, and it works, but it can be slow with lots of objects. In Swiss-PDB viewer, you are

[PyMOL] Rtools Question

Hello all, This may have already been answered but I don't see it in the archives. I've got rTools working under MacPyMol and the effects are great. I'm working with a scene that has many objects loaded at once and I want to have some of them move independently over each other. So far I can o

Re: [PyMOL] Rtools Question

; wrote: > Tony, > I was wondering if you could e-mail me or post the details of how > you got rTools to work with MacPymol as opposed to X11 pymol for the > Mac. I've fiddled with it a bit, but I cannot seem to get the movie > commands to work. > > Thanks, >

[PyMOL] Breaking down PDB files

Hey everyone, I know I should be past this, but I can't seem to figure out how to do this. I have a couple of crystal structures that contain multiple copies in the asymmetric unit, and I would like to superimpose each copy to see what the differences are. One way is to break the PDB file int

[PyMOL] Quicktime movies from PyMol

Hey Everyone, I was just looking through website and noticed references to MacPyMol being able to export Quicktime movies directly. However I cannot find the settings/commands to make this happen. Does anyone know how to do this? I have methods for assembling the quicktime movies after rende

[PyMOL] Never mind

Found it. . .never mind. . .it was in the export movie option in the file menu. . .I just wonder why I never noticed it before.