[PyMOL] dimer interface

___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237

[PyMOL] density around ligand

-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206

[PyMOL] view's in pymol and movie

/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] sticks with different radii

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206

[PyMOL] vacuum electrostatics

Hi Shawn, As you can see when you select the generate electrostatic surface within PyMol - Warren has stated that it is unvalidated experimental code and the results should be viewed with skepticism. If you want publishable electrostatics calculated using more realistic estimates of

[PyMOL] Apple hiring engineers to increase OpenGL support!

) that Warren hand delivered to Apple! Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] Translating and rotating

no problem in my case, I want to move all atoms anyway, relative to an electron density map. But I don't see how I can move the atoms at all using the mouse - all I change is the camera view. Konrad. Hi Konrad, If you left-click once in the lower right hand corner of the viewer where the

[PyMOL] python script question

Hello PyMol gurus, I am trying to make a simple movie with my molecule rotating 360 degrees. There are two molecules superimposed and one of them is turned on for 6 frames then off for 6 frames. Hopefully this won't give anyone epileptic seizures. So here is a part of my python script. The

[PyMOL] Help with labels?

running npymol on OS X. == Scott Classen, Ph.D. University of California, Berkeley Department of Molecular Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==

[PyMOL] saving images

the lines. THanks again Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] saving images

Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] OS X Users: PyMOL 0.97 and APBS via fink - a success story!

Delano. Scott Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] light source inside a molecule??

On Sep 7, 2004, at 6:33 PM, av...@lbl.gov wrote: Hi, I was wodering if it is possible to change the light source to a ligand inside a protein, so it creates a glowing effect? Anton Vila Scott Classen, Ph.D. ACS Postdoctoral Fellow Department

[PyMOL] How to make spacefill effect?

is the option to Show Spheres. I think that's what you're looking for. Ciao, Scott On Aug 12, 2004, at 3:05 AM, Liu Shiyong wrote: Where is the sphere usage? thanks Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology

[PyMOL] question about electrostatic maps

Hello Qun, I think you will find what you want here: http://agave.wustl.edu/apbs/ On Aug 4, 2004, at 8:55 AM, Qun Wan wrote: Hi, I want to get electrostatic map of my protein, which need APBS installation. However, I have a PC with platform of windows XP and a mac with platform of OSX.2.8.

[PyMOL] PyMOL] question about electrostatic maps

with platform of OSX.2.8. I do not know if they are they OK for APBS installation and running? And how? Thanks! Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand

[PyMOL] having problems with batch rendering

Hello Fellow PyMOLers, I have submitted a huge movie (i.e. 520 frames rendered at 1280x854) job to pymol on one of our linux grunts. PyMOL, much to my surprise actually recognized that the grunt has two multithreaded processors and subsequently split the rendering job amongst the available

Re: [PyMOL] having problems with batch rendering

root 34 19 0 0 0 SWN 0.0 0.0 0:00 1 ksoftirqd_CPU1 9 root 34 19 0 0 0 SWN 0.0 0.0 0:00 2 ksoftirqd_CPU2 Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206

[PyMOL] having problems with batch rendering

Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] Is exporting CGOs vertices possible?

Begin forwarded message: From: Scott Classen clas...@berkeley.edu Date: March 10, 2004 4:20:53 PM PST To: Warren DeLano war...@delanoscientific.com Cc: pymol-users@lists.sourceforge.net Subject: Is exporting CGOs vertices possible? Hello Fellow PyMOLers, I am interested in using another

[PyMOL] cartoons

from IBM. Click Now! http://ads.osdn.com/?ad_id=1356alloc_id=3438op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott Classen, Ph.D

Re: [PyMOL] adjust surface?

(Ph) 504-865-6785 (FAX) amul...@tulane.edu Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] Selecting a lot of residues

__ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] PyMOL 0.92 via FINK?

, and help us add new features and functionality. Click here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users Scott

[PyMOL] Is it possible to specify the resolution for a GRASP output rgb file?

, jp Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

[PyMOL] Get rid of border around my images !!

, Somehow I keep getting a dotted border on the edge of the image whenever I have been saving images the past few times. I don't know if I turned something on. Can't figure out what though! How can I get rid of it in Pymol? Thanks, Raji Scott Classen, Ph.D. ACS

[PyMOL] surface settings?

. surface_best 0.2 surface_color default surface_debug 0 surface_miserable 0.8 surface_mode 0 surface_normal 0.5 surface_poor 0.89 surface_proximity on surface_quality 0 Thanks, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu

[PyMOL] default atomic radii

Hi Warren, What are the default atomic radii in PyMol? How are they calculated/determined? Thanks, Scott Classen == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology

Re: [PyMOL] RE: PyMOL v0.88 Released

I missing the pint or something here or am I being premature? (I am using MacOSX 10.2.6 plus all the latest updates to date And Apple's X11 Beta 3 - XFree86 4.2.1) == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California

[PyMOL] how to change radius of cylindrical helix

cartoon_rect_width, 0.3 Good Luck, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX

[PyMOL] Will a faster graphics card speed up ray tracing?

Warren, Does PyMOL ray tracing speed depend on the graphics card? I am curious what factors (hardware or software) effect rendering speed. Thanks, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley

[PyMOL] Stereo labeled figs?

has been made on this? Many thanks, Camille p.s. I'm running npymol on OS X. == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 237 Hildebrand Hall

[PyMOL] Stereo labeled figs?

in stereo. == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==

Re: [PyMOL] Loss of resolution when printing or converting to PDF

them to PDF with Acrobat, the resulting .pdf file looks much worse (on my LCD screen) than the original .png. Is there a way around this problem? Could it be the colors that I'm using in Pymol that's causing this trouble? -Fred == Scott Classen

[PyMOL] isodot vs isomesh

Of course I didn't try: load dif.ccp4 isodot void, dif, 1.0 color black, void show dots, void until after sending the email below. sorry, Scott On Tuesday, February 25, 2003, at 12:59 PM, Scott Classen wrote: PyMolers, Is it possible to display a map (ccp4) as dots rather than a mesh

[PyMOL] multiple h bonds

, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==

[PyMOL] electron density maps

around my ligand? Thanks, Scott == Scott Classen clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 229 Stanley Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==

[PyMOL] PyMOL input for the Mac and movie question

, Scott == Scott Classen clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular Cell Biology 229 Stanley Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ==