Re: [PyMOL] Homologous modelling

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] dimer interface

amp;op=click ___ 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 Cali

[PyMOL] view's in pymol and movie

d to rotate around x,y, and Z and move in x, y and z? I'm sure it can be done, but haven't figured it out. Thanks in advance Mike -- Mike Osborne Iric-Institut de Recherche en Immunovirologie et Cancérologie Université de Montréal 2950 Chemin Polytechnique Pavillon Marcelle-Coutu

[PyMOL] density around ligand

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, Berk

[PyMOL] sticks with different radii

ers 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

[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 dielect

[PyMOL] Apple hiring engineers to increase OpenGL support!

ic 3D) 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 m

[PyMOL] overlay ligands inside of protein

atom selections without performing any fitting. USAGE rms_cur (selection), (selection) ~ Best of luck, Scott ~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology Un

[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 pro

[PyMOL] exporting surfaces

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] Help with labels?

;t find a reply to the original question on stereo figs on the >> BB. I am also trying to label specific residues in my stereo figure. >> Older messages on the BB seem to imply this can"t be done in pymol. >> Do you know if any progress has been made on this? >&

[PyMOL] saving images

times it doesn't save 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] OS X Users: PyMOL 0.97 and APBS via fink - a success story!

ichael Lerner, Jack Howrath, and Warren 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] saving images

ANy ideas? Thanks -GC ~~~~~~~~ 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??

lude an example figure, but it was too big for the PyMol list. Good luck, Scott On Sep 8, 2004, at 11:47 AM, av...@lbl.gov wrote: Hi Scott, Thank you for the help. I'm totally unfamiliar with PovRay. When you say "You can write out the primitives from PyMol" what do you me

[PyMOL] non_bonded size

archives and googled "PyMol non-bonded sphere size" and have had no luck. Suggestions? Best regards, Alex ~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebr

[PyMOL] light source inside a molecule??

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 of

[PyMOL] Why isn't PyMOL version 1.0 yet?

Hi Warren, I don't mean to be a pest, but when will PyMOL (which by the way ROCKS!) reach the seemingly unattainable status of version 1.0 ? Ciao, Scott ~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology U

[PyMOL] How to make spacefill effect?

choices. Nine lines down 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 Fell

[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 Hildeb

[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.

Re: [PyMOL] having problems with batch rendering

PU0 8 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 H

[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 proc

[PyMOL] having problems with batch rendering

the GUI, but when I try to submit it as batch mode I'm getting all these rendering errors. I would really like to get this to work so I can split up my rendering job over several machines. Should I be importing other modules at the very beginning? Thanks, 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] Is exporting CGOs vertices possible?

Begin forwarded message: From: Scott Classen Date: March 10, 2004 4:20:53 PM PST To: Warren DeLano Cc: pymol-users@lists.sourceforge.net Subject: Is exporting CGOs vertices possible? Hello Fellow PyMOLers, I am interested in using another program (Blender) to do some more complicated

[PyMOL] cartoons

inux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users ~~~~~~~

Re: [PyMOL] adjust surface?

A 70118-5698 504-865-6742 (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

[PyMOL] Selecting a lot of residues

knapp.com __ ~~~~ 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] oops

ignore that last post it was meant for a fink maillist 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.

[PyMOL] pymol 0.90-2 fails to compile

ntax error before "uint64_t" /usr/include/libkern/OSByteOrder.h:292: syntax error before "uint16_t" /usr/include/libkern/OSByteOrder.h:301: syntax error before "uint32_t" /usr/include/libkern/OSByteOrder.h:310: syntax error before "uint64_t" make[1]: ***

[PyMOL] Mac questions

On Nov 3, 2003, at 1:37 AM, Einat Sitbon wrote: Several questions regarding pymol on macs. 1)I'm using a G3. will version 0.93 work on it as the 0.90 version does? It should. I'm still waiting for 0.93 to be released via fink, because my compiling skills are minimal. 2)The interface for ma

[PyMOL] PyMOL 0.92 via FINK?

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 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290

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

0? Thanks, 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, P

[PyMOL] ray trace stereo

op around in the settings Good luck 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] 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 Bio

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

at 0.86-3. Am 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 Univ

[PyMOL] PyMOL manual

work up a PyMol manual? How is this going? Do you have a projected release date for the new manual? Thanks, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular & Cell Bio

Re: [PyMOL] Labels

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] how to change radius of cylindrical helix

0 set 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 510.643.9

[PyMOL] Alpha Channel Support

at we can throw those pesky SGIs away? 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 510.643.9

[PyMOL] Stereo pictures, light vector and shadows

2.png turn y,-6 Cheers, Warren == 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] 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?

per depth when the figure is finally viewed 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 ==

[PyMOL] Stereo labeled figs?

you know if any progress 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 &

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

n linux? How does one make a "big" png? Is it a command-line option, or you just make the window the size of the screen? Thanks Denis ========== Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Departm

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

n. Likewise, when I convert 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 ====

[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

[PyMOL] isodot vs isomesh

void show dots, void but it didn't seem to work. Any help would be greatly appreciated, Scott ====== Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular & Cell Biology 237 Hildebr

[PyMOL] color tube by temp factor

Hello fellow PyMolers, Can PyMol color a tube by main chain temperature factor? How? Please help Thanks, Scott == Scott Classen, Ph.D. clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular & Cell Biology

[PyMOL] nice povray settings?

== 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] 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] help with surface parameters

ate a fairly tight molecular surface and I just can't figure it out. ANy help would be appreciated. Thanks in advance, Scott ====== Scott Classen clas...@uclink4.berkeley.edu University of California, Berkeley Department of Molecular & Cell

[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

PyMOL. 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 ==