[PyMOL] ImportError

Dear developers, just to inform, after some reinitializations of Pymol 0.99rc6 (pre-compiled) in a same session, I have got the message bellow (restarted the program and it was ok again). (I don't know if its due to my Linux installation or Pymol). Cheers, Ricardo Error: 3 ImportError Excep

[PyMOL] AMD64 X2+Quadro FX1300+Fedora5

although stereo mode was not tested yet. Kind regards, Ricardo Aparicio http://www.iqm.unicamp.br/profs/aparicio.html

Re: [PyMOL] stereo: should wait for LCD solutions in near future?

--Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Ricardo Aparicio Sent: Monday, March 20, 2006 2:17 PM To: pymol-us...@lists.sf.net Subject: [PyMOL] stereo: should wait for LCD solutions in near future? Dear al

[PyMOL] stereo: should wait for LCD solutions in near future?

chance that in near future a technology based on LCD monitors may become available at reasonable price and competitive image quality? (intrinsic horizontal low resolution of LCD 3D options seems to be a problem) Comments are welcomed. Cheers, Ricardo Aparicio http://store.sharpsystems.com

[PyMOL] labels again

you have any reference (paper published or web) where I can see PyMOL-made figures containing labels? Thank you very much for your help. Regards, Ricardo Aparicio PhD Student Sao Paulo - BR

[PyMOL] soap-film II

With respect to my previous question, any option in PyMOL would be useful, not necessarily a polygonal surface. Any ideas are welcomed. Thank you, Ricardo Ricardo Aparicio wrote: Dear PyMOL users: To make a structural alignment (2 pdb files) more informative, it would be

[PyMOL] soap-film

iated. Thank you in advance, Ricardo Aparicio PhD Student USP - Sao Paulo Brazil

Re: [PyMOL] transparent sphere

Hi, the PyMOL Current Capabilities (v0.80) include "Transparent surfaces and spheres" (http://pymol.sourceforge.net/) Another option would be use NCSMASK (ccp4) and control the "transparency" level by changing the GRID, it worked for me. Good luck, Ricardo Aparici

[PyMOL] util.mroll & movie rate

is an easier answer to this question) Thank you in advance, Ricardo Aparicio PhD Student Brazil

[PyMOL] selecting atoms from a mask

advance, Ricardo Aparicio PhD Student Brazil

[PyMOL] stereo pictures

o sense in capture the image from the screen with png command. 2) how to make stereo figures using PyMol. If necessary we have SGIs with stereo here. Thank you very much, Ricardo Aparicio PhD student, USP Sao Paulo Brazil

[PyMOL] PyMol module _cmd version

s API version 1009, module _cmd has version 1007. Where can I get the correct "module_cmd" ?? I am using Linux Mandrake 8.0 on a PIII500 MHz. Does this problem could be solved installing new PyMol version? Thank you again, Ricardo Aparicio PhD Student

[PyMOL] transparency question

s it map considered a "surface" by PyMol?? I think not, that is the reason by which transparency doesn't have any effect in the mask. 2- Is it possible to obtain a "surface" from a map? I think not, just to confirm. Thank you very much, Ricardo Aparicio PhD Student -

[PyMOL] "ray" doubts

of figures published (in the case of a paper)? - does it renderize(?) all the active objects in the screen? - after finished ray process, if the image is rotated, is it necessary to renderize again (I think no, just to confirm) Many thanks, Ricardo Aparicio PhD Student - USP Sao Paulo - Brazil

Re: [PyMOL] Selecting objects to move

I'm new too but I think on-line manual can help you. http://pymol.sourceforge.net/html/toc.html Good luck, Ricardo Leslie Hall wrote: > > Hello, > > I have just started using PyMol and had a question about moving selected > objects in an animation. > Here is basically what I want to do.

[PyMOL] state variables

help is very welcomed. In short: 1) how to make a rough, not detailed mask around my pdb? Is "surface" option the right way? 2) what parameters do have influence in making a "rough" surface, what are their functions and default values? Thanks in advance, Ri