[PyMOL] DALI alignment visualization

I have a set of structures that are structurally aligned to a template structure by DALI. DALI provides the transformation matrices so I can transform mol A to mol B. I was wondering if anyone had a clever phyton script to do this for not just a pair but for many at once. Thanks in advance, - E

[PyMOL] pymol transitions recorded as movie?

I regularly use the F function keys in PyMol to store conformations and call them back in a presentation. I really like the transition effects. Is it possible to record those transitions as a movie and use them in a Powerpoint presentation? Thanks in advance, - Eva

[PyMOL] Is .psw file cross platform?

Hi, If I create a .psw file in Windows and send it to someone with an Apple, can that person view it under Mac OS? Thanks a lot! - Eva

[PyMOL] making movies from

When I save scenes in Pymol and replay them by pressing the functions keys, I get nice transition effects. Is it possible to record that as a movie and save it as QuickTime for presentation or Flash for a web site? Thanks in advance - Eva

[PyMOL] cartoon representation error

Hi, Once in a while when I try to display a chain or segment of a molecule in cartoon representation, it shows up as ribbon. What might be the problem and is there a fix? Thanks in advance, - Eva

[PyMOL] clear "glassy" surface and ribbon shown together

I am trying to show the surface and ribbon representations together. I want to give a nice glassy look of the surface but it does not work too well. Does anyone have ideas on how to achieve that? I know I can do it in PovRay but I'd love to achieve that effect in PyMol with no extra program. Thank

[PyMOL] adding user defined colors to "color by element" list

Hi, I'd like to add user defined colors to the "color by element" list. How is this done? Also, I'd like to order them by my preference. Thanks in advance for the help. - Eva

[PyMOL] coloring based on sequence identity

Hi, I'd like to color a molecule based on its sequence similarity to another molecule. Can this be done in Pymol? Thanks in advance. - Eva

[PyMOL] Saving high resolution images

Hi, I'd like to save an image in high resolution for a poster. The requested size is 20" by 30". I calculated that it would correspond to a 6000 x 9000 pixel image. How can I create such a large ray traced image without crashing the computer? Many thanks in advance for the help. Best, - Eva

[PyMOL] coloring residues by a certain property

color scale from blue to red or any other color? Many thanks, Eva Vanamee eva.vana...@mssm.edu

[PyMOL] move_zone, move_object

Hi, Is there an equivalent to the move_zone, move_objects command of O in PyMOL? Thanks in advance, Eva Vanamee

[PyMOL] Pymol 0.98 standalone vs. PyMol 0.97 in Phenix under linux

Hi, I have just installed linux (SUSE 9.2) on my PC and downloaded PyMol v.0.98. I see some ghosting when I resize the window (the right vertical menu bar resizes with a delay and several intermediate steps are seen before it reaches its final position). I also downloaded PHENIX which has PyMol v

[PyMOL] "elegant" installation under linux

in advance, - Eva Vanamee