Re: [PyMOL] Question about Pymol movie

Liyang, This will only be of use to you if you happen to be a PyMOL subscriber, but there is an example movie script somewhat like this in the official online documentation: http://delsci.info/dsc/dokuwiki/doku.php?id=example:animation:granzyme_h ydrolysis Cheers, Warren > -Original Message

Re: [PyMOL] select by absolute coordinate

Martin, It is remarkable that a question like this hasn't come up before, but it reveals a rather large whole in PyMOL's selection language: though we have some proximity operators, we are not currently able to select atoms based on absolute or relative coordinate vector relationships. So t

Re: [PyMOL] select by absolute coordinate

Am 04.03.2009 um 06:46 schrieb Warren DeLano: Hey Warren, It is remarkable that a question like this hasn't come up before, but it reveals a rather large whole in PyMOL's selection language: though we have some proximity operators, we are not currently able to select atoms based on absol

[PyMOL] .phs file open in PyMol

Hello, I have experimental phases/map_coeff's in a .phs file. Can anyone tell me how to most easily get them read read into PyMol to display electron density? I assume I need to convert the file somehow first, I usually use mapman for this utility but don't see an option for .phs files. Thanks

Re: [PyMOL] select by absolute coordinate

Hi, I have a couple of quick notes about your specific application: This works well when bilayers are flat. So, it works well for small bilayers and it works well at the beginning of a simulation. For medium to large bilayers, undulations throughout the simulation will cause this algorithm to bre

[PyMOL] drawing a spring/arrow with pymol

Dear pymol users I am running SMD simulation. I want to draw arrow/spring to display direction of pulling of my ligand. i know it is possible with VMD. but i am more attracted to graphics in Pymol. is it some way i can draw arrow or spring connecting two atoms. please let me know -- Falgun H sha

Re: [PyMOL] select by absolute coordinate

Am 04.03.2009 um 17:32 schrieb Michael Lerner: Hey Michael You probably know all of this, but I thought I'd mention it in case someone was tempted to just take your code and apply it individually to each frame of a simulation without really thinking about it. Unfortunately, I've seen peo

[PyMOL] rotation

I have a homodimer. I place it at an arbitrary place on the screen, where it looks nice. Now move the monomers apart from each other in x. translate [10, 0, 0], object molA translate [-10, 0, 0], object molB Then I want to rotate each monomer 90 deg so that each monomer's contribution to

Re: [PyMOL] rotation

Dave, origin molA rotate y,90,molA origin molB rotate y,90,molB origin all Cheers, Warren > -Original Message- > From: David Garboczi [mailto:dgarbo...@niaid.nih.gov] > Sent: Wednesday, March 04, 2009 10:05 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] rotation > > I

Re: [PyMOL] drawing a spring/arrow with pymol

Falgun, We don't have an arrow primitive, but you can use the distance command to connect two atoms: dist spring, selection1, selection2, label=0 for example: fragment val dist spring, valCG1, valCG2, label=0 Cheers, Warren F

Re: [PyMOL] .phs file open in PyMol

Hi, > I have experimental phases/map_coeff's in a .phs file. Can anyone tell me > how to most easily get them read read into PyMol to display electron > density? I assume I need to convert the file somehow first, I usually use > mapman for this utility but don't see an option for .phs files. Fi

[PyMOL] Ca trace

Colleagues, If the PDB file contains only Ca atoms and PyMOL shows them as non-bonded atoms what one should do to display them as a ribbon? The 1rh2 entry is one of them. Thank you. ___ Vaheh To the extent this electronic communication or any of its attachments contain inform