Re: [PyMOL] Different color on each side of strand

Hi, Keitaro, On 03/08/2011 03:11 AM, Keitaro Yamashita wrote: > Dear Hongbo, > > For example, user can put something like light source and "front" is > defined as the side light hits. > (though it would be undefined If sheet plane is placed parallel to the ray..) and even the same strand can have

Re: [PyMOL] Question about the .obj file saved by Pymol

Hi Francois, Woops--sorry for the delay. I think only the outside vertices are sent. To get the inside, try set surface_cavity_mode, 2 before surfacing and exporting. You can also set that to '3' to include pockets as well as cavities. Cheers, -- Jason On Wed, Mar 2, 2011 at 3:04 AM, Franc

Re: [PyMOL] CGO objects don't disappear when they should...

Hi Nicolas, It sounds like you have the "all_states" option set. So, to only have one object state shown at a time, try unset all_states Also, deleting anything in PyMOL is easy: delete objName or through the cmd API: cmd.delete("objName") Cheers, -- Jason On Mon, Mar 7, 2011 at 9:11 PM,

Re: [PyMOL] Different color on each side of strand

Dear Hongbo, For example, user can put something like light source and "front" is defined as the side light hits. (though it would be undefined If sheet plane is placed parallel to the ray..) But I think any definition is ok if front and back could be alternated easily by user operation. Cheers

Re: [PyMOL] CGO objects don't disappear when they should...

Hi Jason, Thanks for your reply. No, I'm not deleting the cgo objects after the relevant frames. Actualy, I don't know how. This what I wanted to do though. I was able to achieve a workaround. Each time load_cgo() is called to create a box, a loop will go through all later time steps adding an em

Re: [PyMOL] CGO objects don't disappear when they should...

Hi Nicolas, Are you hiding or deleting the boxes after the relevant frame passes? This is hard to debug without seeing sample code. Cheers, -- Jason On Mon, Mar 7, 2011 at 8:39 PM, Nicolas Bigaouette wrote: > Hi all, > > I'm usin pymol to vizualize my molecular dynamics code. Particle position

Re: [PyMOL] CGO objects don't disappear when they should...

Sorry I forgot to give system informations. I'm using ArchLinux x86_64 with pymol compiled from svn (revision 3837) under python 2.7.1-7 I've tried going back up to revision 3037, but older then around 3200 I get "Fatal Python error: can't initialize module sglite". Everything newer then 3200-som

[PyMOL] CGO objects don't disappear when they should...

Hi all, I'm usin pymol to vizualize my molecular dynamics code. Particle positions is saved in a single .xyz file. An example is: 2 0.0 fs -- MD of 2 particles (position in Angstrom) A0.0000.0000.000 E 13.0200.0000.000 2 0.00050 fs -- MD of 2 particles (positi

Re: [PyMOL] Different color on each side of strand

how do you define "front" and "back" sides of sheets in general? On 03/07/2011 01:32 AM, Keitaro Yamashita wrote: > Dear all, > > Sorry for my unclear explanation. > > I made a picture explaining what I'd like to do. > I want to color the front and back of sheets separately. > > Jason said it shou

Re: [PyMOL] Different color on each side of strand

Not sure if this is possible but it would be a nice feature to have. Since it mimics the way helices are drawn, when cartoon_highlight_color is set. Cheers, Carsten > -Original Message- > From: Keitaro Yamashita [mailto:yamash...@castor.sci.hokudai.ac.jp] > Sent: Sunday, March