From: Sajeewa P. <saj...@gm...> - 2012-03-16 19:32:15
|
Hello everyone, I have created molecular tunnels for two starting points using CAVER and saved them as two different pse(Pymol session) files. Is there any way I can superimpose the two tunnels? Can I superimpose the two pse files (I tried and it doesn't happen. One pse overrides the other). I want to compare the two tunnels visually which are in different files. Could you please give me any suggestion as to how I should do this? Thank you Sajeewa Dewage |
From: Jason V. <jas...@sc...> - 2012-03-16 20:32:14
|
Hi Sajeewa, load sessionA.pse load sessionB.pse, partial=1 This will essentially merge sessionA and sessionB. Make sure sessionA and sessionB do not have objects with the same names--it'll just confuse PyMOL if they do. To transform the mesh/surfaces after aligning the proteins see the matrix_copy (http://pymolwiki.org/index.php/Matrix_Copy) command. Cheers, -- Jason On Fri, Mar 16, 2012 at 3:32 PM, Sajeewa Pemasinghe <saj...@gm...> wrote: > Hello everyone, > > I have created molecular tunnels for two starting points using CAVER and > saved them as two different pse(Pymol session) files. Is there any way I can > superimpose the two tunnels? Can I superimpose the two pse files (I tried > and it doesn't happen. One pse overrides the other). I want to compare the > two tunnels visually which are in different files. Could you please give me > any suggestion as to how I should do this? > > Thank you > > Sajeewa Dewage > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Jason V. <jas...@sc...> - 2012-03-17 01:07:19
|
Sajeewa, > 1) Is there a way of changing the object names in a session file so that > pymol will not get confused when I merge two sessions having objects with > the same name? You need to ensure that each session has file names that will not collide with name in other sessions. Rename each object to something unique and re-save the session files. Use the "set_name" command or A > Rename Object for each object. > 2) If I am merging three session files, will it look like > > load sessionA.pse > > load sessionB.pse,partial=1 > > load sessionC.pse,partial=2 Partial is a binary flag: load sessionA.pse load sessionB.pse, partial=1 load sessionC.pse, partial=1 ... Cheeres, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |