[PyMOL] disjoint surfaces
Hi, I imported into Blender (a 3D modelling and animation software) a surface created in PyMOL and I realized that there are some disjoint surfaces inside. Is it possible to remove these surfaces in PyMOL? Thank you, Raluca -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] disjoint surfaces
Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly are you having problems with? In what way are things disjointed ? Best, Shiven On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi, I imported into Blender (a 3D modelling and animation software) a surface created in PyMOL and I realized that there are some disjoint surfaces inside. Is it possible to remove these surfaces in PyMOL? Thank you, Raluca -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ~^v^~ the cgull ... -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] disjoint surfaces
Hi Raluca, So I am guessing this something like the surface being in fragments, with small vertices floating within the larger object? Unfortunately there is no easy way to do this from within PyMOL, unless you can separate out the residues/atoms that are contributing the disjointed meshes into new objects and then turn them off before export. Right now the best thing I can think of going into edit mode in Blender and deleting those vertices by hand. :-( Best, Shiven On Mon, Dec 21, 2009 at 12:11 PM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Thank you Shiven, I know how to remove the double vertices in Blender but I would like to remove them directly from PyMOL. By disjoint meshes I mean non-connected meshes, inside my mesh I have some smaller meshes that are non connected to the big mesh. I would like to know how to remove these meshes before saving. Thank you, Raluca On Mon, 21 Dec 2009 11:24:11 -0500 Shiven Shandilya shiven.shandi...@gmail.com wrote: Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly are you having problems with? In what way are things disjointed ? Best, Shiven On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi, I imported into Blender (a 3D modelling and animation software) a surface created in PyMOL and I realized that there are some disjoint surfaces inside. Is it possible to remove these surfaces in PyMOL? Thank you, Raluca -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ~^v^~ the cgull ... -- ~^v^~ the cgull ... -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] List of Groups
How would someone get the list of groups in a pymol session? get_object_list doesn't have them and the only commands I can find in cmd that have the word group in them seems to be group and ungroup (if my quick regex search worked right). Thanks, David -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] List of Groups
David, I think groups are treated like objects (see help group). So, one can type print cmd.get_names(objects) and all the objects (proteins, groups, etc) will be returned. For example: group a group b group c print cmd.get_names(objects) The problem is that other objects will be returned, too. So, if you don't use special naming for your groups, they will run together with other objects. -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Dec 21, 2009 at 6:45 PM, David Hall dwash59_2...@yahoo.com wrote: How would someone get the list of groups in a pymol session? get_object_list doesn't have them and the only commands I can find in cmd that have the word group in them seems to be group and ungroup (if my quick regex search worked right). Thanks, David -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Linux 195.22 Nvidia binary driver + 120Hz LCD Samsung 2233RZ + Quadro FX 3700 + Nvidia 3D vision = working quad buffered stereo
Hi all, Just wanted to mention that I've updated some of the info on the wiki here: http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options#LCD_Displays_.28120_Hz.29 to note that quad buffered stereo (QBS) on the 120Hz Samsung 2233RZ LCD monitor works on Linux. It's nowhere as cheap as the Zalman solution but will work with any other visualization apps out there that have QBS support which don't support the Zalman. HTH, Sabuj Pattanayek -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net