Re: [PyMOL] Alpha setting of CGO spheres
Great, thanks! Matt On 01/20/2015 08:01 PM, Osvaldo Martin wrote: Hi Matt, Try removing the BEGIN sph1 = [ALPHA, 0.5, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph1, sph1, 1) sph2 = [ALPHA, 1.0, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph2, sph2, 1) Cheers, Osvaldo. On Tue, Jan 20, 2015 at 7:19 PM, Matthew Baumgartner mp...@pitt.edu mailto:mp...@pitt.edu wrote: Hi, I'm having some trouble using CGO spheres. When I create one, it is not visible in the viewer, although there is an (apparently empty) object in the object pane. It is somewhat confusing because with some parameters the spheres ARE visible when ray tracing, although they are still not visible when non ray traced. I have not had this problem in the past, although I haven't tried in a while ( 1 year). I am using pymol v1.7.4.0 which is up to date from the SVN repository (revision 4107). And I am on Ubuntu 14.04. I reproduced this problem on another computer running 1.7.x. To reproduce: pymol -k #to eliminate setting in the .pymolrc In pymol: from pymol.cgo import * sph1 = [BEGIN, ALPHA, 0.5, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph1, sph1, 1) This loads a seemingly empty object that is not visible when ray tracing. Setting the Alpha parameter to 1.0 allows it to be visible when ray tracing, but not under normal conditions. sph2 = [BEGIN, ALPHA, *1.0*, COLOR, 1.0, 1.0, 1.0, SPHERE, -3.818, -28.181, -15.016, 0.5] cmd.load_cgo(sph2, sph2, 1) Do you have any idea what the problem might be or settings that I could check? Thanks, Matt Baumgartner -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto: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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ 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] Clip surface only
if you have access to Gimp or photoshop and want to do this in just a few minutes… clip and render the surface how you want it, then without moving anything, unclip and render just the ligand. In any bitmap editing program layer the ligand image over the clipped surface image and merge the two into one image. On Jan 21, 2015, at 2:57 PM, Markus Heller mhel...@cdrd.ca wrote: Hello all, I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only. I haven't found anything on the web, only that it was not possible a few years ago. Surely this has changed? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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] Clip surface only
Hey :) If you want to do it using only Pymol in just a few minutes, try this: set auto_zoom, 0 scale=1.0 import numpy M=numpy.array(cmd.get_view()).reshape(6,3) cmd.pseudoatom(dummy,pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:]))) hide everything, (not ligand) within 150 of dummy Adjust the scale to get a more curved or more planar clip. Hope it helps, Tsjerk On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg h.adam.steinb...@gmail.com wrote: if you have access to Gimp or photoshop and want to do this in just a few minutes… clip and render the surface how you want it, then without moving anything, unclip and render just the ligand. In any bitmap editing program layer the ligand image over the clipped surface image and merge the two into one image. On Jan 21, 2015, at 2:57 PM, Markus Heller mhel...@cdrd.ca wrote: Hello all, I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only. I haven't found anything on the web, only that it was not possible a few years ago. Surely this has changed? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ 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] Clip surface only
Hello all, I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only. I haven't found anything on the web, only that it was not possible a few years ago. Surely this has changed? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mhel...@cdrd.ca | www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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] Clip surface only
Thanks to both of you, guys. I settled on something far more trivial, sparked by the hide everything command in Tsjerk’s suggestion ☺ Involves a tiny bit of manual labor but works for me. Cheers and Thanks! Markus From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Wednesday, January 21, 2015 1:49 PM To: H. Adam Steinberg Cc: Markus Heller; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Clip surface only Hey :) If you want to do it using only Pymol in just a few minutes, try this: set auto_zoom, 0 scale=1.0 import numpy M=numpy.array(cmd.get_view()).reshape(6,3) cmd.pseudoatom(dummy,pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:]))) hide everything, (not ligand) within 150 of dummy Adjust the scale to get a more curved or more planar clip. Hope it helps, Tsjerk On Wed, Jan 21, 2015 at 10:21 PM, H. Adam Steinberg h.adam.steinb...@gmail.commailto:h.adam.steinb...@gmail.com wrote: if you have access to Gimp or photoshop and want to do this in just a few minutes… clip and render the surface how you want it, then without moving anything, unclip and render just the ligand. In any bitmap editing program layer the ligand image over the clipped surface image and merge the two into one image. On Jan 21, 2015, at 2:57 PM, Markus Heller mhel...@cdrd.camailto:mhel...@cdrd.ca wrote: Hello all, I'm trying to show a ligand in a binding site, and I'd like to selectively clip the surface only. I haven't found anything on the web, only that it was not possible a few years ago. Surely this has changed? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147tel:%28604%29%20827-1147 Direct: (604) 827-1122tel:%28604%29%20827-1122 | F: (604) 827-1299tel:%28604%29%20827-1299 | E: mhel...@cdrd.camailto:mhel...@cdrd.ca | www.cdrd.cahttp://www.cdrd.ca Follow us: This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Tsjerk A. Wassenaar, Ph.D. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet___ 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] unable to export obj
Hi, I am trying to get a .obj file, but fail when setting up surface_type to 2. More explicitly: load 1ppe.pdb, 1ppe set surface_type, 2 hide everything show surface shows a nice triangulated surface. However, save myscene.obj saves an empty file. I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works well when surface_type is set to 0, or 1. Any help? Best, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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] different colours for isomeshes in version 1.7.4.0
Hi Gerhard, works for me. Note that the mesh_color setting will take priority over the object color, so once you set the global setting, the color command will have no effect anymore on the mesh. Try to restore the default: # default will take object color set mesh_color, default # clear object settings unset mesh_color, * # test fetch 1ubq, map, type=2fofc, async=0 isomesh m1, map, 1 isomesh m2, map, 2 color blue, m1 color red, m2 Cheers, Thomas On 19 Jan 2015, at 08:58, Gerhard Fischer gf...@cam.ac.uk wrote: Hi, since upgrading to 1.7.4.0 (both when compiling manually and installing the package through Yast on openSUSE 13.2), I can no longer give different isomeshes (of electron density maps) separate colours. The only way to change the colour seems to be through changing the global mesh_color-setting, but not through the GUI or the color-command. Is this a bug, a feature or maybe just something specific to my system? Any ideas? Best regards, Gerhard -- Gerhard Fischer, PhD Postdoctoral Research Associate University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge United Kingdom -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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
