[PyMOL] Fwd: drawing trajectory files
Colleagues, When I load an amber topology file and associated trajectory file, the lines for all heteroatoms are drawn as dashed lines (but bonds to hydrogens drawn as solid lines). I can’t seem to find a flag that would turn this feature off… I’d rather see all bonded atoms connected as solid lines. I couldn’t find an explanation on the WIKI (earlier versions of pymol didn’t behave this way). Everything else works fine (movie plays as it normally would). Any advice would be appreciated. Thanks, Mike -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ 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] Testing if a .pml script is run in command line mode
Dear list, Moving a bit further with this, I have been trying to find an easy way to iterate through the list of scene names. Or to get them somehow. I don't seem to be able to find any information about this and thought someone probably already knew. Thanks in advance! Folmer 2016-01-27 14:07 GMT+01:00 Folmer Fredslund : > Dear Tsjerk, > > Thanks! simply including > if '-c' in invocation._argv > in the script works fine for me, > > Best, > Folmer > > 2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar : > >> Hey Folmer, >> >> You can check if '-c' not in invocation._argv >> Of course, you'd also need to check combinations, so it would be matching >> -.*c.* on the elements in _argv. >> >> There probably is a way to check for the GUI directly though. >> >> Hope it helps, >> >> Tsjerk >> >> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund >> wrote: >> >>> Hi there, >>> >>> I was wondering if there is a way to check if a .pml is being run in >>> command line mode (pymol -c), i.e. without the GUI. >>> >>> The reason I'm asking, is because I am making some scripts for figures, >>> and save the representations as scenes. It would be nice to both be able >>> to view them (running the .pml normally) and also make raytraced png's >>> when the .pml is being run in commandline mode. >>> >>> Best regards, >>> Folmer Fredslund >>> >>> >>> -- >>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>> Monitor end-to-end web transactions and take corrective actions now >>> Troubleshoot faster and improve end-user experience. Signup Now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >>> ___ >>> 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. >> >> > > > -- > Folmer Fredslund > -- Folmer Fredslund -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] loading trajectory file
Hi everybody, How can I load a gromacs trajectory file in PyMOL? Thank you, Mohammad.-- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] drawing trajectory files
Hi Mike, These bonds have bond order zero. Incentive PyMOL 1.8 renders those as dashed lines and sticks. Previous versions of PyMOL had no proper support for zero-order bonds, they did render as solid lines, but had no stick representation. You can set all bond orders to 1 with: PyMOL>valence 1, *, * Or PyMOL can guess the bond orders for you, if double bonds matter: PyMOL>valence guess, *, * I will look into the amber topology loading code to see if we are importing those bonds wrong. Cheers, Thomas On 01 Feb 2016, at 07:08, Michael F. Summers wrote: > Colleagues, > > When I load an amber topology file and associated trajectory file, the lines > for all heteroatoms are drawn as dashed lines (but bonds to hydrogens drawn > as solid lines). > I can’t seem to find a flag that would turn this feature off… I’d rather see > all bonded atoms connected as solid lines. I couldn’t find an explanation on > the WIKI (earlier versions of pymol didn’t behave this way). Everything else > works fine (movie plays as it normally would). Any advice would be > appreciated. > > Thanks, > > Mike -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 ___ 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] PyMOL-users Digest, Vol 116, Issue 15
Hi Annemarie, Have you tried the following? cmd.translate([x,y,z], object='membrane') replace x,y,z with your translation vector. Cheers, Julian On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie wrote: > I am trying to show some cell surface receptors and to indicate their > position relative to the membrane. > > I thought to indicate the plane of the membrane by a flat disk, a ago > cylinder. > > x1,y1,z1 = 0, -1, 0 # start point > r1,g1,b1 = 1, 1, 0 # color (yellow) > x2,y2,z2 = 0, -2, 0 # end point > r2,g2,b2 = 1, 1, 0 # color (yellow) > radius = 100 > cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, > b2 ], "membrane" ) > > When I try to move this cylinder into the correct position > with cmd.transform_selection, > using the transformation parameters extracted from get_view (reordering > them as needed) > I get the error message "Selector-Error: Invalid selection name “membrane” > “ > > The same transform command works fine if I apply it to a pseudo atom > originally generated with coordinates 0,0,0. > > Any suggestion how else I could indicate the membrane, or how I could > place my ego object parallel > to the screen yz plane? I have to be able to do this in a reproducible > fashion, as I have to do this > for a large number of constructs that bend my receptors relative to the > membrane in various ways. > > Thanks for your help > Annemarie > ___ > > Dr. Annemarie Honegger PhD > Department > of Biochemistry > Zürich University > Winterthurerstrasse 190 > CH-8057 Zürich > Switzerland > > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > ___ > 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 > -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] superimposition of 2 ligand molecules
Hi, have a look at the 'align' command: http://pymolwiki.org/index.php/Align Best, Julian On Thu, Jan 28, 2016 at 7:13 AM, leila karami wrote: > Dear pymol users, > > I have 2 ligand molecules having similar backbone. There is little > difference between them. When I load them in pymol, I have following figure: > https://www.dropbox.com/s/k4g53p0qoxp58zs/pymol.png?dl=0 > > I want to have these 2 ligands in superimposed form such as following: > https://www.dropbox.com/s/v75uhrghy4johjy/pymol_2.png?dl=0 > > Please guide me to do that. > > Best, > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > ___ > 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 > -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] problem saving very large ray traced pngs
Dear all: I'm ray tracing images from a script with the png command, but am having problems saving images larger than ~ 6000x6000. While I get perfect images at 6000x6000, anything larger writes small, empty files (219kb instead of ~50Mb like expected). Is there some sort of buffer size that needs to be raised to write larger images? Thanks, Dan -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] loading trajectory file
Can I load the gromacs trajectory files or just the amber trajectory files? On Monday, February 1, 2016 10:17 PM, mohammad r wrote: Hi everybody, How can I load a gromacs trajectory file in PyMOL? Thank you, Mohammad. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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] PyMOL-users Digest, Vol 116, Issue 15
Hi Annemarie, It's actually quite simple to generate a real membrane around your protein and, e.g., to show the head groups. Do you have a PDB ID for the protein, or are they in-house models? Cheers, Tsjerk On Mon, Feb 1, 2016 at 10:57 PM, Julian Heinrich wrote: > Hi Annemarie, > > Have you tried the following? > cmd.translate([x,y,z], object='membrane') > > replace x,y,z with your translation vector. > > Cheers, > Julian > > On Sat, Jan 30, 2016 at 8:33 AM, Honegger Annemarie > wrote: > >> I am trying to show some cell surface receptors and to indicate their >> position relative to the membrane. >> >> I thought to indicate the plane of the membrane by a flat disk, a ago >> cylinder. >> >> x1,y1,z1 = 0, -1, 0 # start point >> r1,g1,b1 = 1, 1, 0 # color (yellow) >> x2,y2,z2 = 0, -2, 0 # end point >> r2,g2,b2 = 1, 1, 0 # color (yellow) >> radius = 100 >> cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, >> b2 ], "membrane" ) >> >> When I try to move this cylinder into the correct position >> with cmd.transform_selection, >> using the transformation parameters extracted from get_view (reordering >> them as needed) >> I get the error message "Selector-Error: Invalid selection name >> “membrane” “ >> >> The same transform command works fine if I apply it to a pseudo atom >> originally generated with coordinates 0,0,0. >> >> Any suggestion how else I could indicate the membrane, or how I could >> place my ego object parallel >> to the screen yz plane? I have to be able to do this in a reproducible >> fashion, as I have to do this >> for a large number of constructs that bend my receptors relative to the >> membrane in various ways. >> >> Thanks for your help >> Annemarie >> ___ >> >> Dr. Annemarie Honegger PhD >> Department >> of Biochemistry >> Zürich University >> Winterthurerstrasse 190 >> CH-8057 Zürich >> Switzerland >> >> >> >> -- >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> ___ >> 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 >> > > > > -- > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > ___ > 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. -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140___ 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
