[PyMOL] electrostatic potential as cartoon?
Hi everyone, is there a way to color by electrostatic potential but display the structure as cartoon? a workaround could be : color white, molecule color red, resn asp+glu+thr+ser etc.. color blue, resn arg+lys ... but this seems rather flimsy. Thank you and best wishes for the new year. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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
ers 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 -- 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=/4140 ___ 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 -- 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=/4140___ 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 H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 <tel:608%2F592-2366> H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- 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=272487151=/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 -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- 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=272487151=/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] bonds in ligands for MD simulations?
Dear everyone, I have a MD simulation of coarse grain molecules, therefore not defined as typically for normal protein/ligands, but as beads. I want to represent it using Pymol, and need to define bonds between the beads. The problem is that I have 400 copies of my ligand, and all with the same name. I want to link bead1 with bead2, all having the name LIG. How can I do it? The CONECT record works only to define connections on a one-on-one basis, so it would be horrible for the whole file. I tried the bond command in pymol with the following argument, but it doesn't work: PyMOLbond resi LIG and name B1, resi LIG and name B2 Editor-Warning: bonds cannot be created between objects, only within. I guess this command line will create also bonds between B1 to all the 399 other LIG B2... (If resi would take into account the residue number, it would work?) here is what the pdb file looks like: ATOM6129B1LIG97740.880 105.97099.0901.000.00 ATOM6130B2LIG97741.700 105.20097.1801.000.00 ATOM6131B3LIG97741.880 104.86094.7501.000.00 ... ATOM6138B1LIG978116.680 127.990 105.9901.000.00 ATOM6139B2LIG978117.300 129.230 107.7201.000.00 ATOM6140B3LIG978119.340 130.290 108.5901.000.00 ... thank you for your help. best Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 07 http://www.ibcp.fr -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ 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] white background is black when opaque_background is on
Hi all,
when I use :
cmd.set('''opaque_background''','''0''',quiet=0)
cmd.bg_color('white')
the background is black. If I set the background back to opaque, then it
turns white.
Is there a way to keep the background white at all times when setting
the opacity off?
I'm using pymol 1.7.2. It didn't happen on previous versions.
(as a workaround, i could comment the opaque background off, and
decomment it when I ray trace the image, but it would be nice to have
the full settings working initially without having to edit too much the
.pml ...)
thanks
Vincent
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
--
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Re: [PyMOL] white background is black when opaque_background is off
Sorry, I meant in the title, opaque_background set to off.
Le 9/16/14 3:03 PM, vincent Chaptal a écrit :
Hi all,
when I use :
cmd.set('''opaque_background''','''0''',quiet=0)
cmd.bg_color('white')
the background is black. If I set the background back to opaque, then
it turns white.
Is there a way to keep the background white at all times when setting
the opacity off?
I'm using pymol 1.7.2. It didn't happen on previous versions.
(as a workaround, i could comment the opaque background off, and
decomment it when I ray trace the image, but it would be nice to have
the full settings working initially without having to edit too much
the .pml ...)
thanks
Vincent
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
--
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Manually upgrade your production database.
When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
___
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--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
--
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce.
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk___
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Re: [PyMOL] drawing arows, CONE cgo doesn't work. -- SOLVED
Hi all, I managed to solve the problem by looking at the cgo_arrow.py of Thomas Holder in the wiki: http://www.pymolwiki.org/index.php/Cgo_arrow my line was incorrect: cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, b1 ], cone_a ) correct line: cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, 0.0, r1, g1, b1, r1, g1, b1, 1.0, 0.0 ], cone_a ) of course, with the definition of x0, y0, etc... and the from pymol.cgo import Have a good day. Vincent Le 8/26/14 12:19 AM, Andreas Warnecke a écrit : Hej, if you simply copy-paste the wiki entry into PyMOL you will get the error. This code is intended to be run as a block (e.g. from script) and creates e.g. problems with indentation, or other errors. A simple solution would be to wrap the commands to a block using python and python end. Either you include them in what copy paste (the whole shabang): python # axes.py from pymol.cgo import * from pymolimport cmd from pymol.vfont import plain # create the axes object, draw axes with cylinders coloured red, green, #blue for X, Y and Z obj= [ CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0., CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0., CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0, ] # add labels to axes object (requires pymol version 0.8 or greater, I # believe cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]]) # then we load it into PyMOL cmd.load_cgo(obj,'axes') python end OR you can enter the lines/ copy paste sequentially. If you are interested in arrows/ cones, have a look at the cgo_arrow script: http://www.pymolwiki.org/index.php/Cgo_arrow Hope this helps. Cheers, Andreas On Mon, Aug 25, 2014 at 5:48 PM, vincent Chaptal vincent.chap...@ibcp.fr mailto:vincent.chap...@ibcp.fr wrote: Hi, I'm trying to draw arrows in Pymol 1.7.2 for mac, à la http://www.pymolwiki.org/index.php/Axes When I run the script for the Axes_with_nice_cones, I have the error message: File /Applications/MacPyMOL.app/pymol/modules/pymol/parser.py, line 464, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1 CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0] ^ SyntaxError: invalid syntax As a workaround, I tried to use the cylinder syntax (bellow, by replacing CYLINDER by CONE), pymol loads the object but doesn't draw anything. cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, b1 ], cone_a ) Can someone tell me what is going on and how I can draw a cgo CONE in pymol? It looks very nice. Thank you Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 tel:%2B33%204%2037%2065%2029%2001 http://www.ibcp.fr -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ 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 -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ 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] drawing arows, CONE cgo doesn't work.
Hi, I'm trying to draw arrows in Pymol 1.7.2 for mac, à la http://www.pymolwiki.org/index.php/Axes When I run the script for the Axes_with_nice_cones, I have the error message: File /Applications/MacPyMOL.app/pymol/modules/pymol/parser.py, line 464, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1 CONE, 0.0, 0.0, l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0] ^ SyntaxError: invalid syntax As a workaround, I tried to use the cylinder syntax (bellow, by replacing CYLINDER by CONE), pymol loads the object but doesn't draw anything. cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, b1 ], cone_a ) Can someone tell me what is going on and how I can draw a cgo CONE in pymol? It looks very nice. Thank you Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ 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 with distance
Hi, I've just purchased v1.6 and installed it under MacOS 10.6.8. I have a problem with using distance from a script, as well as via the wizard. my pdb has 12 chains. when I type: distance d1, molA and chain a and resi 53 and name o, molA and chain d and resi 8 and name n the distance is drawn between: chain M and resi 7 and atom cg, and chain I and resi 53 and atom o. I don't understand the error. So I turned to the wizard -measurement. I click on the atoms that are in front of me, and the distance is drawn again between chain M and resi 7 and atom cg, and chain I and resi 53 and atom o. For a proof, I'm pasting the top screen where the names of the atoms I clicked is: You clicked /molA//A/SER`53/O Selector: selection sele defined with 1 atoms. You clicked /molA//D/GLY`8/N) I was previously under 1.3 and didn't have this problem. Can you help me? Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-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] disconnected loop in pymol
Hi, I've seen this when using modeller and then working in coot to change parts of my model. The pdb looked like this: ATOM 2 CA ALA A 61 19.187 -16.491 60.818 1.00 7.01 AC ATOM 3 CB ALA A 61 17.667 -16.537 61.040 1.00 7.01 AC ATOM 4 C ALA A 61 19.475 -16.919 59.419 1.00 7.01 AC ATOM 5 O ALA A 61 20.559 -16.678 58.892 1.00 7.01 AO ATOM 6 N GLY A 62 18.489 -17.575 58.780 1.00 9.64 N ATOM 7 CA GLY A 62 18.677 -18.017 57.433 1.00 9.64 C ATOM 8 C GLY A 62 19.240 -19.399 57.475 1.00 9.64 C ATOM 9 O GLY A 62 19.501 -20.003 56.436 1.00 9.64 O The missing 'A' for the GLY at the end of the line was preventing the cartoon. Writing back the A did the trick. vincent Anastassis Perrakis wrote: Dear all, I have a small domain which is mostly loops, its a Cys-knot. All residues are in the preferred Rama regions, and all atoms are present in the PDB, but Pymol decides to 'break' my cartoon! Would anyone have a solution to force pymol draw a nice loop where the break is? (see small image attached) Thanks in advance, Tassos -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] COVER image
Hello, I am trying to make a picture for a cover and I am wondering how to make a vertical image. (Pymol creates horizontal images, and journal covers are vertical) Is there a way to creates those vertical images other than turning the image 90 degrees with the 'turn z, 90' command? thanks vincent -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer. -- -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer. --
[PyMOL] manual docking problem
Hi, I have a little problem with manual docking. I load 2 pdb as 2 different objects. I define the mouse in editing mode and shift+left-click to turn and shift+middle-button tu drag. unfortunatly, the molecule splits in two and loops and helices streches to follow one piece of the protein. any ideas to keep the protein as one single piece? I am using version 0.98 on windows xp. thanks vincent Vincent Chaptal CNRS, LEBS-bat 34 1 Av de la terrasse 91 198 gif sur Yvette tel: 01 69 82 42 04 fax: 01 69 82 31 29 http://www.lebs.cnrs-gif.fr/
