Re: [PyMOL] pymol question
Hi, You can draw a CGO circle in the yz plane using: x1,y1,z1 = -0.1, 0, 0 # start point r1,g1,b1 = 1,0,0 # color (red) x2,y2,z2 = 0.1, 0, 0 # end point r2,g2,b2 = 1,1,0 # color (yellow) radius = 10 cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" ) To make it transparent, change it to cmd.load_cgo( [ 25.0, 0.25, 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" ) The 9.0 stands for CYLINDER, but you'd need to 'from pymol.cgo import *' to be able to use the keywords. Likewise, 25.0 stands for ALPHA, controlling the transparency. Note that the cylinder may not look quite round. It will do when you raytrace it. I couldn't find a setting for cgo display quality... Anyway, it may be that Micheals suggestion is better, but since the question was for a cylinder... And with a bit of Python scripting such a circle could be drawn with a given center and normal axis. Hope it helps, Tsjerk On Tue, Jul 7, 2009 at 12:54 AM, Michael Lerner wrote: > I'm sure there's a way to actually draw a circle, but for your particular > use it might be better to use a sphere. If you're comfortable with python > scripting, you can use CGO objects. If not, you might do something like > this: > > fetch 1hhp > create thing, resi 24 and name ca # create a new object from some single > atom selection > alter thing, vdw=10.0 # set desired radius > rebuild # necessary if spheres have already been shown > show spheres, thing > alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords > set sphere_transparency, 0.5, thing # make it transparent > zoom > ray > > you can also use something like select + within to select all residues > within a cutoff, but I got the impression you wanted a nice visualization. > > > Hope that helps, > > -michael > > On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen > wrote: >> >> Does anyone know how to draw a circle with a given radius in pymol? I have >> a distance that I want to use to see what residues lie on the end of that >> radius, but I have no idea how to write the command to draw the circle. >> Could someone help me please? >> >> >> -- >> >> ___ >> 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 > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > > -- > > ___ > 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. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry ___ 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] CAVER question
BS"D Dear All, I addressed this question to the CAVER contact address, but it bounced. I downloaded and tested the latest CAVER plugin on Linux and it worked fine. I also wanted to test this under OSX, but the "readme" file says that one needs JRE 1.6, and the latest upgrade to JRE on the Mac gave 1.5.0_19-b02-306. I tried it anyways, and it seems to give the initial window, but when it goes to make the search for a cavity it fails claiming that it can't find any. This was true under OSX 10.4.11 and 10.5.7 (same JRE version). This was the same test file that worked on Linux. Suggestions? Thanks Harry - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry___ 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] unexpected EOF while parsing
I am new to pymol and python. I have a number of cross sections of lysozyme. I want to display them one by one, color them using a script file that I have written earlier, and save the image. I have written a script file that I had hoped would do this. I have a couple problems with script file, but the one that is frustrating me the most is that immediately after the beginning of for loop pymol says that there in an unexpected EOF. The other problem is that when I try to use the variable pdb, pymol does not use the value of the variable, but the variable name itself. I have pasted my script file below and part of the log file. from pymol.cgo import * import colorsys,sys,re from pymol import cmd z=-8.153 inc=0.5 Sections=100 for j in range(0, Sections): pdb="c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_" + str(z) + ".pdb" load pdb @c:/b_color8.plm png pdb delete pdb z=z+inc PyMOL>@c:/Users/jouko/CrossSections.plm PyMOL>from pymol.cgo import * PyMOL>import colorsys,sys,re PyMOL>from pymol import cmd PyMOL>z=-8.153 PyMOL>inc=0.5 PyMOL>Sections=100 PyMOL>for j in range(o, Sections): Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 256, in parse exec(layer.com2+"\n",self.pymol_names,self.pymol_names) File "", line 1 for j in range(o, Sections): ^ SyntaxError: unexpected EOF while parsing PyMOL>pdb="c:/Users/jouko/Desktop/Research/Lysozyme/DensityCube_Lysozyme2-4a/DensityCube_Lysozyme2-4a_" + str(z) + ".pdb" PyMOL>load pdb ExecutiveProcessPDBFile-Error: Unable to open file 'pdb'. Thanks in advance for your advice. Jouko -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/blackberry ___ 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 question
I'm sure there's a way to actually draw a circle, but for your particular use it might be better to use a sphere. If you're comfortable with python scripting, you can use CGO objects. If not, you might do something like this: fetch 1hhp create thing, resi 24 and name ca # create a new object from some single atom selection alter thing, vdw=10.0 # set desired radius rebuild # necessary if spheres have already been shown show spheres, thing alter_state 1, thing, x,y,z = 50,60,10 # set desired x,y,z coords set sphere_transparency, 0.5, thing # make it transparent zoom ray you can also use something like select + within to select all residues within a cutoff, but I got the impression you wanted a nice visualization. Hope that helps, -michael On Mon, Jul 6, 2009 at 5:01 PM, Benjamin Michael Owen wrote: > Does anyone know how to draw a circle with a given radius in pymol? I have > a distance that I want to use to see what residues lie on the end of that > radius, but I have no idea how to write the command to draw the circle. > Could someone help me please? > > > -- > > ___ > 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 > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- ___ 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] pymol question
Does anyone know how to draw a circle with a given radius in pymol? I have a distance that I want to use to see what residues lie on the end of that radius, but I have no idea how to write the command to draw the circle. Could someone help me please? -- ___ 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
