[PyMOL] rotate
Hello, I would like to rotate a group of atoms around an axis defined by line connecting two atoms in the group. Is it possible in Pymol ? How to do it ? -- Thank you and Regards, Vivek Ranjan -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ 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] rotate
Is it possible to define an arbitrary axis (say a line connecting two atoms). Thanks, Vivek On Wednesday, December 28, 2011, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Vivek, Check out the rotate command (http://pymolwiki.org/index.php/Rotate). Cheers, -- Jason On Wed, Dec 28, 2011 at 1:58 PM, Vivek Ranjan vran...@gmail.com wrote: Hello, I would like to rotate a group of atoms around an axis defined by line connecting two atoms in the group. Is it possible in Pymol ? How to do it ? -- Thank you and Regards, Vivek Ranjan -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thank you and Regards, Vivek Ranjan -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ 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] Script for Torsion angles
Check get_dihedral. On Mon, Sep 5, 2011 at 6:56 PM, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Hi Martin, Whilst I have no competence what so ever in scripting, I believe the measurement wizard does offer you the torsion angle option only it is listed as a dihedral. Hope this helps Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -Original Message- From: Martin Hediger [mailto:ma@bluewin.ch] Sent: Friday, 2 September 2011 9:49 p.m. To: pymol-users Subject: [PyMOL] Script for Torsion angles Dear List Does anyone have a script to calculate torsion angles lying around? Ideally, i would like to be able to enter x1, x2, x3, x4 and get the (smaller) angle between the two normals of the planes defined by x1, x2, x3 and x2, x3, x4, respectively. For some odd reason the measurment wizard in my PyMOL install does not display torsion angles..!? Kind regards and thanks for any feedback. Martin -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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 -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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 -- Thank you and Regards, Vivek Ranjan -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ 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] about script
Hello, I ran a script in pymol run axes.py once. After killing pymol and restarting it, pymol always runs the script. Any reason for this behavior ? I was also wondering if there is a way to display just one axis in pymol without running a script ? -- Thank you and Regards, Vivek Ranjan -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ 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] print quality pictures
Hello, Once I get a high quality picture from pymol, I want to put some labels, combine a few of them together, add some arrows and texts, etc. Any suggestions on what is a good way to do that so that I don't lose resolution ? I generally crop the pictures in gimp to get rid of the white space around, then insert them in a powerpoint and resize them to fit a few together on one slide, then add texts, labels, arrows, etc. Save the slide in as a jpg and then crop it again. But I believe that even though I starts with a high resolution pictures created by pymol, I end up with not so good picture due to the procedure I described above. -- Thank you and Regards, Vivek -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ 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] python
Hello, How can I find out what version of python my current installation of pymol is using ? -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] how to run a python script
Hello, I am trying to run a simple python script from Pymol and cannot run it: *** # axes.py from pymol.cgo import * from pymol import 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') *** I saved the above in a file named axes.py and put it in the same directory from where I type pymol (on ubuntu linux). Then I type run axes.py in pymol command bar. I get the following error message: * Traceback (most recent call last): File /usr/local/lib/python2.6/dist-packages/pymol/parser.py, line 334, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File /usr/local/lib/python2.6/dist-packages/pymol/parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) IOError: [Errno 2] No such file or directory: 'axes.py' *** Any help ? -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] cctbx
Hello, I downloaded a pymol script from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ called draw_cell.py. I have Python 2.6.5, numpy version: 1.3.0, I downloaded cctbx for unix (self extracting files) and installed cctbx in my $HOME/bin/. I have also included the line (. /home/vranjan/bin/cctbx_build/setpaths.sh) in my .bashrc then ran the command from another window cctbx.version and found cctbx version to be 2010_03_29_2334 When I type run draw_celll.py in pymol window I get the following error: *** PyMOLls draw_cell.py draw_cell.py PyMOLrun draw_cell.py Traceback (most recent call last): File /usr/local/lib/python2.6/dist-packages/pymol/parser.py, line 334, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File /usr/local/lib/python2.6/dist-packages/pymol/parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) File draw_cell.py, line 3, in module from cctbx import uctbx, sgtbx ImportError: No module named cctbx PyMOL: normal program termination. ** any help ? -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] how to run a python script
Thanks for your mail. I did two things: (i) typed the entire path starting from /home/../../draw_cell.py (ii)cd /home/../../ and then run draw_cell.py. It still gives me the same error of not finding cctbx. I checked if I am in the correct directory by typing pwd and got the correct answer. When I do ls draw_cell.py it prints the filename. I guess the problem is that pymol cannot recognise cctbx, even though my path to cctbx are correctly set as I can run cctbx commands from any directory. Is there a resolution ? or I need to reinstall pymol ? Thanks again, Vivek Ranjan On Fri, Jul 9, 2010 at 4:01 PM, Paul Rigor (uci) paul.ri...@uci.edu wrote: Hi, Your assumptions are correct, as I've copied and tested your code, which works fine from the current working directory where I ran the pymol start script. It's probably a quirk w/ your installation? Otherwise, you can just specify the full path to your script or cd into the folder... either way. Goodluck, Paul On Fri, Jul 9, 2010 at 11:01 AM, Robert Campbell robert.campb...@queensu.ca wrote: On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan vran...@gmail.com wrote: Hello, I am trying to run a simple python script from Pymol and cannot run it: snip I saved the above in a file named axes.py and put it in the same directory from where I type pymol (on ubuntu linux). Then I type run axes.py in pymol command bar. I get the following error message: * Traceback (most recent call last): File /usr/local/lib/python2.6/dist-packages/pymol/parser.py, line 334, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File /usr/local/lib/python2.6/dist-packages/pymol/parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) IOError: [Errno 2] No such file or directory: 'axes.py' *** Any help ? Try typing the command pwd within PyMOL to see if it reports that you are in the directory that you think you are. Also try typing ls axes.py to see if it can see it. Are you sure you haven't made a typo in the name of the file? Otherwise I don't see why what you have done shouldn't work. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- Paul Rigor http://www.ics.uci.edu/~prigor -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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 -- Thank you and Regards, Vivek Ranjan -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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] dihedral angle
Hello, When I cntrl+right-click on a bond, it is supposed to give the dihedral angle. However, it gives something else. E.g. the angle in question has actual dihedral angle of 180 degrees. However, it shows -56.9 degrees. Please let me know how this works ? -- Thank you and Regards, Vivek Ranjan -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ 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 display problems
There are problems in display window of pymol in ubuntu 9.04. The one that I install from repository completely blocks the CPU. When I compile the latest one on my machine (version 1.2b6pre), the display window does not show up most of the time. The commands buttons do not show up all the time. Has someone noticed it ? -- Thank you and Regards, Vivek Ranjan -- ___ 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] compilation problem with the latest pymol
I downloaded the latest pymol by using the following command: svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol Then, while running the command python setup.py install, I encountered the following: In file included from layer5/main.h:35, from layer0/Block.c:20: layer0/os_python.h:28:19: error: Python.h: No such file or directory In file included from layer0/Block.c:20: layer5/main.h:45: error: expected ‘)’ before ‘*’ token layer5/main.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token error: command 'gcc' failed with exit status 1 Any help ?? Thanks, Vivek -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ 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] reorienting a chain
Hello Warren, Thank you very much for your advice. I guess I was not being very clear. what i meant was that i would also like to save the coordinates of this reoriented polymer. Let me be clear: I have a polymer aligned along y-axis. I change some of the dihedral angles. As a result, the chain is pointing in some arbitrary direction. So, I want to re-orient the polymer along the y-axis and then save the coordinates of this reoriented polymer. I used the command orient from the installed pymol on my system (version 1.0r2). But when I try to save the polymer, it still saves the same coordinates as the one before reorientation. Please let me know if something can be done ? Thank you, Vivek On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano war...@delsci.com wrote: You can save a copy of the original and then superimpose the copy back onto it # using fab command from the latest 1.2 beta to create poly-ala fab AAA, pol # create copy of the polymer create copy, pol # adjust a torsion set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60 # superimpose back on the original copy fit pol, copy Cheers, Warren From: Vivek Ranjan [mailto:vran...@gmail.com] Sent: Tue 6/2/2009 10:57 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] reorienting a chain Hello, I have a long chain of polymer. Once I change some dihedral angles, it orients in a different direction. I would like the chain to be reoriented in the same direction as it initially was. Is it possible within pymol ? How can I achieve this ? -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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 -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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] reorienting a chain
Hello, I have a long chain of polymer. Once I change some dihedral angles, it orients in a different direction. I would like the chain to be reoriented in the same direction as it initially was. Is it possible within pymol ? How can I achieve this ? -- Thank you and Regards, Vivek Ranjan -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ 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] diehedral angle
Hello, I would like to change some of the diehedral angles in a polymer systems. I know how to measure diehedral angle. However, I don't know how to change it ? Any advice is greatly appreciated. -- Thank you and Regards, Vivek Ranjan -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
