[PyMOL] change angle
Hello, I have an xyz file with coordinates of atoms in a molecule. I want to change some of the bond angles ? I wonder if its doable in pymol ? I can easily change dihedral, but I could not figure out the same for the angles ? Please let me know. -- Thank you and Regards, Vivek Ranjan -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ 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 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] 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 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
[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
[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
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 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
Re: [PyMOL] reorienting a chain
Hello, I tried the following with your advice: (i) load select.pdb (ii) @beauty.pdb (iii) @script.pdb (iv) save 165.pdb (v) orient select (vi) cmd.matrix_copy(None, "select") (vii) reset (viii) save new.pdb There is no difference in 165.pdb and new.pdb. Let me be clear: Once I change some of the dihedrals in select.pdb, the resulting 165.pdb is oriented in an arbitrary direction. I want to reorient it along one of the axes (preferably along the original Y-axis) and save the resulting coordinates. No matter what I do, I get the same output file. Is there a way. I have attached all the files I am using, in case someone wants to see and comment. Basically, I want to (a) change dihedrals in select.pdb, (b) resulting in 165.pdb, (c) and rotate 165.pdb back to align with select.pdb and save the coordinates of aligned molecule to new.pdb. Please let me know if it can be done. Thank you, Vivek Ranjan On Wed, Jun 3, 2009 at 5:17 PM, Warren DeLano wrote: > Vivek, > > Please see the example I posted today for Sean Law -- the cmd.matrix_copy > command embedded therein (followed by "reset") performs exactly the action > you're looking for. > > Cheers, > Warren > ____ > From: Vivek Ranjan [mailto:vran...@gmail.com] > Sent: Wed 6/3/2009 9:26 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: 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 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
[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
[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] coordinate transformation
Hello, I am trying to modify dihedral angles of a polymer chain. Once I perform all the required steps, I am able to orient the chain and align the chain along the same axis as the original chain. But unfortunately, pymol moves the chain to a different position. Basically, it changes the coordinates in a way that the center of the chain is at the origin. I want the chain to lie along the original chain with backbones coinciding with each other (almost). Is that possible in pymol ? -- Thank you and Regards, Vivek Ranjan -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 BlackBerry® 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 9-12, 2009. Register now! 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] dihedral
Helllo, I am using pymol to change dihedral angles in a polymer chain. However, dihedral angles have poor precision. If I want to set them to, say 150, it never gets me that. I always get something like 149.5. I would like it to be 150.00. At least that precision. I was not able to find set_dihedral in the source code. Wondering if someone has some idea how a better precision can be achieved. Perhaps a tolerance issue that can be fixed easily. Please let me know. -- 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] 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: *** PyMOL>ls draw_cell.py draw_cell.py PyMOL>run 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 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) 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 > wrote: >> >> On Fri, 09 Jul 2010 13:46:57 -0400 Vivek Ranjan wrote: >> >> > Hello, >> > >> > I am trying to run a simple python script from Pymol and cannot run it: >> >> >> >> > 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 >> 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] 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] pymol fetch
Hello, There is a script supercell at "http://pymolwiki.org/index.php/Supercell";. It uses the following example: run supercell.py fetch 2x19, async=0 Where is "2x19"... I mean the pdb file for this example is in which directory under pymol ? -- 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] need more info
Hello, First, thanks a lot for your help. Pymol with cctbx works now for me. I changed the script "pymol" and replaced "/usr/binpython" to "python" and thats it. Few more questions: (i) draw_cell.py uses lavv.pdb as an example. Where can I find this pdb file ? Basically, I am making my own pdb file for a crystal system, the file lavv.pdb can help me figure out how to put crystal information in my own pdb file. (ii) I used "draw_cell_param" command to put crystal information at command prompt. Then I wanted to change radius, etc. How to undo what has already be drawn so that I can re-sketch ? Or killing the pymol, starting it again, and loading everything again is the only option ? Similarly, is there a way to turn off labels ? (iii) For the same reason as stated above, I would like to know how to get the file for 2x19 ? When I issue the command "fetch 2x19" it draws a structure. Where is the pdb file for it and how to get it to my computer ? Please let me know. -- 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] need more info
Thank you once again. I have been trying to change the color of the cell. cell = [] cell.append(CYLINDER) cell = cell + vert_000 + vert_100 + [radius] + [0,0,0] + [1,0,0] cell.append(CYLINDER) cell = cell + vert_000 + vert_010 + [radius] + [0,0,0] + [0,1,0] cell.append(CYLINDER) if I put cell.append(CYLINDER, [COLOR, 0, 0, 1]), pymol complains "TypeError: append() takes exactly one argument". If I add a line "cell.extend([COLOR, 0.0, 0.0, 1.0])" after the above cell.append(CYLINDER), nothing displays. There is also very little description of cgo on "http://pymol.sourceforge.net/newman/user/S0500cgo.html"; How to change the color of the cell ? What is append(), and extend() ? Is there a document that describes complete functionalities of CGO ? Basically, I would like learn how CGO, python, and openGL are connected within pymol. Please let me know. Thank you again, Vivek Ranjan On Tue, Jul 13, 2010 at 12:13 PM, Robert Campbell wrote: > Hello Vivek, > > On Tue, 13 Jul 2010 11:21:03 -0400 Vivek Ranjan wrote: > >> Hello, >> >> First, thanks a lot for your help. Pymol with cctbx works now for me. >> I changed the script "pymol" and replaced "/usr/binpython" to "python" >> and thats it. Few more questions: >> >> (i) draw_cell.py uses lavv.pdb as an example. Where can I find this >> pdb file ? Basically, I am making my own pdb file for a crystal >> system, the file lavv.pdb can help me figure out how to put crystal >> information in my own pdb file. > > That would be "1avv" not "lavv". All PDB structure codes begin with a number. > You could use "fetch 1avv" to get it, but I guess you know that. > >> (ii) I used "draw_cell_param" command to put crystal information at >> command prompt. Then I wanted to change radius, etc. How to undo what >> has already be drawn so that I can re-sketch ? Or killing the pymol, >> starting it again, and loading everything again is the only option ? >> Similarly, is there a way to turn off labels ? > > The only way to "undo" what you have done is to delete the objects created by > draw_cell_param (or similarly with draw_cell) and rerun the draw_cell_param > function. You'll find the delete function under the "A" menu next to the > object name or simply type "delete cell*" to delete all objects whose name > begins with "cell". > > As far as the labels go, you'll note that two objects are created by the > draw_cell function. One object is the cell border and the second is the > labels. Simply click on the name of the labels and they will turn off. This > is true of any object. > >> (iii) For the same reason as stated above, I would like to know how to >> get the file for 2x19 ? When I issue the command "fetch 2x19" it draws >> a structure. Where is the pdb file for it and how to get it to my >> computer ? > > The fetch command should leave the 2x19.pdb file in the directory from which > you started PyMOL. > > 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 > 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 > -- 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] 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] 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] remote desktop problems
Hello, I am running a remote desktop on my windows machine to work on my office linux machine. When I launch pymol, it fails with the following message: freeglut (pymol): ERROR: Internal error in function fgOpenWindow X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 4 (X_DestroyWindow) Resource id in failed request: 0x0 Serial number of failed request: 27 Current serial number in output stream: 30 PyMOL: abrupt program termination. Any help ? Most other graphics application work just fine. -- Thank you and Regards, Vivek Ranjan -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ 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
