[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

Re: [PyMOL] Script for Torsion angles

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[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

Re: [PyMOL] 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

[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 R

[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

Re: [PyMOL] reorienting a chain

ose 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 ch

Re: [PyMOL] reorienting a chain

ne. 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&#

[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/Bloc

[PyMOL] pymol display problems

. 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

[PyMOL] coordinate transformation

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

[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 Regar

[PyMOL] dihedral

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] how to run a python script

ymol_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' ******

[PyMOL] cctbx

ortError: 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 pho

Re: [PyMOL] how to run a python script

nd 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 ?

[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

[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 Re

[PyMOL] need more info

ommand "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 W

Re: [PyMOL] need more info

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. >

[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 aro

[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, Vi

[PyMOL] remote desktop problems

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