[PyMOL] Coordinates of a mesh

Hi, I actual try to get the coordinates of the mesh from a protein/selection. At first I run the following command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) There I get points shifted by one axis or something like that. Then somebody here from the mailinglist tells me that I have to use

Re: [PyMOL] Coordinates of a mesh

Check this, and tell if it works. http://pymolwiki.org/index.php/Matrix_Copy Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/ 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/25 Bjoern-oliver Gohlke bjoern-oliver.goh...@student.uni-tuebingen.de The error I

Re: [PyMOL] Coordinates of a mesh

Hi Bjoern, Please do also give a more explicit account of what you want to achieve in the end and what you've tried to get there, including the commands used. Cheers, Tsjerk 2011/8/25 Troels Emtekær Linnet tlin...@gmail.com: Check this, and tell if it works.

[PyMOL] Fog settings for indicidual portions of molecules

This is a very basic question, but I have been having trouble with this for a couple of days. I am working in pymol for Windows, but have access to Mac pymol if the problem is a windows-specific problem. I am working on a figure showing the sticks of one molecule interacting with the surface

Re: [PyMOL] Get pymol 1.4.1 source to windows. Easy.

I don't know what the current stance on such things is, and Schrodinger's acquisition of PyMOL might have changed things, but I remember two very clear messages from Warren relating to Windows compilation. I'd read these and think about them pretty carefully before you go out of your way to do the

[PyMOL] bbPlane script SyntaxError: invalid syntax

Hi all, Can anyone help me with a problem that I am having trying to run a python script? I am trying to run the bbPlane script from the PyMOLWiki http://www.pymolwiki.org/index.php/BbPlane I have copied the script from the web page, to a plain text document, saved it as bbPlane.py but when I

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

Hi Adam, I just copy/pasted the script you attached in your email and it worked fine. There are, however two spaces on line 14--maybe the parser thinks it found a block indent? Try erasing line 14 (the line following from chempy import cpv) and re-running the script. Cheers, -- Jason On Thu,

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

Hi Adam, Here's an alternative script... The command is pplanes (peptide-planes): run triangles.py pplanes selection[, color[, alpha[, state[, name Hope it helps, Tsjerk On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg a...@steinbergs.us wrote: Hi all, Can anyone help me with a

Re: [PyMOL] Fog settings for indicidual portions of molecules

Hi Andrew, On Thu, Aug 25, 2011 at 8:51 AM, Malaby, Andrew andrew.mal...@umassmed.edu wrote: I am working on a figure showing the sticks of one molecule interacting with the surface of another.  I am trying to keep my normal coloring in a figure, but make background portions of the molecule

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

I erased all of the spaces in the blank lines and now the script works. When I erased them in line 14 then it found them in kine 38, etc. You may want to update the script on the WIki to one without spaces. I am trying to follow the example in the Wiki to make sure it works before I try it on

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

Hi Adam, I updated the wiki page to remove the spurious spaces--good idea. I am trying to follow the example in the Wiki to make sure it works before I try it on my pdb. However, when I run the command bbPlane i. 4-10 I get a new error: PyMOLbbPlane i. 4-10 Traceback (most recent call

Re: [PyMOL] bbPlane script SyntaxError: invalid syntax

Thanks Tsjerk, When I run this script, I see: PyMOLpplanes selection, (sele) Selector-Error: Invalid Selection Name. ( selection and n. ca )-- I have tried selecting just one n and ca in the pdb, tried selecting multiple n and ca, tried a bunch of other selections, but it's not working. What