Re: [PyMOL] bbPlane script "SyntaxError: invalid syntax"

Thanks Tsjerk, When I run this script, I see: PyMOL>pplanes 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.

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: > > PyMOL>bbPlane i. 4-10 > Traceback (most recent

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] Fog settings for indicidual portions of molecules

Hi Andrew, On Thu, Aug 25, 2011 at 8:51 AM, Malaby, Andrew 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 lighter.  I have tried "

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 wrote: > Hi all, > Can anyone help me with a problem that I am havi

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,

[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 I have copied the script from the web page, to a plain text document, saved it as "bbPlane.py" but when

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] 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 o

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 : > Check this, and tell if it works. > > http://pymolwiki.org/index.php/Matrix_Copy > >

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 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/25 Bjoern-oliver Gohlke < bjoern-oliver.goh...@student.uni-tuebingen.de> > The err

Re: [PyMOL] Coordinates of a mesh

The error I get is from the following command: super 1A9U, mesh ExecutiveAlign: invalid selections for alignment. I think that the problem is that I try to align the mesh points with an protein. In my understanding, I need this one to run the get_object matrix command. Or do I understand somet

Re: [PyMOL] Coordinates of a mesh

Can you provide the error message? 2011/8/25 Bjoern-oliver Gohlke < bjoern-oliver.goh...@student.uni-tuebingen.de> > 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] )

[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 u