[Chimera-users] Command line

[Elaine Meng]

Hi Ryan,
You may have sent your message twice -- looks the same though, so I'm replying to the second...

(A) coloring by secondary structure.  You would just use the "color" command with strand, helix, or coil as the specifier.  For example:

color yellow strand

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/color.html>

about command-line specifiers, see the "built-in classifications" section:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin>

(B) text file with summary info.  We don't have commands for that.  For things that are Chimera attributes, for example areaSAS for residues, you would open Render by Attribute (under Tools... Depiction or Structure Analysis), show the desired attribute in the histogram, and then use that tool's File menu to save the attribute values to a file.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>
 
The number of ions, ligands, chains aren't attributes as far as I know.  You would have to do something yourself such as "select ligand" and then see how many residues were selected.

(C) coloring surface by hydrophobicity.  Menu item "Presets... Interactive 3" does this, but if you want to specify your own colors and use the command line, you would use the "rangecolor" command.  The hydrophobicity we have built into Chimera is Kyte-Doolittle amino acid hydrophobicity, attribute name kdHydrophobicity.  Each protein residue has a single value (it is not per-atom).   Your command could be something like

rangecolor kdHydrophobicity min turquoise 0 white max tan

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>

To color surface only (not also atoms, ribbons) you would just put ",s" right after "kdHydrophobicity" -- no spaces.  Or, instead of a command, you could use Render by Attribute (mentioned above) graphical interface for coloring.  If you wanted to use some other hydrophobicity scale for residues or atoms, you could create an "attribute assignment file" and read it in to Chimera.  Some example files are provided for other residue-based scales. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Apr 20, 2011, at 10:25 PM, Ryan Doherty wrote:

> I searched the online documents and was unable to find out how to perform certain actions via the command line.  
> 
> Can you let me know how to perform the following commands via the command line:
> 
> Color secondary structure (and set color for Helix, Strand & Coil)
> Create a text file with a summary of attributes (ie. # of ions, # of ligands, # of chains, areaSAS for each selected residue)
> Color surface based on hydrophobicity
> Thanks!
> Ryan