[Chimera-users] Hydrophobicity surface

[Elaine Meng]

Hi Anne,
This is a commonly encountered issue: by default the whole macromolecule is enclosed in one surface.  However, there are at least a couple ways to tell Chimera to enclose each chain in a separate surface instead:

(1) use command "split" to put the separate chains into separate models.  The advantage is that it's easy; if you only have that one structure, all you have to do is enter the command:

split

and then use the hydrophobicity preset again (or show surface and apply your own hydrophobicity coloring scheme with the Render by Attribute tool or the "rangecolor" command). Possible disadvantages of split are if you have already saved positions (from "savepos") they will not work with the new split models, and if you already made the surface around both, it will not go away automatically.  You would either need to close that surface (say from Model Panel, under Favorites in the menu) or just close everything, then reopen the structure and split before showing any molecular surfaces.  If your original structure is model #0 with chains A and B, split will replace that with new models #0.1 with chain A and #0.2 with chain B. One way to control which models are shown/hidden is with the "S" checkboxes in the Model Panel.

(2) use command "surfcat" to tell Chimera exactly which atoms should be grouped together into a surface.  The advantages are that any saved positions will continue to work, and the first surface enclosing both will automatically go away.  The possible disadvantage is that one should be careful not to include waters and stuff like that in the specification.  For example, just today I used the following when making some figures:

surfcat achain :.a&protein
surfcat bchain :.b&protein
surface achain
surface bchain

... where the surfcat commands specify atoms with a particular chain ID that are also protein (not solvent, ions, etc.).  Then you can use the preset again or show surface and apply your own coloring scheme with Render by Attribute or rangecolor.  Of course you could undisplay a chain and its surface, for example:

~surf achain
~ribbon :.a
~display :.a

... where these commands hide the surface, ribbon, and atoms/bonds, respectively.

Commands documentation:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Command-line atom specification:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Jun 19, 2013, at 10:06 AM, Anne Simonsen wrote:

> Dear Chimera helpers,
> 
> I'm trying to make a figure showing the hydrophobic surface of one chain (chain A in attached IGA1.pdb file) with a peptide (chain B) shown as ribbon with residues, but I then get a "hole" in the A surface around the peptide (see attached figure). Can you please advice?
> 
> Thank you!
> 
> Best wishes,
> Anne
> 
> -- 
> Anne Simonsen, PhD, Professor
> Dept. of Biochemistry, Institute of Basic Medical Sciences
> University of Oslo, P.B. 1112 Blindern
> 0317 Oslo, Norway
> 
> Visiting address:
> Domus Medica, room 3174
> Sognsvannsveien 9
> 0372 Oslo
> 
> Phone: +47 22 851110
> Fax: +47 22 851058
> Mobile: +47 99350960
> email: anne.simonsen at medisin.uio.no
> http://www.med.uio.no/imb/english/research/groups/autophagy/
> 
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