[Chimera-users] surface ESP in chimera

Elaine Meng meng at cgl.ucsf.edu
Fri May 30 16:21:41 PDT 2014


Dear Sankar Basu,
I will try to answer your questions below.

On May 29, 2014, at 12:59 PM, sbasu at ffame.org wrote:

> Dear Chimera group,
> Could you please help us resolving the following issues ?
> 
> 1. Is there a way to load a pre-computed solvent accessible surface (i.e.,
> coordinates of dot surface points stored in a PDB format against source
> atom types) on top of a protein molecule ? [kindly see the attached
> example file]

The basic problem is that PDB-format files are for atoms, not surface dots. If you want to read/write dot surfaces, a format designed for that purpose is MS (*.ms, *.dms), which Chimera can read:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/dms.html>

> 
> 2. Is there a way to print / write the actual dot surface points generated
> by Chimera into a file (preferably in a PDB format with the source atom
> records) ?

If you are showing a molecular surface in Chimera, you can write it to the MS format mentioned above using the "Write DMS" tool (in menu under Tools... Structure Editing).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/dms.html#writedms>

> 
> 3. Is there a way to actually compute the electrostatic potentials (ESP)
> on the solvent accessible surface by chimera using a Delphi interface ? In
> that case, how can one set the delphi parameters (e.g., partial charges /
> atomic radii / percentage grid fills / boundary conditions) according to
> his likings ?

(A) Chimera includes a DelPhiController tool (in menu under Tools... Surface/Binding Analysis) in which you can specify the parameters including charge and radius files.  You have to get the DelPhi program and the charge and radius files separately, but it sounds like you already did that.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/delphicontroller/delphicontroller.html>

 In my opinion it can be difficult to get charges and radii assigned correctly because the atom names must match the entries in the charge and radius files.  This can involve a lot of tedious editing of the PDB file.  After you run DelPhi to get the phi map, you can use Electrostatic Surface Coloring (in menu under Tools... Surface/Binding Analysis) to color the molecular surface.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

(B) If your goal is ESP visualization, e.g. coloring the surface, rather than quantitative calculations, you might instead try the Coulombic Surface Coloring tool (in menu under Tools... Surface/Binding Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
See also this tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

(C) If you would rather have a Poisson-Boltzmann-type calculation rather than Coulombic, yet another approach is to use the PDB2PQR tool (in menu under Tools... Structure Editing) and then use its output with the APBS tool (in menu under Tools... Surface/Binding Analysis).  That will take care of the atom-naming issues which are often problematic in using DelPhi, and you don't have to get the programs separately.  They are run using web services.  If you take this approach, I recommend you use Chimera 1.9.  APBS creates a *.dx file which you can use with Electrostatic Surface Coloring.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>

> 4. We have computed ESP on solvent accessible surface (MS - connolly)
> using a standalone version of delphi. When we load the phimap.phi onto the
> chimera-generated surface to obtain the ESP-colored surface map, we find
> ambiguities between the surface coloring and the actual values of the
> potentials (almost the entire surface is showing red / white whereas there
> are obviously positive patches from the actual numbers) ! We suspect that
> it is due to the inconsistency between two surfaces.

Maybe the issue is that by default, Electrostatic Surface Coloring doesn't evaluate the potential at the solvent-excluded Connolly surface but instead at points 1.4 angstroms outward (approximate location of solvent-accessible surface, which isn't shown in Chimera.  Connolly called his surface solvent-accessible but in Fred Richards' terminology it is instead the solvent-excluded surface.<http://en.wikipedia.org/wiki/Frederic_M._Richards> ). The reasoning  for this offset is explained in the documentation, but if you don't want to do that you can change it: click the Options button on that tool, change "Surface offset" to 0.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

> Lastly,
> 
> 5. A trivial question is how to select residue(s) by residue sequence
> number (e.g., 108 or 108-VAL) from the select drop-down list ? We do not
> seem to find that option.

You can't do it from the menu.  Instead you could use a command:

select :108

... some explanation:
:108 means residues numbered 108 in all chains
:108.a means residue 108 in chain A
:val means all valines 
:val.a means all valines in chain A
etc. ... for more about command line atom-specification:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

>                      thanks and regards,
>                      Sankar Basu

You're welcome. 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






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