[Chimera-users] surface ESP in chimera

sbasu at ffame.org sbasu at ffame.org
Fri May 30 16:33:43 PDT 2014


Dear Dr. Meng,

Many many thanks. The whole picture seems to be clear now.

regards,
sankar


> 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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