[chimerax-users] CastP surfaces in ChimeraX/ Chimera

[Y. Mutum]

Hi Elaine

Could you please describe the sightly tedious way - I'm slightly interested in keeping on using ChimeraX

Get Outlook for Android<https://aka.ms/ghei36>

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, January 19, 2021 11:50:50 PM
To: Y. Mutum <ym337 at cam.ac.uk>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera

Hi Yaikhomba,
I tried to describe it earlier, but I probably wasn't clear.  You would need to calculate the surface for the whole protein (not just those atoms) but then just show the contributions to that  overall  surface from the pocket atoms.  That is exactly what the castp tool in Chimera does in an automated way, but you would have to do it manually in ChimeraX.  I.e. instead of opening a separate coordinate file for those atoms, just select or specify them within the overall structure and show the parts of the overall surface resulting from those atoms.  That is what I was saying would be tedious in ChimeraX, listing all of those atoms in the command line for selection or surfacing.
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 19, 2021, at 3:40 PM, Y. Mutum <ym337 at cam.ac.uk> wrote:
>
> Hi Elaine
>
> I got a workaround but there are a few 'finishing-touch' problems.
>
> In this case, as it is just for proof-of-principle, let's take the small pdb: 1bxw, as in the CastP website. I downloaded its generated surfaces, loaded them in pymol. The first one, 'poc0001', enders the surface as a thin surface - almost like a folded paper (attached as an image here - black background image).
>
> I later exported these set of atoms forming 'poc001', as a .cif file. Then, opened this set of atoms in ChimeraX and generated a surface. The surface does look similar. However, ChimeraX renders this surface, as a continuous 3D blob, as it appears from a distance (picture attached - in the white background).
> I played around with a couple of options in surface command (such as >>> suface zone #1 near sel distance 2), but am unable to get it work - like 'paper thin'.
>
> Is there a way to make the surface thin, like the one pymol generates (image attached in black background). I think in this case, it looks as if pymol has ignored the outer surface, so, just the 'inner suface' if my description is alright.
>
> I have attached the set of atoms (1poc.cif), relevant for this pocket (poc0001), just in case, you may need it.
>
> Thanks
> Yaikhomba
>
>
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: 19 January 2021 17:28
> To: Y. Mutum <ym337 at cam.ac.uk>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
>
> Hi Yaikhomba,
> When Chimera shows Castp results, it is not showing a surface that Castp calculated, but instead molecular surface (calculated in Chimera) for a list of atoms from Castp.  Castp calculates which atoms are in each pocket, then Chimera calculates molecular surface and shows the patches of surface contributed by those atoms.
>
> Your structure is a huge complex.  You could try making very small changes in probe radius or VDW radii in Chimera, or (instead of split) using surfcat to specify a different surface to enclose each protein instead of the default enclosing all the proteins in one giant surface, e.g. after opening your 3cx5 castp results:
>
> surfcat one :.a & protein
> surf one
> surfcat two :.b & protein
> surf two
> [... etc. for all protein chains]
>
> ... but then using the dialog, the pocket surfaces would look messier because you'd have all the interchain interface surfaces in addition to the outside surface of the whole complex.
>
> I don't think Castp was originally meant for use on large complexes, but instead to explore the shape of individual proteins.
>
> However, if you cannot get the molecular surface calculated in Chimera, for a given pocket you could manually take the list of atoms and show molecular surface for those atoms in ChimeraX, but it would be tedious.  We don't have a tool in ChimeraX for automatically showing Castp results, so you would have to look in the .poc file with a text editor, find all the atoms associated with the pocket of interest (maybe pocket ID number is the next-to-last column?), and then show the molecular surface from those atoms using a ChimeraX command.  Sometimes the same atom contributes to more than one pocket.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jan 19, 2021, at 7:10 AM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> >
> > Hi
> >
> > Is there a way to open the results from CastP results in 'ChimeraX' and visualise the surfaces calculated using CastP? In this case, the pdb is 3cx5, and the surfaces are calculated from CastP webserver.
> >
> > Just on using Chimera (version 1.15c) - I have also tried to open the CastP results using 'Chimera', but the molecular surfaces display are failing (picture attached). I followed up the abberant surface-calculation problems inhttps://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html.
> >
> > However, the display surfaces are all still failing - I tried the first 2 suggestions relevant to mine, but they are still failing. The first - which involves splitting the chain using the command 'split', shuts down the Castp: surfaces-window in Chimera and I can't see of a way to retrieve this CastP window with the list of surfaces.
> >
> > As, I do not want to split the model, I tried the second suggestion of 'surfcat one' (as CastP server selects atoms from multiple chains to create surfaces).
> >
> > I am not sure if I want to mess up with the Vanderwaal radii (the third suggestion) either, as these surfaces were calculated in CastP with a specific probe radius.
> >
> >  Would you have any suggestions of how to use ChimeraX to open and analyse molecular surfaces calculated by CastP? Last, but not the least, if suppose you have to end up using Chimera if ChimeraX doesn't support .poc files, could you please suggest this work-around for opening these problematic CastP-calculated-surfaces in Chimera?
> >
> > Thanks
> > Yaikhomba
>
> <Pymol_surface.png><ChimeraX_surface.png><1poc.cif>_______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210120/5ebdfac9/attachment.html>