[chimerax-users] CastP surfaces in ChimeraX/ Chimera
Elaine Meng
meng at cgl.ucsf.edu
Tue Jan 19 17:04:17 PST 2021
Hi Yaikhomba,
You would look in the *.pocInfo file to see a list of the pockets, their ID numbers, and sizes (area and volume). Then if you decide you want to see a pocket with a specific ID, then you would find all the atoms in the *.poc file with that ID number in the next-to-last column. (Would probably be easiest to first sort on that column and then simply divide the file into the atom lists for the different pockets.) Then in ChimeraX you would open the overall structure and then list those atoms in the "surface" command.
For example, in 2gbp I decided wanted to look at pocket 33. I find all the atoms in the *.poc file with 33 in the next-to-last column (there happen to be 26 of those) and then I open 2gbp in ChimeraX and list those atoms in a "surface" command:
open 2gbp
surface /A:16 at ce1:91 at ca,nd2,o:93 at cb,n,oe2:107 at ce2,oh:109 at ca:110 at cg2,n,o,og1:112 at og:152 at ce1:153 at cb,cd:154 at cg,n,od1,od2:256 at nd2,od1:261 at oe1:195 at oh visible 1
**THE SURFACE COMMAND IS ALL ONE LINE even though the mail program display will probably split it up**
Unfortunately, even though this is a completely enclosed pocket (0 openings) according to Castp and Chimera displays it as such, in ChimeraX the shape of the surface is slightly different and it has some holes, see screenshot with Chimera on left and similar view in ChimeraX on right:
I tried changing some parameters but none of them made it look the same as in Chimera... perhaps not a surprise because the calculation is done in a different way. I tried slight changes in probe radius, which you could also try, and grid spacing. Decreasing the grid spacing significantly and rapidly increases calculation time (and is most definitely not recommended on your giant structure, as it would probably "hang" Chimera) and still doesn't get rid of the holes.
Since the holes are so persistent and stay in much the same location, I wonder if there might be a bug, or whether it is a consequence of the different calculation methods. Let's see what the others say...
So this may or may not get you what you want. Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jan 19, 2021, at 4:08 PM, Y. Mutum <ym337 at cam.ac.uk> wrote:
>
> I'm sorry - there's a typo in my previous email.
>
> **
> I've a couple of cryo-EM density maps, which I want to display along with the surface.
> **
>
> Get Outlook for Android
>
> From: Y. Mutum <ym337 at cam.ac.uk>
> Sent: Wednesday, January 20, 2021 12:06:49 AM
> To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
>
> Hi Elaine
>
> Could you please describe the sightly tedious way to generate that type of surface - I'm slightly interested in keeping on using ChimeraX and giving it a try.
>
> This is because there are a couple of volume media that I want to display asking with the surface. Also, not to mention the good graphics in ChimeraX is quite easy to use too.
>
> Thanks
> Yaikhomba
>
> Get Outlook for Android
>
> From: Y. Mutum <ym337 at cam.ac.uk>
> Sent: Wednesday, January 20, 2021 12:04:45 AM
> To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
>
> Hi Elaine
>
> Could you please describe the sightly tedious way - I'm slightly interested in keeping on using ChimeraX
>
> Get Outlook for Android
>
> 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>_______________________________________________
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