CastP surfaces in ChimeraX/ Chimera
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 in https://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
[cid:8c139fcc-51aa-496c-9f20-9c01badbbe12]
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@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
I forgot to mention that unlike Chimera, the default in ChimeraX is to show separate surfaces for each chain. So if your intent was to analyze the shape of the overall complex, if you are trying to use ChimeraX to view Castp results, you may want to use the ChimeraX "surface" command "enclose" option to make one big surface around all of the protein chains instead of the default separate surface for each chain.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html
Again, I don't think the original intent of Castp was for analyzing the shapes of such large multiprotein complexes, so you may be stretching the useful limits of the tool.
Elaine
On Jan 19, 2021, at 9:28 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
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@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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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
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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine
Could you please describe the sightly tedious way - I'm slightly interested in keeping on using ChimeraX
Get Outlook for Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 Androidhttps://aka.ms/ghei36
________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 Androidhttps://aka.ms/ghei36
________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: Wednesday, January 20, 2021 12:06:49 AM To: ChimeraX Users Help chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@ce1:91@ca,nd2,o:93@cb,n,oe2:107@ce2,oh:109@ca:110@cg2,n,o,og1:112@og:152@ce1:153@cb,cd:154@cg,n,od1,od2:256@nd2,od1:261@oe1:195@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@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@cam.ac.uk Sent: Wednesday, January 20, 2021 12:06:49 AM To: ChimeraX Users Help chimerax-users@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@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine,
The Chimera pocket surface of 2gbp does look nicer without as many holes. Unfortunately the Chimera surface is wrong. This is a common problem with the MSMS surface calculation code in Chimera. As you know it crashes for large molecules, but even when it does not crash it sometimes gives obviously incorrect surfaces.
Here is a picture of the 2gbp pocket surface from Chimera 1.15 where I did not limit it to just one connected piece. Notice that the surface piece in the upper right intersects the middle (reddish) surface piece -- the two patches of surface pass through each other. There should be a hole at that position in the surface but the MSMS algorithm missed it. The same thing happens with the surface pieces at the left -- it intersects the middle piece in two places (where you see the red poking through). Again that is wrong -- different regions of a solvent excluded surface can't intersect other regions. The correct surface has two holes there.
ChimeraX shows the correct holes and but is uglier due to the grid approximation used by the ChimeraX surface algorithm. For these very small surface blobs (a few atoms) the MSMS algorithm will give more faithful shape but wrong lack of holes.
Tom
Chimera surface with incorrect self-intersections.
ChimeraX surface has no self-intersections
On Jan 19, 2021, at 5:04 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
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@ce1:91@ca,nd2,o:93@cb,n,oe2:107@ce2,oh:109@ca:110@cg2,n,o,og1:112@og:152@ce1:153@cb,cd:154@cg,n,od1,od2:256@nd2,od1:261@oe1:195@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:
<Screen Shot 2021-01-19 at 4.55.55 PM.png>
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@cam.ac.uk mailto:ym337@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@cam.ac.uk mailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:06:49 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cam.ac.uk mailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cam.ac.uk mailto:ym337@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@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cam.ac.uk mailto:ym337@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 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@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
On Jan 19, 2021, at 4:06 PM, Y. Mutum ym337@cam.ac.uk wrote:
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 https://aka.ms/ghei36 From: Y. Mutum ym337@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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 https://aka.ms/ghei36 From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
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________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
[cid:B5D81530-D170-48D3-8A64-30E31B753AE7]
On Jan 19, 2021, at 4:06 PM, Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> wrote:
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 Androidhttps://aka.ms/ghei36
________________________________ From: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
openhelp:user/commands/open.html 3lbw addhhelp:user/commands/addh.html
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
selecthelp:user/commands/select.html #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surfacehelp:user/commands/surface.html #1 enclose #1 ~surfacehelp:user/commands/surface.html#~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 08:07 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
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________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
[cid:B5D81530-D170-48D3-8A64-30E31B753AE7]
On Jan 19, 2021, at 4:06 PM, Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> wrote:
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 Androidhttps://aka.ms/ghei36
________________________________ From: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Tom, Elaine
You could regard this as an independent email. I missed out on another important thing to ask: on how to color this castP-pocket surface by, say electrostatic potential.
Once, I generated the surface using the commands using the distance cutoff command, I tried to color the surface of this pocket, using hydrophobicity.
First run the comands, open 1blw; addh; open 1poc001.cif; sel #2 @<1; surface #1 enclose #1; ~surface ~sel
Then, color by hydrophobicity.
mlp sel
However, the resulting hydrophobicity-colored-surface is very different from the pocket that we saw earlier (image attached - white background). I also tried to first color the whole pdb: 3blw by hydrophobicity, then, carve out using the command:
sel #2 @<1; surface #1 enclose #1; ~surface ~sel
But then the pocket-surface is not colored (image in black background).
I agree that the CastP-pocket might not necessarily indicate the surface of the atoms in-selection, in ChimeraX, as we see in the example above. And that we might have to fill up the patches/holes. But is there a rough fix - show the pocket, yet color the pocket by say, electrostatic potential?
It would be very helpful.
Thanks Yaikhomba ________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 13:15 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu; Elaine Meng meng@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
open 3lbw addh
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
select #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surface #1 enclose #1 ~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
________________________________ From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 08:07 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
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________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
[cid:B5D81530-D170-48D3-8A64-30E31B753AE7]
On Jan 19, 2021, at 4:06 PM, Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> wrote:
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
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________________________________ From: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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 Androidhttps://aka.ms/ghei36
________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Hi Yaikhomba, (1) I am skeptical that those large holes have anything to do with hydrogens. (I am pretty sure that the Castp algorithm does not add atoms that are not in the original structure.) One possibility is that they are the intersections described by Tom. Another possibility is that you didn't include all of the atoms for a pocket. Remember that the atoms for a single pocket are not necessarily together in the poc file, they can be sprinkled throughout the file. Again if you are showing pocket N then you look for lines where N is in the next-to-last column.
(2) the "mlp" command recalculates the surface. If you want to make "mlp" use the already existing surface instead of making a new one, you have to use the "mlp" command option "surfaces" with the model number of the already existing surface. See the "mlp" manual page. https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html
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 20, 2021, at 5:58 AM, Y. Mutum ym337@cam.ac.uk wrote:
Hi Tom, Elaine
You could regard this as an independent email. I missed out on another important thing to ask: on how to color this castP-pocket surface by, say electrostatic potential.
Once, I generated the surface using the commands using the distance cutoff command, I tried to color the surface of this pocket, using hydrophobicity.
First run the comands, open 1blw; addh; open 1poc001.cif; sel #2 @<1; surface #1 enclose #1; ~surface ~sel
Then, color by hydrophobicity.
mlp sel
However, the resulting hydrophobicity-colored-surface is very different from the pocket that we saw earlier (image attached - white background). I also tried to first color the whole pdb: 3blw by hydrophobicity, then, carve out using the command:
sel #2 @<1; surface #1 enclose #1; ~surface ~sel
But then the pocket-surface is not colored (image in black background).
I agree that the CastP-pocket might not necessarily indicate the surface of the atoms in-selection, in ChimeraX, as we see in the example above. And that we might have to fill up the patches/holes. But is there a rough fix - show the pocket, yet color the pocket by say, electrostatic potential?
It would be very helpful.
Thanks Yaikhomba From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 13:15 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu; Elaine Meng meng@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
open 3lbw addh
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
select #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surface #1 enclose #1 ~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 08:07 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
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From: Tom Goddard goddard@sonic.net Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
<3cx5_pockets.jpg>
On Jan 19, 2021, at 4:06 PM, Y. Mutum ym337@cam.ac.uk wrote:
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
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From: Y. Mutum ym337@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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<Screenshot 2021-01-20 at 13.54.44.png><Screenshot 2021-01-20 at 13.53.56.png>
Hi Yaikhomba,
The CastP server says it ignores all hydrogens. If you add hydrogens in ChimeraX it will of course change the surface, maybe more holes, maybe fewer.
The reason there is a hole in a pocket surface is because the patch of surface that fills the hole is closest to some atom which is not listed as one of the pocket lining atoms by the .poc file. Why would CastP leave out such an atom? There are lots of reasons. It is not easy for CastP to figure out which atoms line the pocket. It depends on the atom radii that surely differ by small amounts between CastP and ChimeraX. If CastP includes more atoms lining the pocket this creates more fragments of surface outside the pocket, so there is a tradeoff, it doesn't want to include more than are needed.
In summary the holes are to be expected. Because of bugs in the Chimera surface calculation those holes sometimes get filled so it may look better than the ChimeraX surface. You could fiddle with the ChimeraX surface probeRadius (a bit larger might help reduce holes) or the ChimeraX atom radii (again a bit larger might reduce holes). But ultimately it would require a more sophisticated algorithm than CastP to minimize holes, and the surface calculation would need to be part of the algorithm. Notice that on the CastP web site it does not show pocket surfaces -- instead it uses translucent spheres of various sizes that fill the pocket. That is a better way to avoid holes than trying to depict a partial solvent excluded surface as in ChimeraX.
Tom
Here is how CastP shows the 3lbw pockets using translucent spheres of various sizes to avoid the problem with holes. Probably CastP defines the pocket using these spheres.
On Jan 20, 2021, at 5:15 AM, Y. Mutum ym337@cam.ac.uk wrote:
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
open help:user/commands/open.html 3lbw addh help:user/commands/addh.html
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
select help:user/commands/select.html #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surface help:user/commands/surface.html #1 enclose #1 ~surface help:user/commands/surface.html#~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
From: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Sent: 20 January 2021 08:07 To: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
Get Outlook for Android https://aka.ms/ghei36 From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
<3cx5_pockets.jpg>
On Jan 19, 2021, at 4:06 PM, Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> wrote:
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 https://aka.ms/ghei36 From: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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 https://aka.ms/ghei36 From: Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cam.ac.uk mailto:ym337@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@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.uk mailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@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@cam.ac.uk mailto:ym337@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 applewebdata://BA47BFFF-53DC-404B-9BA1-9C69D3DF07A9.
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@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<1poc001.cif><Screenshot 2021-01-20 at 13.02.41.png><Screenshot 2021-01-20 at 12.54.52.png><Screenshot 2021-01-20 at 12.54.04.png><Screenshot 2021-01-20 at 13.10.07.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
CASTp uses Delaunay triangulation, alpha shape, and discrete flow (not spheres nor solvent-excluded nor solvent-accessible surfaces), as outlined at the CASTp website and described in more depth in the cited publications.
http://sts.bioe.uic.edu/castp/background.html
Elaine
On Jan 20, 2021, at 9:34 AM, Tom Goddard goddard@sonic.net wrote:
Hi Yaikhomba,
The CastP server says it ignores all hydrogens. If you add hydrogens in ChimeraX it will of course change the surface, maybe more holes, maybe fewer.
The reason there is a hole in a pocket surface is because the patch of surface that fills the hole is closest to some atom which is not listed as one of the pocket lining atoms by the .poc file. Why would CastP leave out such an atom? There are lots of reasons. It is not easy for CastP to figure out which atoms line the pocket. It depends on the atom radii that surely differ by small amounts between CastP and ChimeraX. If CastP includes more atoms lining the pocket this creates more fragments of surface outside the pocket, so there is a tradeoff, it doesn't want to include more than are needed.
In summary the holes are to be expected. Because of bugs in the Chimera surface calculation those holes sometimes get filled so it may look better than the ChimeraX surface. You could fiddle with the ChimeraX surface probeRadius (a bit larger might help reduce holes) or the ChimeraX atom radii (again a bit larger might reduce holes). But ultimately it would require a more sophisticated algorithm than CastP to minimize holes, and the surface calculation would need to be part of the algorithm. Notice that on the CastP web site it does not show pocket surfaces -- instead it uses translucent spheres of various sizes that fill the pocket. That is a better way to avoid holes than trying to depict a partial solvent excluded surface as in ChimeraX.
Tom
Here is how CastP shows the 3lbw pockets using translucent spheres of various sizes to avoid the problem with holes. Probably CastP defines the pocket using these spheres.
<3lbw_castp.png>
On Jan 20, 2021, at 5:15 AM, Y. Mutum ym337@cam.ac.uk wrote:
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
open 3lbw addh
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
select #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surface #1 enclose #1 ~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
From: Y. Mutum ym337@cam.ac.uk Sent: 20 January 2021 08:07 To: Tom Goddard goddard@sonic.net Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
Get Outlook for Android
From: Tom Goddard goddard@sonic.net Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
<3cx5_pockets.jpg>
On Jan 19, 2021, at 4:06 PM, Y. Mutum ym337@cam.ac.uk wrote:
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@cam.ac.uk Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help chimerax-users@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@cgl.ucsf.edu Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@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@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@cgl.ucsf.edu Sent: 19 January 2021 17:28 To: Y. Mutum ym337@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@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@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@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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<1poc001.cif><Screenshot 2021-01-20 at 13.02.41.png><Screenshot 2021-01-20 at 12.54.52.png><Screenshot 2021-01-20 at 12.54.04.png><Screenshot 2021-01-20 at 13.10.07.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Thanks Tom, Elaine. I understand somewhat and to move on with what we have.
Yaikhomba ________________________________ From: Tom Goddard goddard@sonic.net Sent: 20 January 2021 17:34 To: Y. Mutum ym337@cam.ac.uk Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The CastP server says it ignores all hydrogens. If you add hydrogens in ChimeraX it will of course change the surface, maybe more holes, maybe fewer.
The reason there is a hole in a pocket surface is because the patch of surface that fills the hole is closest to some atom which is not listed as one of the pocket lining atoms by the .poc file. Why would CastP leave out such an atom? There are lots of reasons. It is not easy for CastP to figure out which atoms line the pocket. It depends on the atom radii that surely differ by small amounts between CastP and ChimeraX. If CastP includes more atoms lining the pocket this creates more fragments of surface outside the pocket, so there is a tradeoff, it doesn't want to include more than are needed.
In summary the holes are to be expected. Because of bugs in the Chimera surface calculation those holes sometimes get filled so it may look better than the ChimeraX surface. You could fiddle with the ChimeraX surface probeRadius (a bit larger might help reduce holes) or the ChimeraX atom radii (again a bit larger might reduce holes). But ultimately it would require a more sophisticated algorithm than CastP to minimize holes, and the surface calculation would need to be part of the algorithm. Notice that on the CastP web site it does not show pocket surfaces -- instead it uses translucent spheres of various sizes that fill the pocket. That is a better way to avoid holes than trying to depict a partial solvent excluded surface as in ChimeraX.
Tom
Here is how CastP shows the 3lbw pockets using translucent spheres of various sizes to avoid the problem with holes. Probably CastP defines the pocket using these spheres.
[cid:368602D5-1797-4B85-84F0-56F224366DA2] On Jan 20, 2021, at 5:15 AM, Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> wrote:
Hi Elaine, Tom
I have figured out the surface holes problem. It seems to be a problem of the hydrogens, that were not added in the pdb. However, there're a few finishing-touch problems.
The approach I took was add hydrogens in the parent pdb (pdb: 1blw in this case), then to take the atoms relevant for that CastP-calculated pocket (say poc0001) from pymol as described earlier, select these corresponding atoms in the original pdb 'within a certain distance', then to generate a surface of these in ChimeraX. The commands I used were, (in order) :
open 3lbw addh
Then, open the 1poc001.cif (atoms for that pocket poc001 saved from pymol)
select #2 @<1 (This distance parameter is varied 2.5 A, 1 A to illustrate a point described later) surface #1 enclose #1 ~surface ~sel
There are no holes in this new surface, provided the distance is 'optimum' for that surface. The problem with this approach seems to be that the surface generated is quite dependent on the distance cut-off chosen - please have a look at the screenshots (for selected within a distance of 2.5 A and 1.0 A (images attached in black and blue background respectively). You can see different levels of holes, depending on the distance chosen.
This surface is compared with the script in the previous email (image attached as white background), where there are a few holes. I actually, like the script generated by Tom - it is quite convenient for loading surfaces for these pockets of large pdb models, except for the holes - which I assume a way around is to add the hydrogens. Is there a way to modify this script - I am not sure of what exact distance parameters to use, once we have added the hydrogens in the parent pdb. In other words, I am also not sure how to 'enclose' this surface generated. Could you please have a look at this script?
Please feel free to correct this approach - I might not be entirely correct in adding the hydrogens either. I tried adding hydrogens to the pdb: 3lbw before running Tom's script, but these hydrogens seems to mess the surface originally intended (more holes - see image attached in pink background).
Another thing - there are other unconnected patches in my approach, as we increase this distance. Some of these surface patches are unconnected with the actual pocket and quite far away. I am not exactly sure how to get rid of these patches - could you please suggest ways to remove these fragmented patches? I tried the argument visiblePatches in the commands described above:
~surface ~sel enclose protein visiblePatches 1
But this is giving an error. I am not sure how to just show only the main surface (in this case, largest patch)
The atoms contributing to the pocket in observation, generated from pymol, -1poc0001.cif, is attached, just in case you need it.
Thanks Yaikhomba
________________________________ From: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Sent: 20 January 2021 08:07 To: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Wow! This is amazing! Thanks a lot everyone ! Tom, Elaine. Thanks Yaikhomba
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________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Wednesday, January 20, 2021 6:19:33 AM To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] CastP surfaces in ChimeraX/ Chimera
Hi Yaikhomba,
The .poc file has the format of a PDB file with pocket numbers at the end of each atom line. I wrote some example Python code to read that in ChimeraX and define names pocket1, pocket2, ... which are atom specifiers for the atoms lining each pocket.
https://rbvi.github.io/chimerax-recipes/castp/castp.html
There are over 500 pockets for the complex III structure 3cx5.
Some day we will probably implement the Chimera CASTP tool in ChimeraX.
Tom
<3cx5_pockets.jpg>
On Jan 19, 2021, at 4:06 PM, Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> wrote:
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
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________________________________ From: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Sent: Wednesday, January 20, 2021 12:04:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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
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________________________________ From: Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 19, 2021 11:50:50 PM To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> Sent: 19 January 2021 17:28 To: Y. Mutum <ym337@cam.ac.ukmailto:ym337@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@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@cam.ac.ukmailto:ym337@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@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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<1poc001.cif><Screenshot 2021-01-20 at 13.02.41.png><Screenshot 2021-01-20 at 12.54.52.png><Screenshot 2021-01-20 at 12.54.04.png><Screenshot 2021-01-20 at 13.10.07.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Tom Goddard -
Y. Mutum