Displaying and calculating protein surface enclosed pockets
Good day I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software. Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question. I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket. How can I display the "negative" (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details. If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed. Thank you Matthias Fellner
Dear Mathias, Chimera automatically excludes water from the molecular surface calculation, so in general (unless something is weird about your input file) you wouldn’t have to worry about that. One approach is to only show the surface of the protein for the atoms lining the pocket. In most cases, the pocket is not completely enclosed, however, so there will be an opening and somewhat rough edges. For example, see this figure in the “structure analysis and comparison” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces> Another difficulty is that of figuring out which atoms line the pocket and thus which surface patches to show. If you use the CASTp interface, that is taken care of; CASTp calculates pocket areas/volumes and figures out which sets of atoms define each pocket and tunnel. You can fetch directly from the CASTp database (if your structure of interest is in the PDB, its results may already be there) or upload a structure to the CASTp server and have the results emailed to you. In the latter case, you can still use the Chimera interface to view the results; this lists pocket volumes and areas calculated with both molecular surface and solvent-accessible surface, number of openings, etc. More about the Chimera-CASTp interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html> As for display, all of the above are just showing parts of the surface of the protein. A different approach is to calculate a separate surface of the void space. There are several programs, mainly separate from Chimera. (For example, CAVER doesn’t have a Chimera plugin.) (A) Chimera does have a Surfnet tool (in menu under Tools… Surface/Binding Analysis) that you may want to take a look at. Personally, I have had trouble getting a nice display of pocket or tunnel volume with this tool. I usually get a bunch of smaller blobs instead of the desired one filling the whole pocket. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html> (B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates “density” maps filling void spaces, and you can open and view these maps in Chimera’s Volume Viewer. Just like other density maps, you could adjust the isosurface level, do coloring, etc. There are probably others. WIth A or B, you can measure volume enclosed in surfaces with Chimera’s Measure and Color Blobs tool (in menu under Tools… Surface/Binding Analysis). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 30, 2015, at 8:34 PM, Matthias Fellner <mfellner@chemistry.otago.ac.nz> wrote:
Good day
I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.
Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.
I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.
How can I display the “negative” (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.
If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.
Thank you Matthias Fellner
Thank you very much for the detailed answer and especially the links to other software options. This will help a lot! Matthias Fellner ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: 02 May 2015 04:23 To: Matthias Fellner Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Displaying and calculating protein surface enclosed pockets Dear Mathias, Chimera automatically excludes water from the molecular surface calculation, so in general (unless something is weird about your input file) you wouldn’t have to worry about that. One approach is to only show the surface of the protein for the atoms lining the pocket. In most cases, the pocket is not completely enclosed, however, so there will be an opening and somewhat rough edges. For example, see this figure in the “structure analysis and comparison” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces> Another difficulty is that of figuring out which atoms line the pocket and thus which surface patches to show. If you use the CASTp interface, that is taken care of; CASTp calculates pocket areas/volumes and figures out which sets of atoms define each pocket and tunnel. You can fetch directly from the CASTp database (if your structure of interest is in the PDB, its results may already be there) or upload a structure to the CASTp server and have the results emailed to you. In the latter case, you can still use the Chimera interface to view the results; this lists pocket volumes and areas calculated with both molecular surface and solvent-accessible surface, number of openings, etc. More about the Chimera-CASTp interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html> As for display, all of the above are just showing parts of the surface of the protein. A different approach is to calculate a separate surface of the void space. There are several programs, mainly separate from Chimera. (For example, CAVER doesn’t have a Chimera plugin.) (A) Chimera does have a Surfnet tool (in menu under Tools… Surface/Binding Analysis) that you may want to take a look at. Personally, I have had trouble getting a nice display of pocket or tunnel volume with this tool. I usually get a bunch of smaller blobs instead of the desired one filling the whole pocket. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html> (B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates “density” maps filling void spaces, and you can open and view these maps in Chimera’s Volume Viewer. Just like other density maps, you could adjust the isosurface level, do coloring, etc. There are probably others. WIth A or B, you can measure volume enclosed in surfaces with Chimera’s Measure and Color Blobs tool (in menu under Tools… Surface/Binding Analysis). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 30, 2015, at 8:34 PM, Matthias Fellner <mfellner@chemistry.otago.ac.nz> wrote:
Good day
I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.
Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.
I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.
How can I display the “negative” (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.
If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.
Thank you Matthias Fellner
Dear all, do you know if it is possible to label the different strands and helices on a protein with something like B1, B2, H1, H2, etc. ? The label option does not contain this possibility. Thanks, Marco Dr.Marco Sette, Ph.D. Assistant professor of Biochemistry Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette Il 01/05/2015 18.23, Elaine Meng ha scritto:
Dear Mathias, Chimera automatically excludes water from the molecular surface calculation, so in general (unless something is weird about your input file) you wouldn’t have to worry about that.
One approach is to only show the surface of the protein for the atoms lining the pocket. In most cases, the pocket is not completely enclosed, however, so there will be an opening and somewhat rough edges. For example, see this figure in the “structure analysis and comparison” tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces>
Another difficulty is that of figuring out which atoms line the pocket and thus which surface patches to show. If you use the CASTp interface, that is taken care of; CASTp calculates pocket areas/volumes and figures out which sets of atoms define each pocket and tunnel. You can fetch directly from the CASTp database (if your structure of interest is in the PDB, its results may already be there) or upload a structure to the CASTp server and have the results emailed to you. In the latter case, you can still use the Chimera interface to view the results; this lists pocket volumes and areas calculated with both molecular surface and solvent-accessible surface, number of openings, etc. More about the Chimera-CASTp interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
As for display, all of the above are just showing parts of the surface of the protein. A different approach is to calculate a separate surface of the void space. There are several programs, mainly separate from Chimera. (For example, CAVER doesn’t have a Chimera plugin.)
(A) Chimera does have a Surfnet tool (in menu under Tools… Surface/Binding Analysis) that you may want to take a look at. Personally, I have had trouble getting a nice display of pocket or tunnel volume with this tool. I usually get a bunch of smaller blobs instead of the desired one filling the whole pocket. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html>
(B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates “density” maps filling void spaces, and you can open and view these maps in Chimera’s Volume Viewer. Just like other density maps, you could adjust the isosurface level, do coloring, etc.
There are probably others. WIth A or B, you can measure volume enclosed in surfaces with Chimera’s Measure and Color Blobs tool (in menu under Tools… Surface/Binding Analysis). <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 30, 2015, at 8:34 PM, Matthias Fellner <mfellner@chemistry.otago.ac.nz> wrote:
Good day
I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.
Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.
I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.
How can I display the “negative” (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.
If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.
Thank you Matthias Fellner
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. http://www.avast.com
2dlabels seem appropriate for the job. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html ---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne ---------------------------------------- On 5/7/15, 12:04, "MarcoSette" <sette@uniroma2.it> wrote:
Dear all,
do you know if it is possible to label the different strands and helices on a protein with something like B1, B2, H1, H2, etc. ? The label option does not contain this possibility. Thanks, Marco
Dr.Marco Sette, Ph.D. Assistant professor of Biochemistry Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Il 01/05/2015 18.23, Elaine Meng ha scritto:
Dear Mathias, Chimera automatically excludes water from the molecular surface calculation, so in general (unless something is weird about your input file) you wouldn¹t have to worry about that.
One approach is to only show the surface of the protein for the atoms lining the pocket. In most cases, the pocket is not completely enclosed, however, so there will be an opening and somewhat rough edges. For example, see this figure in the ³structure analysis and comparison² tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html #surfaces>
Another difficulty is that of figuring out which atoms line the pocket and thus which surface patches to show. If you use the CASTp interface, that is taken care of; CASTp calculates pocket areas/volumes and figures out which sets of atoms define each pocket and tunnel. You can fetch directly from the CASTp database (if your structure of interest is in the PDB, its results may already be there) or upload a structure to the CASTp server and have the results emailed to you. In the latter case, you can still use the Chimera interface to view the results; this lists pocket volumes and areas calculated with both molecular surface and solvent-accessible surface, number of openings, etc. More about the Chimera-CASTp interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
As for display, all of the above are just showing parts of the surface of the protein. A different approach is to calculate a separate surface of the void space. There are several programs, mainly separate from Chimera. (For example, CAVER doesn¹t have a Chimera plugin.)
(A) Chimera does have a Surfnet tool (in menu under ToolsŠ Surface/Binding Analysis) that you may want to take a look at. Personally, I have had trouble getting a nice display of pocket or tunnel volume with this tool. I usually get a bunch of smaller blobs instead of the desired one filling the whole pocket.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfne t.html>
(B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates ³density² maps filling void spaces, and you can open and view these maps in Chimera¹s Volume Viewer. Just like other density maps, you could adjust the isosurface level, do coloring, etc.
There are probably others. WIth A or B, you can measure volume enclosed in surfaces with Chimera¹s Measure and Color Blobs tool (in menu under ToolsŠ Surface/Binding Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pick blobs.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 30, 2015, at 8:34 PM, Matthias Fellner <mfellner@chemistry.otago.ac.nz> wrote:
Good day
I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.
Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.
I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.
How can I display the ³negative² (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.
If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.
Thank you Matthias Fellner
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. http://www.avast.com
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes :)) thanks a lot. Marco Dr.Marco Sette, Ph.D. Assistant professor of Biochemistry Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette Il 07/05/2015 13.33, Repic Matej ha scritto:
2dlabels seem appropriate for the job.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html
---------------------------------------- Matej Repic Ecole Polytechnique Fédérale de Lausanne SB - ISIC - LCBC BCH 4108 CH - 1015 Lausanne
----------------------------------------
On 5/7/15, 12:04, "MarcoSette" <sette@uniroma2.it> wrote:
Dear all,
do you know if it is possible to label the different strands and helices on a protein with something like B1, B2, H1, H2, etc. ? The label option does not contain this possibility. Thanks, Marco
Dr.Marco Sette, Ph.D. Assistant professor of Biochemistry Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Il 01/05/2015 18.23, Elaine Meng ha scritto:
Dear Mathias, Chimera automatically excludes water from the molecular surface calculation, so in general (unless something is weird about your input file) you wouldn¹t have to worry about that.
One approach is to only show the surface of the protein for the atoms lining the pocket. In most cases, the pocket is not completely enclosed, however, so there will be an opening and somewhat rough edges. For example, see this figure in the ³structure analysis and comparison² tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html #surfaces>
Another difficulty is that of figuring out which atoms line the pocket and thus which surface patches to show. If you use the CASTp interface, that is taken care of; CASTp calculates pocket areas/volumes and figures out which sets of atoms define each pocket and tunnel. You can fetch directly from the CASTp database (if your structure of interest is in the PDB, its results may already be there) or upload a structure to the CASTp server and have the results emailed to you. In the latter case, you can still use the Chimera interface to view the results; this lists pocket volumes and areas calculated with both molecular surface and solvent-accessible surface, number of openings, etc. More about the Chimera-CASTp interface: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
As for display, all of the above are just showing parts of the surface of the protein. A different approach is to calculate a separate surface of the void space. There are several programs, mainly separate from Chimera. (For example, CAVER doesn¹t have a Chimera plugin.)
(A) Chimera does have a Surfnet tool (in menu under ToolsŠ Surface/Binding Analysis) that you may want to take a look at. Personally, I have had trouble getting a nice display of pocket or tunnel volume with this tool. I usually get a bunch of smaller blobs instead of the desired one filling the whole pocket.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfne t.html>
(B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates ³density² maps filling void spaces, and you can open and view these maps in Chimera¹s Volume Viewer. Just like other density maps, you could adjust the isosurface level, do coloring, etc.
There are probably others. WIth A or B, you can measure volume enclosed in surfaces with Chimera¹s Measure and Color Blobs tool (in menu under ToolsŠ Surface/Binding Analysis).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pick blobs.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 30, 2015, at 8:34 PM, Matthias Fellner <mfellner@chemistry.otago.ac.nz> wrote:
Good day
I am a PhD student at the University of Otago New Zealand. First I would like to thank you for this very useful software, I use it for all my protein crystallography pictures and a lot of analysis as well, I always cite your citation for sure when I publish using your software.
Normally I get very far with your tutorials but this time I failed to achieve my goal and I wanted to write a direct question.
I have a protein with an active site pocket. I can display the surface of the protein and then I see the pocket inside but I am really interested in the enclosed surface = the active site pocket.
How can I display the ³negative² (enclosed) surface area and possibly calculate its volume. Can this be done with the pdb file or is such an analysis only possible based on the electron density. I learned how to manipulate the density map in chimera, so if this is the only way I should also be able to do it if you explain the details.
If I get this done I wanted to ask if there is a way to ignore water molecules from the displaying of surfaces and later calculations or if I should simply work with a pdb which has the waters removed.
Thank you Matthias Fellner
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. http://www.avast.com
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
--- Questa e-mail è stata controllata per individuare virus con Avast antivirus. http://www.avast.com
participants (4)
-
Elaine Meng -
MarcoSette -
Matthias Fellner -
Repic Matej