.sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie
Hi Natalie, Chimera does not know the *.sld file type. Can SYBYL save this file in a format Chimera knows, such as VRML? <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> If not, you could try opening the structure (PDB or Mol2 file) in Chimera, instead of the surface file, and have Chimera calculate the surface. In Chimera, you can display the surface with "Actions... Surface... show". The default in Chimera is also to use a 1.4 Angstrom probe. That would generate both the inner and outer surfaces, which you could see by slicing the structure in the Side View (under Favorites menu). There will probably be differences in the surface due to the different default atomic radii in Chimera and SYBYL, but I would not expect them to be large. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 21, 2009, at 10:34 AM, Xarana wrote:
Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this “inner surface” with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie
Hi Elaine, Thank you very much for your quick help. That really helped a lot and the differences are small. One last question: Is there a possibility to only show this "inner surface" without the outer one for more clarity? I have to compare in 10 different structures (NMR solved) the extent of this cavities. And sadly SYBYL is not able to save as any other file format. Best wishes, Natalie Bordag PhD student -----Ursprüngliche Nachricht----- Von: Elaine Meng [mailto:meng@cgl.ucsf.edu] Gesendet: Montag, 21. September 2009 22:28 An: Xarana Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera Hi Natalie, Chimera does not know the *.sld file type. Can SYBYL save this file in a format Chimera knows, such as VRML? <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> If not, you could try opening the structure (PDB or Mol2 file) in Chimera, instead of the surface file, and have Chimera calculate the surface. In Chimera, you can display the surface with "Actions... Surface... show". The default in Chimera is also to use a 1.4 Angstrom probe. That would generate both the inner and outer surfaces, which you could see by slicing the structure in the Side View (under Favorites menu). There will probably be differences in the surface due to the different default atomic radii in Chimera and SYBYL, but I would not expect them to be large. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 21, 2009, at 10:34 AM, Xarana wrote:
Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this inner surface with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.409 / Virus Database: 270.13.110/2385 - Release Date: 09/20/09 17:51:00
Hi Natalie, It is unfortunately a bit tricky to show just the inner pocket surface of a molecule in Chimera. Here's one way. Create the surface then use the following command to make it possible to select the separate connected pieces of the surface: ac Sc (This runs the keyboard shortcut "Sc" - split connected pieces of selected surface.) Now select the outer surface with the mouse (ctrl-click) and use a command to delete it: ac Ds (Keyboard shortcut "Ds" - delete selected surface pieces.) These steps that change the molecular confuse Chimera and the Actions / Surface menu then doesn't work on the inner piece. The problem is that the molecular surface no longer matches the atomic coordinates in the way Chimera expects. To get those menu entries to work delete the atomic model and reload another copy. A drawback of all this is that it will no longer color the surface to match the atoms. Tom -------- Original Message -------- Subject: [Chimera-users] Thanks for the help, Is it possible to only show the "inner surface"? From: Xarana To: chimera-users Date: 9/22/09 2:07 AM
Hi Elaine, Thank you very much for your quick help. That really helped a lot and the differences are small. One last question:
Is there a possibility to only show this "inner surface" without the outer one for more clarity? I have to compare in 10 different structures (NMR solved) the extent of this cavities. And sadly SYBYL is not able to save as any other file format.
Best wishes, Natalie Bordag PhD student
-----Ursprüngliche Nachricht----- Von: Elaine Meng Gesendet: Montag, 21. September 2009 22:28 An: Xarana Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera
Hi Natalie, Chimera does not know the *.sld file type. Can SYBYL save this file in a format Chimera knows, such as VRML? <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
If not, you could try opening the structure (PDB or Mol2 file) in Chimera, instead of the surface file, and have Chimera calculate the surface.
In Chimera, you can display the surface with "Actions... Surface... show". The default in Chimera is also to use a 1.4 Angstrom probe. That would generate both the inner and outer surfaces, which you could see by slicing the structure in the Side View (under Favorites menu). There will probably be differences in the surface due to the different default atomic radii in Chimera and SYBYL, but I would not expect them to be large.
I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2009, at 10:34 AM, Xarana wrote:
Hi, My interest is a 4 helix protein which has a cavity inside. A colleague generated with a 1,4 Angström probe this "inner surface" with Sybyl for me and exported the surface as .sld file. Can I import this file into chimera somehow? Alternatively, can I generate such a surface with chimera? My knowledge of protein visualization is limited and I am very thankful for any help Thank you very much in advance. Best Wishes Natalie
No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.409 / Virus Database: 270.13.110/2385 - Release Date: 09/20/09 17:51:00
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Hi Natalie, If the inner surface is totally disconnected from the outer surface (like an inside "bubble"), it is fairly easy: - Ctrl-click to select the surface - use command: ac Sc (this makes the disconnected parts into separate "surface pieces" that can be controlled separately; choose "Favorites... Command Line" from the menu to get the command line) - Ctrl-click empty space to clear selection - Ctrl-click outer surface to select it (now the inner surface will not be selected) - choose "Actions... Inspect" from the menu to open the Selection Inspector. In that dialog, Inspect "Surface Piece" and set "displayed" to "false." That will undisplay the outer surface, leaving the inner surface. If there are other pieces to turn off, repeat by selecting them and using the Selection Inspector to undisplay them. If inner and outer surfaces are connected, however, it may be difficult to just show the part you want. You can select sets of atoms and use "Actions.... Surface... hide/show" to hide or show their surface patches, but the problem is that it can be hard to figure out which atoms go with which surface patches, and some atoms might even form parts of both the inner and outer surfaces. A third possibility is to use the Surface Zone tool (under Tools... Surface/Binding Analysis). In that case you would need to put some atom in the middle of the inner surface, select it, and then use some cutoff from that atom. You can add a single atom with Build Structure (under Tools... Structure Editing), Add Atoms section, "atom" (make sure to put atom in a "new model") and then move it relative to your first structure by checking/unchecking the boxes under the Command Line and using the mouse. It can be hard to get the atom where you want it, and even if that part is successful, it may work very well either if a spherical cutoff does not separate the inner and outer surfaces. The "Structure Analysis and Comparison" tutorial includes showing just the surface of a binding pocket: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html#surfaces> 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 Sep 22, 2009, at 2:07 AM, Xarana wrote:
Hi Elaine, Thank you very much for your quick help. That really helped a lot and the differences are small. One last question:
Is there a possibility to only show this "inner surface" without the outer one for more clarity? I have to compare in 10 different structures (NMR solved) the extent of this cavities. And sadly SYBYL is not able to save as any other file format.
Best wishes, Natalie Bordag PhD student
-----Ursprüngliche Nachricht----- Von: Elaine Meng [mailto:meng@cgl.ucsf.edu] Gesendet: Dienstag, 22. September 2009 20:23 An: Xarana Cc: chimera-users@cgl.ucsf.edu Betreff: Re: [Chimera-users] Thanks for the help, Is it possible to only show the "inner surface"? Hi Natalie, If the inner surface is totally disconnected from the outer surface (like an inside "bubble"), it is fairly easy: - Ctrl-click to select the surface - use command: ac Sc (this makes the disconnected parts into separate "surface pieces" that can be controlled separately; choose "Favorites... Command Line" from the menu to get the command line) - Ctrl-click empty space to clear selection - Ctrl-click outer surface to select it (now the inner surface will not be selected) - choose "Actions... Inspect" from the menu to open the Selection Inspector. In that dialog, Inspect "Surface Piece" and set "displayed" to "false." That will undisplay the outer surface, leaving the inner surface. If there are other pieces to turn off, repeat by selecting them and using the Selection Inspector to undisplay them. If inner and outer surfaces are connected, however, it may be difficult to just show the part you want. You can select sets of atoms and use "Actions.... Surface... hide/show" to hide or show their surface patches, but the problem is that it can be hard to figure out which atoms go with which surface patches, and some atoms might even form parts of both the inner and outer surfaces. A third possibility is to use the Surface Zone tool (under Tools... Surface/Binding Analysis). In that case you would need to put some atom in the middle of the inner surface, select it, and then use some cutoff from that atom. You can add a single atom with Build Structure (under Tools... Structure Editing), Add Atoms section, "atom" (make sure to put atom in a "new model") and then move it relative to your first structure by checking/unchecking the boxes under the Command Line and using the mouse. It can be hard to get the atom where you want it, and even if that part is successful, it may work very well either if a spherical cutoff does not separate the inner and outer surfaces. The "Structure Analysis and Comparison" tutorial includes showing just the surface of a binding pocket: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html#surfaces> 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 Sep 22, 2009, at 2:07 AM, Xarana wrote:
Hi Elaine, Thank you very much for your quick help. That really helped a lot and the differences are small. One last question:
Is there a possibility to only show this "inner surface" without the outer one for more clarity? I have to compare in 10 different structures (NMR solved) the extent of this cavities. And sadly SYBYL is not able to save as any other file format.
Best wishes, Natalie Bordag PhD student No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.409 / Virus Database: 270.13.112/2387 - Release Date: 09/21/09 17:55:00
participants (4)
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Elaine Meng -
Natalie Bordag -
Tom Goddard -
Xarana