Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take. (1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid. (2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above. The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users@cgl.ucsf.edu I hope this helps, Elaine ----------------------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 5, 2008, at 4:52 PM, Tom Ferrin wrote:
------- Forwarded Message
Date: Wed, 30 Apr 2008 17:20:27 -0400 From: Jose Gascon <jose.gascon@uconn.edu> To: tef@cgl.ucsf.edu Subject: midasplus
Dear Prof. Ferrin
I am an Assistant Professor in the Chemistry Department at UConn, I am interested in calculating the solvent accessible area of a protein. I looked up on the internet and found that the program midasplus is suppose to do that. The links seem to be outdated and I was not been able to find the program. I assume that midasplus has probably evolved to other programs such as chimera. I understand that you were involved in the development of this program.
At the end, given a pdb input file, I am just interested in obtaining a grid of x,y,z coordinates representing the SAS. Do you know if there is such a program? Is DMS, from midasplus, still available somewhere?
Thanks for your help.
Sincerely,
Jose A. Gascon
-- Jose A. Gascon - Assistant Professor 55 North Eagleville Rd. Department of Chemistry University of Connecticut - (860) 486-0591 Storrs, CT 06269 http://gascon.chem.uconn.edu
------- End of Forwarded Message
Hi Jose, And if for some reason you still want to use DMS, you can obtain it here: http://www.cgl.ucsf.edu/Overview/software.html#dms --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 5, 2008, at 5:15 PM, Elaine Meng wrote:
Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots
You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take.
(1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces
Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render
The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid.
(2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html
Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above.
The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera- users@cgl.ucsf.edu
I hope this helps, Elaine ----------------------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On May 5, 2008, at 4:52 PM, Tom Ferrin wrote:
------- Forwarded Message
Date: Wed, 30 Apr 2008 17:20:27 -0400 From: Jose Gascon <jose.gascon@uconn.edu> To: tef@cgl.ucsf.edu Subject: midasplus
Dear Prof. Ferrin
I am an Assistant Professor in the Chemistry Department at UConn, I am interested in calculating the solvent accessible area of a protein. I looked up on the internet and found that the program midasplus is suppose to do that. The links seem to be outdated and I was not been able to find the program. I assume that midasplus has probably evolved to other programs such as chimera. I understand that you were involved in the development of this program.
At the end, given a pdb input file, I am just interested in obtaining a grid of x,y,z coordinates representing the SAS. Do you know if there is such a program? Is DMS, from midasplus, still available somewhere?
Thanks for your help.
Sincerely,
Jose A. Gascon
-- Jose A. Gascon - Assistant Professor 55 North Eagleville Rd. Department of Chemistry University of Connecticut - (860) 486-0591 Storrs, CT 06269 http://gascon.chem.uconn.edu
------- End of Forwarded Message
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine and Tom, Thanks for the thorough answer. This is exactly what I was looking for. I appreciate the time you took to write this. With best regards, Jose. On Mon, 2008-05-05 at 17:15 -0700, Elaine Meng wrote:
Dear Jose, Prof. Ferrin forwarded your question to me. Our program Chimera, the successor to MidasPlus, can calculate the solvent-accessible surface area. It is available for download for Windows, Mac OSX, Linux and other platforms. The features I will mention are relatively new, so you would need to get a recent version such as the May 1 snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots
You would first load the structure in Chimera (File... Open for a local file, File... Fetch by ID to get it directly from the PDB). Then there are a couple of different approaches you could take.
(1) simply show a molecular surface in Chimera (Actions... Surface... show) or command "surface". The total will be reported in the Reply Log (under Favorites in the menu). You can use the solvent- accessible value or solvent-excluded as you prefer. The difference is explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces
Besides the total, the values per atom and per residue are assigned as "attributes" named areaSAS and areaSES for solvent-accessible and solvent-excluded, respectively. You can see a histogram of the values by opening "Render by Attribute" (under Tools... Depiction), and you can write out the values to a file by choosing File... Save Attributes from that dialog's menu. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render
The Render dialog can be set to show the values for "atoms" or "residues" (simply the sum over the atoms in each residue). What it writes out are the atom (or residue) specifiers and the value for each, not a grid.
(2) instead of doing the calculation in Chimera, you can send the coordinates to a web server with the tool "Area/Volume from Web" (under Tools... Surface/Binding Analysis). There are various options for what you want to calculate.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.htm...
Again you get the values assigned as attributes (but this time atoms only) and can view and save them in the same way as described for #1 above.
The help links above are part of the User's Guide, which is also accessible from the Help menu of Chimera, once you have downloaded it (Help... User's Guide, Search Documentation, Tutorials). If you still have trouble you can send questions to chimera-users@cgl.ucsf.edu
I hope this helps, Elaine ----------------------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On May 5, 2008, at 4:52 PM, Tom Ferrin wrote:
------- Forwarded Message
Date: Wed, 30 Apr 2008 17:20:27 -0400 From: Jose Gascon <jose.gascon@uconn.edu> To: tef@cgl.ucsf.edu Subject: midasplus
Dear Prof. Ferrin
I am an Assistant Professor in the Chemistry Department at UConn, I am interested in calculating the solvent accessible area of a protein. I looked up on the internet and found that the program midasplus is suppose to do that. The links seem to be outdated and I was not been able to find the program. I assume that midasplus has probably evolved to other programs such as chimera. I understand that you were involved in the development of this program.
At the end, given a pdb input file, I am just interested in obtaining a grid of x,y,z coordinates representing the SAS. Do you know if there is such a program? Is DMS, from midasplus, still available somewhere?
Thanks for your help.
Sincerely,
Jose A. Gascon
-- Jose A. Gascon - Assistant Professor 55 North Eagleville Rd. Department of Chemistry University of Connecticut - (860) 486-0591 Storrs, CT 06269 http://gascon.chem.uconn.edu
------- End of Forwarded Message
-- Jose A. Gascon - Assistant Professor 55 North Eagleville Rd. Department of Chemistry University of Connecticut - (860) 486-0591 Storrs, CT 06269 http://gascon.chem.uconn.edu
participants (3)
-
Elaine Meng -
Eric Pettersen -
Jose Gascon