I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database. I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards George
Hi George, In that case (protein is not in the CASTp database), you have to go to the CASTp web server yourself: <http://sts-fw.bioengr.uic.edu/castp/calculation.php> ...to request the new calculation and specify that the results should be e-mailed back to you. Then after you get the e-mail with results attached and put them on your own computer, you can use Chimera to view them. For more about the results files and and how to open them in Chimera, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.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 Oct 24, 2014, at 2:19 PM, George Tzotzos <gtzotzos@me.com> wrote:
I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database.
I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards
George
Thank you Elaine, Much appreciated George On 24Oct, 2014, at 7:34 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, In that case (protein is not in the CASTp database), you have to go to the CASTp web server yourself:
<http://sts-fw.bioengr.uic.edu/castp/calculation.php>
...to request the new calculation and specify that the results should be e-mailed back to you.
Then after you get the e-mail with results attached and put them on your own computer, you can use Chimera to view them.
For more about the results files and and how to open them in Chimera, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.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 Oct 24, 2014, at 2:19 PM, George Tzotzos <gtzotzos@me.com> wrote:
I’m trying to measure to volume and the solvent-exposed area of the binding site of proteins 4fqt and 3n7h. I’m trying to fetch the structures from CASTp to no avail. CASTp informs that these structures are not in its database.
I’ve loaded the structures on Chimera but could not find a way to evoke CASTp. Any suggestions would be most helpful. Best regards
George
participants (2)
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Elaine Meng -
George Tzotzos