castp .poc file is not opened in restored session (plain text version)
Hi,
I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be?
Cheers,
Boaz
P.S. sent again in plain text format since it seems the previous html version has been mangled up
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
On Jul 22, 2011, at 3:26 PM, Boaz Shaanan wrote:
Hi,
I save a session in which I used castp .poc file (very nice indeed!). However, after saving the session, the restored session does not open the .poc file. Is that how it's supposed to be?
Hi Boaz, CASTp session support has been added relatively recently, and therefore is only available in the 1.6 daily build -- not in the 1.5.3 release. Now, if the 1.6 version doesn't restore the .poc file, please let me know! :-)
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 24, 2011, at 3:54 PM, Boaz Shaanan wrote:
Hi Eric,
Indeed with the daily built of 1.6 the castp file opens up too when restoring the session. However, I noted a strange feature in that a hole from castp is split between two monomers. I used the bug report mechanism to report this and attached the session file (bug #9775). I'd appreciate your input on the issue.
Hi Boaz, The most reliable way to match the pocket atoms listed in the .poc file to the PDB is by serial number (due to the vagaries of how CASTp formats the .poc file). Your input PDB (and therefore output PDB) has duplicate serial numbers for corresponding atoms in the two chains. If you open your input PDB in Chimera and write out a new PDB, the new one will have unique serial numbers. You can use that with the CASTp server and get results that Chimera can handle. Sorry for the hassle.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Eric,
OK, thanks for letting me know. I read on the castp site that they can't cope with multiple models (a-la NMR) in the pdb so thought that I managed to circumvent the problem by giving different chain ID's to the two chains that I extracted from the pdb1 files and by deleting the model cards. I didn't realize that there is program that looks into the atom serial numbers in the pdb (none of the crystallographic programs that I use does).
I'll fix the problem and submit again to the castp site.
Thanks a lot for your help.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: Eric Pettersen [pett@cgl.ucsf.edu]
Sent: Tuesday, July 26, 2011 4:23 AM
To: ��� ����
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] castp .poc file is not opened in restored session (plain text version)
On Jul 24, 2011, at 3:54 PM, Boaz Shaanan wrote:
Hi Eric,
Indeed with the daily built of 1.6 the castp file opens up too when restoring the session. However, I noted a strange feature in that a hole from castp is split between two monomers. I used the bug report mechanism to report this and attached the session file (bug #9775). I'd appreciate your input on the issue.
Hi Boaz,
The most reliable way to match the pocket atoms listed in the .poc file to the PDB is by serial number (due to the vagaries of how CASTp formats the .poc file). Your input PDB (and therefore output PDB) has duplicate serial numbers for corresponding atoms in the two chains. If you open your input PDB in Chimera and write out a new PDB, the new one will have unique serial numbers. You can use that with the CASTp server and get results that Chimera can handle. Sorry for the hassle.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (2)
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Eric Pettersen