We sometimes find that a local fasta search against the pdb sequence datafile (for which you need to install fasta package) works better than OCA at EBI, i.e. finds more matches. We have never tracked down why.
But not sure what you mean by using local OCA server. How have you specified this server? And how does it fail? Cheers Martyn -----Original Message----- From: CCP4 bulletin board on behalf of Harry M. Greenblatt Sent: Tue 8/21/2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] problem with Mr Bump? BS"D Dear All, While trying to run Mr. Bump, the program fails just after the FASTA step saying it can't find a file, which should contain the search results. This same job got past this point last week, but fails now. In trying to check out what is going wrong, I used the sequence with our local OCA server, and it works, and even finds four matches. Using the EBI's web site for OCA (used by Mr. Bump), it finds only two matches (same last week), but it *does* succeed. Have other people used Mr. Bump today, or this week? Thanks Harry ------------------------------------------------------------------------- Harry M. Greenblatt Staff Scientist Dept of Structural Biology [EMAIL PROTECTED] Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel
