Hi Doug, The problem could be one of two things. Do you need to set a proxy to access the internet? Alternatively, it might just be that the multiple alignment step is taking a long time to run. We've noticed this if you chose probcons to do the multiple alignment step.
A useful thing to do is turn the debug option on. It will give more feedback about what's happening. Please send me the output from this if it still gives you a problem. Hope this helps. Regards, Ronan -----Original Message----- From: CCP4 bulletin board on behalf of Doug Bailey Sent: Mon 14/01/2008 21:48 To: [email protected] Subject: [ccp4bb] MrBUMP FASTA Hello Everyone, Just to let you know our lab just starting using the MrBUMP program (v0.4.1), so our problem(s) could definitely be from lack of knowledge. Anyway, when we try a FASTA search from CCP4i, either over the internet or locally, things just seem to hang at "Getting Template Sequences and Multiple Alignment" . See output from logfile. Any ideas, directions or suggestions would be greatly appreciated. Thanks in advance, Doug ################################### ### Fasta search ### ################################### Fasta log message: E value used in Fasta search: 2.00e-02 Fasta log message: Performing Fasta search locally Fasta log message: Fasta DB set to: /people5/bhaumik/.ccp4_mrbump/pdb_ATOMseqs.txt Number of templates after user specified chains are included: 169 --------------------------------------- Adding chains from local files... --------------------------------------- Fasta log message: Number of matches: 170 --------------------------------------------------------- Fasta: Getting Template Sequences and Multiple Alignment: --------------------------------------------------------- Douglas Bailey Ph: 301-846-5328 NCI-Frederick Fax: 301-846-6322 1050 Boyles Street E-mail: [EMAIL PROTECTED] Frederick, Maryland 21702
