Re: [ccp4bb] MrBUMP FASTA

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From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-14

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Subject: Re: PERL system call to CCP4
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-14

Subject: Re: MrBUMP FASTA
From: "Keegan, RM (Ronan)" r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-01-14

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: CCP4BB@JISCMAIL.AC.UK
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: baileyd@ncifcrf.gov
Frederick, Maryland 21702

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CCP4bb <-- 2008 <-- January 2008 <-- 14 January 2008

Previous message:
Subject: Re: PERL system call to CCP4
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-14

Next message:
Subject: Re: PERL system call to CCP4
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2008-01-14