-if your sequence_search program finishes properly, related pdb codes
reported automatically at the end of your log file.
The error you see at the end of the file related to the growth of PDB:
nowadays, after clustering PDB, certain clusters have more than 40
members and MAXSEQ apparently was pre-set to 40. We will change it and
recompile the program.
until then you can extract with 'grep' command or any text editor the
related PDB structures from the file
-seq_search takes a long time, because it uses dynamic programming to
align your target with each potential templates (about < 4000
representative PDB str).
-otherwise, I have checked the example, it was running for < 3 hours on
a pc 1.7GH intel3. and ended with the reported error problem I
explained above. i.e. only at the very last stage of collecting related
Alex Brown wrote:
> Hi, again.
> Is there a script that can be used to extract the 'other closely
> related' structures from the 'CHAINS_3.0_40_XN.grp' file, other than
> just using a text-editor search ?
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras