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 ?
-if your sequence_search program finishes properly, related pdb codes are 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 $MODINSTALL6v2/modlib/CHAINS_3.0_40_XN.grp
-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 structures.
best wishes, Andras
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 ? > > Thanks, > > Alex.