Hi All,
I am presently trying to run MALIGN for 15 sequences, taking them from their respective PDB co-ordinates. With upto 5 sequences (taken at random)the multiple alignment is working all right, but it is failing for 6 or more inputs. Here is the .log file "................... openf5___> file does not exist: /disk2/pdb/pdb.ent/List.ent (do not worry about this one) rdpir___E> increase MAXSEQ openf5__E> error openning file rdpir___E> alignment sequence not found in PDB file: 1 ./ ............................"
I've tried several Gap Penalty combinations. Please help me as I'm not sure where the mistake is.
Debashis. ------------------------------------------------------------------------------ ("`-''-/").___..--''"`-._ `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. India. deb@cmb2.saha.ernet.in ------------------------------------------------------------------------------
Debashis wrote: > > Hi All, > > I am presently trying to run MALIGN for 15 sequences, taking them from their > respective PDB co-ordinates. With upto 5 sequences (taken at random)the multiple > alignment is working all right, but it is failing for 6 or more inputs. > Here is the .log file > "................... > openf5___> file does not exist: /disk2/pdb/pdb.ent/List.ent > (do not worry about this one) > rdpir___E> increase MAXSEQ > openf5__E> error openning file > rdpir___E> alignment sequence not found in PDB file: 1 > ./ > ............................" >
The maximal number of sequences set in your program is less than 15. You can find the maximally allowed number of sequences which is set in your program in the header of MODELLER .log output. Now there is no way to change it in the program without recompiling. Please check our web site if there are versions with larger MAXSEQ.
The next release of MODELLER (probably around mid-year) will deal with it more smoothly.
Yours,
Azat.
> I've tried several Gap Penalty combinations. > Please help me as I'm not sure where the mistake is. > > Debashis. > ------------------------------------------------------------------------------ > ("`-''-/").___..--''"`-._ > `6_ 6 ) `-. ( ).`-.__.`) Debashis Mukhopadhyay > (_Y_.)' ._ ) `._ `. ``-..-' Research Fellow,C&MB Div., > _..`--'_..-_/ /--'_.' ,' Saha Institute Of Nuclear Physics, > (il).-'' (li).' ((!.-' 1/AF, Bidhannagar,Calcutta-700 064. > India. > deb@cmb2.saha.ernet.in > ------------------------------------------------------------------------------
-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
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