Don't specify chain IDs in the alignments for PDBs that don't have chain IDs. Similarly, to return to a system with no chain IDs at all, strip the chain IDs out of any PDB that have chain IDs (by looking for <space>CHAINID<space>). Note that this will only work with monomeric PDBs, which is apparently what you are working with so it should work. (It worked for me).
Adding the chain ID to a pdb is tricky, but can be done with some clever perl tricks (read a line, explode the line into an array using whitespace as the delimiter, insert <space>A<space> into the appropriate element, serialize the array and write the resulting line into your new file, read next line, etc).
On Thu, Mar 13, 2003 at 12:07:53PM -0500, Richard Friedman wrote: > Dear Modellers, > > How can I write a pdb file containing a chain specification? > > My top file is > > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined TOP routines > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log > file > SET ALNFILE = 'monomer3.ali' # alignment filename > SET KNOWNS = '1g2i' # codes of the templates > SET SEQUENCE = 'prk7' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom > files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > > CALL ROUTINE = 'model' # do homology modelling > > My ali file is: > > C; alignment > >P1;1g2i > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG > NWVSSRVPADLYAWMREFVKLLK----------------* > >P1;prk7 > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > I was hoping that inclusion of the chain designators in the prk7 > sequence file, would produce a pdb file with the chain designators > included, but that is not what had happened. How can I be sure that the > output file includes the chain designation 'A' on every atom line? > > Thanks and best wishes, > Rich > > > > > -------------------------------------------------------------- > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Medical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "You don't have ot do any more work to write a book. You > already wrote a book. Your course notes are a book. I've > seen them lying on the floor of your office. I've seen > course notes used for books on everything from Math to > Origami. Just hand your course notes in. Make sure you > hand in the ones with the apple juice spilled on it." > -Isaac Friedman, age 13 > > Upon Isaac's attainment of his majority I am discontinuing > the quotes from him. > >