Dear Dr. Andras Fiser,
Sorry for replying you late.
Thank you for your top and alignment files. They are very helpful. To compare your top file with mine, I found that I used a comma between two knows files: SET KNOWNS='template1, template2' although I don't know if it really matter.
Another problem was found by using the debug option: SET OUTPUT_CONTROL= 1 1 1 1. Modeller complained that one of my template was unacceptable, probably that was because its low resolution (2.6 or something) and too many missing atoms. After changing to another template, I got model. Thank you for your help.
Sincerely,
Xiao-Ping
At 07:05 PM 3/28/00 -0500, you wrote: > > Dear Xiao-Ping , > > It is not very fruitful, if you are not showing what exactly you are dealing > with. > > As a last help I send one of mine last application for the very same topic, > hope it helps. > a top file and an alignment file. Structures were generataed without any > problem. > > best wishes, > > Andras > > ########################################### > > INCLUDE > SET OUTPUT_CONTROL= 1 1 1 1 > SET ALNFILE='tetu.pir' > SET KNOWNS='2abc3' '2abc2' > SET SEQUENCE= 'tetu' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 30 > > CALL ROUTINE = 'model' > > > SUBROUTINE ROUTINE = 'transfer_xyz' > > # SET ALIGNMENT_FORMAT = 'PIR' > ## READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS > ## MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4 > READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE > > READ_TOPOLOGY FILE = TOPLIB > READ_PARAMETERS FILE = PARLIB > > CALL ROUTINE = 'create_topology' > > TRANSFER_XYZ CLUSTER_CUT = -1.0 > BUILD_MODEL INITIALIZE_XYZ = OFF > > WRITE_MODEL FILE = MODEL > > RETURN > END_SUBROUTINE > ################################################## > > >P1;2abc3 > structureX:2ezm3:55::99::::: > ----YPSDNEEFDPHEQEDKLADPHEQCEFDCDPYPSDNEEDYPSHEQC----------- > -----------------------------------------* > >P1;2abc2 > structureX:2ezm2:5::48::::: > -------------------------------------------------------SQTCY > LSDKEYHRTCNMKHGSDFEQAPLPWDFHGKLMNYTELKS--* > >P1;tetu > sequence:tetu:::::::: > DCDPKLADNEEDEFDCDPNEEFDPHEDKLADPHEQCEFDCDPYPSDNEEDYPSDNEEDKL > NSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKYE* > > ################################################# > > > -- > , > Andras Fiser, PhD # phone: (212) 327 7206 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras
------------------------------------------------ Xiao-Ping Zhang Department of Biochemistry Stockholm University 106 91 Stockholm Sweden
Phone: 46-08-162582 / 162472 Fax: 46-08-153679 e-mail: zhang@biokemi.su.se