Dear Professor Sali, although I tried to thoroughly read through your documentation, and found several references (and examples) to patching disulphide bridges, I could not get it to work for my particular case. I tried to use Modeller v6a (but we also have Modeller4 in the lab, if that would make any difference). My case might be a bit special: I have got an Xray structure, with missing sidechains+residues. One Cysteine is present, the second missing, There are only 2 in the structure, and there has to be a disulphide bridge between them. I only need a homology model where missing residues and sidechains are completed. So my usual modeller script looks like this: INCLUDE SET ALNFILE = '1fep.ali' SET KNOWNS = '1fep_xr' SET SEQUENCE = '1fep_ok' SET ATOM_FILES_DIRECTORY = '.' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET DEVIATION = 2.0 SET RAND_SEED = -12312 CALL ROUTINE = 'model' Using xray coordinates from 1fep_xr.atm. Now I wanted to add something like PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' which leads to an error of Run READ_TOPOLOGY and GENERATE_TOPOLOGY first. Now I wonder, is this the right way to add my disulphide restraint ? If yes, then what kind of topology should I use and how ? Do I need to build an initial complete model first, and my 10 models afterwards ? Thank you very much in advance, Best wishes, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217
Dear Marc, Did you add the PATCH command within the 'special_patches' routine? You should have something like this in your top file (Please see FAQ #6 in the modeller manual). SUBROUTINE ROUTINE 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' END_SUBROUTINE This should work even if you have missing atoms in one of your CYS residues. Best Wishes, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ Marc BAADEN wrote: > Dear Professor Sali, > > although I tried to thoroughly read through your documentation, > and found several references (and examples) to patching disulphide > bridges, I could not get it to work for my particular case. > > I tried to use Modeller v6a (but we also have Modeller4 in the lab, > if that would make any difference). > > My case might be a bit special: > I have got an Xray structure, with missing sidechains+residues. > One Cysteine is present, the second missing, There are only 2 in > the structure, and there has to be a disulphide bridge between > them. > > I only need a homology model where missing residues and sidechains > are completed. So my usual modeller script looks like this: > > INCLUDE > SET ALNFILE = '1fep.ali' > SET KNOWNS = '1fep_xr' > SET SEQUENCE = '1fep_ok' > SET ATOM_FILES_DIRECTORY = '.' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 10 > SET DEVIATION = 2.0 > SET RAND_SEED = -12312 > CALL ROUTINE = 'model' > > Using xray coordinates from 1fep_xr.atm. > > Now I wanted to add something like > > PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' > > which leads to an error of > Run READ_TOPOLOGY and GENERATE_TOPOLOGY first. > > Now I wonder, is this the right way to add my disulphide restraint ? > If yes, then what kind of topology should I use and how ? > Do I need to build an initial complete model first, and my 10 models > afterwards ? > > Thank you very much in advance, > > Best wishes, > > Marc Baaden > >
Hi Marc! Did you redefine the special_patches routine, i.e. write into your top script: INCLUDE SET ALNFILE = '1fep.ali' SET KNOWNS = '1fep_xr' SET SEQUENCE ='1fep_ok' SET ATOM_FILES_DIRECTORY = '.' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET DEVIATION = 2.0 SET RAND_SEED = -12312 CALL ROUTINE = 'model' STOP ... and then: SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' RETURN END_SUBROUTINE I hope this will work. Nice greetings, Andreas -- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers@mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ###################################################################### On Tue, 11 Sep 2001, Marc BAADEN wrote: > > Dear Professor Sali, > > although I tried to thoroughly read through your documentation, > and found several references (and examples) to patching disulphide > bridges, I could not get it to work for my particular case. > > I tried to use Modeller v6a (but we also have Modeller4 in the lab, > if that would make any difference). > > My case might be a bit special: > I have got an Xray structure, with missing sidechains+residues. > One Cysteine is present, the second missing, There are only 2 in > the structure, and there has to be a disulphide bridge between > them. > > I only need a homology model where missing residues and sidechains > are completed. So my usual modeller script looks like this: > > INCLUDE > SET ALNFILE = '1fep.ali' > SET KNOWNS = '1fep_xr' > SET SEQUENCE = '1fep_ok' > SET ATOM_FILES_DIRECTORY = '.' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 10 > SET DEVIATION = 2.0 > SET RAND_SEED = -12312 > CALL ROUTINE = 'model' > > Using xray coordinates from 1fep_xr.atm. > > Now I wanted to add something like > > PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' > > which leads to an error of > Run READ_TOPOLOGY and GENERATE_TOPOLOGY first. > > Now I wonder, is this the right way to add my disulphide restraint ? > If yes, then what kind of topology should I use and how ? > Do I need to build an initial complete model first, and my 10 models > afterwards ? > > Thank you very much in advance, > > Best wishes, > > Marc Baaden > > -- > Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University > mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de > FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 > >
participants (3)
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Evers Andreas -
Marc BAADEN -
Roberto Sanchez