- modeller_usage - salilab.org

Re: modeller
by Andras Fiser 26 Oct '01

26 Oct '01

Hi Hailong, I include a recent message about the inadequacy of modeller scores when comparing models generated with different sets of restraints. If you want to evaluate your model you can use a wide variety of external programs: http://salilab.org/modeller/methenz/ best Andras Andras Fiser wrote: > > Hi Asim, > > The energy scores in modeller are not comparable if you use different sets of > restraints i.e. including/excluing disulfide restrainst in your case. > > Scores only from the same run i.e. by generating several models, can be > compared. > > otherwise the overall energy score is included in the header of the coordinate > file as "REMARK MODELLER OBJECTIVE FUNCTION: " > > Best, > > Andras > > please take advantage (so others can benefit too) of our modeller user list if > you have other questions. > http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/ > > Asim Kumar Debnath wrote: > > > > Hi Andras: > > I have modeled a protein using your program Modeler. The target > > sequence has two cystine residues which may form a disulfide bond but > > there is no experimental evidence on that. I have modeled both without a > > disulfide bond and with a disulfide bond (by using special_patches > > subroutine). Now I want to compare which one is the energetically best > > probable structure between these two. > > I would greatly appreciate if you could give some advise how to > > proceed in Modeler to find out which one is the most likely model. How > > do I get the overall energy of the 3D-model in your program? > > Thank you in advance for your help. > > Regards, > > > > Asim > > > > ======================================================================= > > > > *** > > *** Asim K. Debnath, Ph.D. > > **** Associate Member > > **** Lindsley F. Kimball Research Institute > > **** *** The New York Blood Center > > **** **** 310 E 67 Th Street > > **** ** **** New York, NY 10021 > > **** **** **** Tel. (212) 570-3373 > > **** ** **** Fax. (212) 570-3299 > > **************** E-mail: asim_debnath(a)nybc.org > > ************** > > > > ======================================================================== > > -- > , > Andras Fiser, PhD # phone: (212) 327 7216 > 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 Hai-Long Wang wrote: > > At 02:20 PM 6/22/2001 -0400, you wrote: > Hi, Andras > > My protein has several disulf bonds. I had tried modeller to built model > protein both with patch and without patch command. When the patch command > not include, the disuf bonds are not there, but it has overall higher > score. Is there any way in modeller to rebuilt the disuf bonds and keep the > rest unchange? > > Thank you. > > Hailong > ****************************************************************************** > Hai-Long Wang Ph.D. Tel: (507)284-5297 > Receptor Biology Laboratory Fax: (507)284-9420 > 1-149, Medical Science Building email: wang.hailong(a)mayo.edu > Mayo Foundation receptor293(a)yahoo.com > Rochester, MN 55905 > **************************************************************************** > ** -- , Andras Fiser, PhD # phone: (212) 327 7216 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

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Re: Modeler help
by Andras Fiser 26 Oct '01

26 Oct '01

Hi Asim, The energy scores in modeller are not comparable if you use different sets of restraints i.e. including/excluing disulfide restrainst in your case. Scores only from the same run i.e. by generating several models, can be compared. otherwise the overall energy score is included in the header of the coordinate file as "REMARK MODELLER OBJECTIVE FUNCTION: " Best, Andras please take advantage (so others can benefit too) of our modeller user list if you have other questions. http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/ Asim Kumar Debnath wrote: > > Hi Andras: > I have modeled a protein using your program Modeler. The target > sequence has two cystine residues which may form a disulfide bond but > there is no experimental evidence on that. I have modeled both without a > disulfide bond and with a disulfide bond (by using special_patches > subroutine). Now I want to compare which one is the energetically best > probable structure between these two. > I would greatly appreciate if you could give some advise how to > proceed in Modeler to find out which one is the most likely model. How > do I get the overall energy of the 3D-model in your program? > Thank you in advance for your help. > Regards, > > Asim > > ======================================================================= > > *** > *** Asim K. Debnath, Ph.D. > **** Associate Member > **** Lindsley F. Kimball Research Institute > **** *** The New York Blood Center > **** **** 310 E 67 Th Street > **** ** **** New York, NY 10021 > **** **** **** Tel. (212) 570-3373 > **** ** **** Fax. (212) 570-3299 > **************** E-mail: asim_debnath(a)nybc.org > ************** > > ======================================================================== -- , Andras Fiser, PhD # phone: (212) 327 7216 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

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Regarding modeller usage
by R Senthil Kumar 25 Oct '01

25 Oct '01

Dear friends, I am Ph.D student doing my work in the field of protein modelling in Center for DNA Fingerprinting & Diagnostics(CDFD),Hyderabad,India. I am having some doubts about Comparative modelling using modeller package.Kindly i request you to clear my doubts. 1.First thing is before submitting to align2D for alignment the sequences in the ali file whether it has to be aligned by some sequence alignment program like clustalW or we can submit the the raw sequence in PIR format in the ali file to align2D.top file?. 2. I am taking three templates for homology modelling for my model.And one of my template has hetroatoms like glucose(ligands) and i want to include those hetroatoms to my model.For that i changed my model.top like this: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'align2d.ali' # alignment filename SET KNOWNS = '1hkca1' '1hkca2' '1bdg' # codes of the templates SET SEQUENCE = 'ppgk' # code of the target SET ATOM_FILES_DIRECTORY = './' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 20 # index of the last model SET HETATM_IO = ON CALL ROUTINE = 'model' # do homology modelling But it is not including the hetroatoms in the model.I don't know why?.Plese help me in this regard. from, Senthil kumar.R

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howto scale weights of restraints
by Evers Andreas 23 Oct '01

23 Oct '01

Hello! Is it possible in MODELLER to change the weight of certain parameters in the optimization process? I am doing homology modelling with incorporation of ligand information as special restraints. The restraints are expressed in terms of knowledge based distance dependent pair potentials between protein and lingand atoms. These pair potentials are expressed in terms of cubic splines. I would like to try if I can improve my results by increasing the scaling weight of my special restraints compared to the predefined restraints which Modeller uses in the model building process. my top file basically looks like this: -------------------------------- INCLUDE SET ALNFILE = '../alis/1dlw_2d.pir' SET KNOWNS = '1dlw' SET SEQUENCE = 'fake' SET ATOM_FILES_DIRECTORY = '../pdbs' SET HETATM_IO = on SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET DYNAMIC_MODELLER = on SET CONTACT_SHELL = 6.00 READ_ATOM_CLASSES ATOM_CLASSES_FILE = 'atmcls-special.lib' READ_PARAMETERS FILE = 'special-pairpot.lib', ADD_PARAMETERS = on END_SUBROUTINE --------------------------------- The file atmcls-special.lib contains the definitions of the atom groups I use, the file special-pairpot.lib contains the restraints for each protein - ligand atom pair, e.g.: --------------------------------- MODELLER12 VERSION: MODELLER FORMAT R 10 60 1 31 2 66 0 L001 P001 1.00 0.00 5.90 0.10 -0.13 -0.05 10.00 9.99 9.95 9.89 9.80 9.68 9.55 9.39 9.21 9.02 8.80 8.57 8.33 8.07 7.80 7.53 7.25 6.96 6.67 6.38 6.09 5.80 5.51 5.23 4.96 4.69 4.44 4.06 3.95 3.59 3.07 2.62 2.26 1.86 1.40 0.95 0.61 0.38 0.17 0.01 -0.10 -0.18 -0.27 -0.36 -0.44 -0.49 -0.50 -0.51 -0.50 -0.50 -0.55 -0.62 -0.70 -0.75 -0.74 -0.73 -0.70 -0.66 -0.64 -0.64 . . . ------------------------------ ... defines the distance distribution between protein and ligand C.3 atoms. Thank you in advance for your help. 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(a)mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################

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PATCH and chains
by Nicolas Le Novere 15 Oct '01

15 Oct '01

dear users, I model a multimeric protein, and I need to patch several disulfide bonds. If I use an alignment like TTTTTT/ TTTTTT/ TTTTTT/ TTTTTT/ TTTTTT* MMMMMM/ MMMMMM/ MMMMMM/ MMMMMM/ MMMMMM* SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126:A' '140:A' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188:A' '189:A' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126:B' '140:B' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188:B' '189:B' # ... RETURN END_SUBROUTINE (which is supposed to work according to the manual) Modeller complains that the synthax '126:A' is not recognized and stops. I then have to fuse all the subunits and perform the following TTTTTT TTTTTT TTTTTT TTTTTT TTTTTT* MMMMMM MMMMMM MMMMMM MMMMMM MMMMMM SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '126' '140' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '188' '189' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '332' '346' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '394' '395' # ... RETURN END_SUBROUTINE Of course at the end I have one huge protein and I have to cut it by hand, not very convenient ... Any idea ? PS: Is it me or an alignment without a final blank line is not read? -- Nicolas Le Novère Neurobiologie Moléculaire, Institut Pasteur, 75724 Paris cedex FRANCE e-mail : lenov(a)pasteur.fr http://www-alt.pasteur.fr/~lenov tel : 33-(0)1-45-68-88-44 fax : 33-(0)1-45-68-88-36

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error 139
by Sherin Yang 14 Oct '01

14 Oct '01

Hi! When I was running Modeler to build a model of protein, the computer always returned the folowing information:your job is failed, error staus 139. Who can tell me the meaning of error staus 139, or where I can find the information about this error code. Good luck! My email: sherin(a)sina.com Sherin

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Problem with SEQUENCE_TO_ALI
by Karl Gruber 04 Oct '01

04 Oct '01

Dear all, I am a new user of Modeller (vers. 4h, June 16, 1997) and I hope that this list is still alive. I have encountered some problems running the scripts 'loop' and 'cluster', which I tried both with my own and the tutorial files. The input and (part of the) output in the case of 'cluster' were as follows: -------------------- INCLUDE DEFINE_STRING VARIABLES = SEQUENCE MODEL CSRFILE SET SEQUENCE = 'pruse1' # sequence code SET MODEL = 'pruse1.B99990002' # one PDB structure SET CSRFILE = 'pruse1.rsr' # restraints file SET ID1 = 2, ID2 = 11 # cluster these models CALL ROUTINE = 'cluster' -------------------- . . . ipdbnam_W> environment variable PDBENT undefined chkseq__E> sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 2 0 #### 1 ALA ----L------ 2 3 0 #### 17 THR ---L------- 2 4 0 #### 17 THR --L-------- 2 5 0 #### 16 SER -L--------- 2 6 0 #### 12 ASN L---------- 2 7 0 #### 7 HSD ----------- 2 8 0 #### 3 ASP ----------- 2 9 0 #### 5 PHE ----------- 2 10 0 #### 16 SER ----------- 2 11 0 #### 20 TYR ----------- chkseq__E> sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 3 2 0 #### 1 ALA ----L------ 3 3 0 #### 17 THR ---L------- 3 4 0 #### 17 THR --L-------- 3 5 0 #### 16 SER -L--------- 3 6 0 #### 12 ASN L---------- 3 7 0 #### 7 HSD ----------- 3 8 0 #### 3 ASP ----------- 3 9 0 #### 5 PHE ----------- 3 10 0 #### 16 SER ----------- 3 11 0 #### 20 TYR ----------- . . (continuing for all 10 structures) . ---------------- I modified '__cluster.top' such that the alignment is written to a file. Obviously only the first amino-acid was copied into the alignment array. ---------------- >P1;pruse1_2 structureM:pruse1.B99990002: 1 : : 521 : :model:model:-1.00:-1.00 L* >P1;pruse1_3 structureM:pruse1.B99990003: 1 : : 521 : :model:model:-1.00:-1.00 L* . . . >P1;pruse1_11 structureM:pruse1.B99990011: 1 : : 521 : :model:model:-1.00:-1.00 L* ----------------- I also tried the following script: ----------------- read_model file = 'pruse1.B99990001', align_codes = 'test' sequence_to_ali add_sequence = off write_alignment file = 'dummy.ali' dummy.ali: >P1;test structureX:test: 1 : : 521 : :undefined:undefined:-1.00:-1.00 L* ----------------- I hope that I did not overlook anything obvious! Any help would be very much appreciated. Yours, Karl --------------------------------------------------------------------- Karl Gruber Institute of Chemistry KFU Graz Heinrichstrasse 28 e-mail: karl.gruber(a)uni-graz.at A-8010 Graz phone: (+43 316) 380-5483 AUSTRIA fax: (+43 316) 380-9850 ---------------------------------------------------------------------

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Restraining a disulphide bridge
by Marc BAADEN 11 Sep '01

11 Sep '01

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

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ref f2c
by Delmiro Fernandez-Reyes 07 Sep '01

07 Sep '01

Hi I am running under linux suse kernel 2.4.x What I did was just install the rpm from suse for the package f2c which contains that libray object. Check the Debian distribution on this package Check on your system under the path where mod binaries are ldd -d mod_xxx Anyway even after a suscesfull linking of that objects to produce the binary for modeller I have an error that I reported to Dr Sali and I am awaiting for his reply Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

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Linux Debian/libf2c
by Decha Enkvetchakul 06 Sep '01

06 Sep '01

I installed Modeller for Debian Linux, but when I try to run the program, it gives the following error: "libf2c.so.0: cannot open shared object file: No such file or directory" I found a file with the above name on the internet, but putting the file on my computer does not work. I still get the same error, even if the file is in the PATH. Any suggestions? Thanks. Decha Enkvetchakul

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