October 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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Installation problem
by Diego Bustos 01 Nov '01

01 Nov '01

Dear All, I am trying to install modeller4 on a new PC with Suse linux7.0. After correction of the default HOSTTYPE setting (for some reason it is set to "i386-linux" on my machine instead of "i486-linux"), the "Install" script finishes surprisingly fast (may be due to the 1.2GHz CPU with RAM memory of 256 Mb) and without any error messages. Afterwards, I can`t started Modeller, because I can`t recognize any executable file. Does anybody know, what this means and how to avoid it? Thank you very much! Diego

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RE:modeller 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 restraints 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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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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