- modeller_usage - salilab.org

can't get disulfides bonds
by Dr Nicolas Le Novere 21 May '01

21 May '01

Dear modellers, [modeller6a] My template contains two disulfides bonds, and the cysteines are conserved in the protein I want to model. Hence, PATCH_SS_TEMPLATE, automatically run by the routine 'model' is suppose to take care of the bonds. It doesn't. Hence my first question: How MODELLER detect SS bonds in templates: SSBOND in the HEADER or CONECT at the end of the PDB file? Then I decided to patch the disulfides manually with INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'a7ggmono2.ali' # alignment filename SET KNOWNS = 'mono2' # codes of the templates SET SEQUENCE = 'a7gg' # 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 STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '127' '141' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '189' '190' RETURN END_SUBROUTINE It did not work either. Any ideas? -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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3d staff
by Joshua Bleeth 06 May '01

06 May '01

Hello, Allow me to introduce myself. My name is Joshua Bleeth, I am lead artist and director of an art-studio based in the Ukraine. My company is called ' Inverse Logic inc.' and is situated in the pleasant town of Kiev. I have a team of 26 very competent and professional artists, each possessing between 5 and 7 years experience working within the Film & Computer-games industry. All are experienced and proficient in: 3DS Max, Character Studio, Corel Draw and Photoshop and many other relatated programs. We have produced high & low polygon models for titles such as: Vicarious Vision's 'Polaris Snocross', Nival's ' Allods - The Sealed Mystery', Deibus's ' Biker Extreme', Clive Barkers "Undying" and recently Pineapple Interactive's 'Crash' which is still in development. Also we have produced many high polygon characters, morph targets and Character Studio sets for 2 Hollywood broadcast projects, but due to the terms laid down in our contract we are as yet unable to mention their names. We are constantly looking to broaden our clientele whenever project commitments allow us to, which is why I am introducing myself to you right now. We are approaching the end of some of our current projects and will soon have artists who are free to start other work. We however, must work remotely and whilst we are aware this may seem like a drawback, we can promise you a very, very swift and professional service. We can also offer the advantage of much lower prices than are available in the USA or UK due to the lower income required to live in the Ukraine. Please rest assured our work is worth 4 or 5 times as much if we were based anywhere else. Regardless of the finances for your project, we will allow you sleep easy at night and not worry at all about your artwork deadlines - if need be, we can work around the clock, 24 hours a day. We would be very pleased to hear from you, and if you like, you may send us some sample work which we shall produce on your approval; if you do not like what we produce then you do not have to pay ( we are very confident you will be delighted with our standard of work ). Should you decide to use us, then work is always delivered via the internet on approval. If you are not happy at all then we shall redo the work until you are happy. Please take the time to view our website which has examples of our artwork dating back over 6 years: www.inverse-logic.com I look forward to hearing your comments and answering any of your questions. I thank you for your time, Joshua Bleeth

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linux installation problem
by Daniel John Rigden 25 Apr '01

25 Apr '01

Hi Everyone Can anyone help with an intallatin problem I'm having? My machine is a PIII 933 running RH7.0. The installation of both f2c and modeller seem to go fine but then when I type mod I get the following /usr/local/bin/modeller4/bin/mod_i386: error while loading shared libraries: libc.so.5: invalid ELF header As a linux novice this means nothing to me. Thanks in advance for your help. Daniel Rigden +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+

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linux installation problem
by Oliver Hucke 19 Apr '01

19 Apr '01

Dear All, I am trying to install modeller4 on a new PC with Suse linux7.1. 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) and without any error messages. Afterwards, modeller can be started (execution of "mod4" without any argument), but when I try to execute the tutorial test cases ("/tutorial-model/run_tops1") I am receiving the following error message from every top-script: /usr/local/bin/modeller4/bin/mod_i486-linux: error while loading shared libraries: /usr/local/bin/modeller4/bin/mod_i486-linux: undefined symbol: acos Execution is terminated and the log files of the scripts are completely empty. Does anybody know, what this means and how to avoid it? Thank you very much! Oliver. ******************************************* Oliver Hucke Institut fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a 79104 Freiburg Germany Tel.: ++49-761-203-6179 Fax : ++49-761-203-6189 email: hucke(a)uni-freiburg.de *******************************************

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spline restraints
by Evers Andreas 18 Apr '01

18 Apr '01

Hello! I want to do homology modelling including information from ligands to model the active site of a protein. I started with hemoglobin as the heme substrate and its topology are already defined in the Modeller4 libraries. As restraints I want to use knowledge based pair potentials between protein and ligand atoms derived from complexes in the PDB and express these restraints as splines. In the top-file, I include the following SPECIAL_RESTRAINTS routine: ######################### 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 ######################### In the file "atmcls-special.lib" I grouped the protein atoms (ATMGRP A001 - A012) and the HEME atoms (A041 - A058) according to SYBYL atom classifications. In the file "special-pairpot.lib" I try to express these pair-potentials as splines. The file looks like this: ######################### MODELLER12 VERSION: USER FORMAT R 10 25 1 31 2 31 0 A001 A041 1.0 0.0 6.0 0.25 -0.05 0.05 values R 10 25 1 31 2 31 0 A002 A041 ... . . . ######################### When I run Modeller it reads the "special-pairpot.lib"-file but then tells me "rdparf__E > increase MATTACNS" and exits. Does anyone know what went wrong? I am not sure if my parameters in the "special-pairpot.lib"-file are set correctly. Thank you very much 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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constraints
by Giulio Rastelli 07 Apr '01

07 Apr '01

Dear modellers, is it possible with Modeller4 to define constraints instead of restraints? I would like to constraint a set of conserved residues to be exactly in the same position as those of the template structure, and was looking for a way to do this without setting explicit distance, angle and torsion restraints. Thank yuo very much, Giulio Rastelli Dipartimento di Scienze farmaceutiche Universita di Modena , Italy

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Cyclic peptide...
by Erika Svangard 03 Apr '01

03 Apr '01

Dear Modellers, I'm trying to generate a model of a cyclic peptide based on a NMR structure of a cyclic peptide. I belive my alignment is fine as all disulfide bonds are conserved, but I wish to patch the N and C termini with a peptide bond. Please, could you suggest how I would do this? I have tried using the link special patch as shown below, but it is not working. I'm not sure if this is correct. I also tried with the reisdue IDs in the opposite order ('29' '1'), but without any luck. I would like your advice. Yours Erika Svangard SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'LINK', RESIDUE_IDS = '1' '29' RETURN END_SUBROUTINE

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TRITON version 2
by Jiri Damborsky 22 Mar '01

22 Mar '01

Dear MODELLERs: We would like to inform you about the release of a new version of the program TRITON (version 2). The program serves for modelling of protein mutants and estimation of their activities. The mutant proteins are constructed by the external program MODELLER using the modelling protocol specifically adjusted for this purpose (new in this version). Mutant activities are estimated from the calculation of reaction pathways using external programs MOPAC and DRIVER. Extensive changes in the graphic interface were made in the version 2 assisting inexperienced users with preparation of calculations. Two wizards, one for construction of mutants and other for reaction mapping, were developed for this purpose. A number of new tools are provided for convenient analysis of results from the calculations, e.g. interactive graphs for animation of the reaction, extraction of charges or calculation of non-bonding interactions. In this version, all necessary external programs (MODELLER 6a, MOPAC 7.01 and DRIVER 1.0) are distributed together with TRITON in a single installation package. This package newly contains also manual, tutorials and example files. The program is available free of charge via web: http://www.chemi.muni.cz/lbsd/triton.html We hope TRITON 2.0 can become a valuable tool in your research projects, but also in education. Jiri Damborsky on behalf of TRITON developers * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Dr. Jiri Damborsky National Centre for Biomolecular Research Masaryk University Kotlarska 2 611 37 Brno Czech Republic e-mail: jiri(a)chemi.muni.cz phone: +420-5-41129 377 FAX: +420-5-41129 506 http://www.chemi.muni.cz/~jiri

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constraining an serine triade
by MarcoBocola 15 Mar '01

15 Mar '01

Hello from Marburg, I want to do homology modelling on serine hydrolases with highly conserved fold and reasonable AA-identity. So the difficulty is to model the active site correctly with respect to the catalytic triade and the backbone nitrogens in the oxyanion hole. These few amino acids should be overlayed as exact as possible. Is there a straightforward way to contstrain modeller only for these higly conserved topology of the catalytic residues within one Angstroem, thus remaining the catalytic hydrogen bond network intact. Any hints on possible protocolls appreciated. Marco

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Modeller4 on IRIX 6.5: additional versions available?
by Allen Smith 03 Feb '01

03 Feb '01

Hi. We're about to start using modeller4 on various IRIX 6.5 machines. These include r5000 (O2s and Indys) and r12000 (an Octane) processors. We are wondering whether the following could be made available: A. A version that will run properly on r12000 machines. These are using a later version of the r10000 processor, with both mips4 and 64-bit capabilities. The existing IRIX 6.5 r10000 versions will run only with a modification to the startup scripts of the LD_LIBRARY64_PATH variable adding /usr/lib64/mips4 to the start of that path. The reason this is necessary is that the -r10000 flag evidently used in compiling the r10000 versions of Modeller adds /usr/lib64/mips4/r10000 to the path of directories searched for libraries. This directory contains libfastm.so, which won't run on r12000 machines (I suspect it has assembler optimizations for r10000). Forcing rld (the runtime loader) to look at /usr/lib64/mips4 first causes it to instead use the more generalized mips4 version of libfastm.so. While this modification enables the tests to run properly, it qualifies as inconvenient and prone to bugs (especially if dealing with other programs such as InsightII that also set LD_LIBRARY64_PATH) and prone to bugs. A generalized mips4, 64-bit version of modeller4 should be compilable via adding: IRIX64 ) FC=f77; FFLAGS="-automatic -L/usr/lib64/mips4 -mips4 -64 -r8 -O2 -GCM:aggressive_speculation=ON -OPT:roundoff=3"; LDFLAGS="-L/usr/lib64/mips4 -Wl,-rpath,/usr/lib64/mips4 -lfastm" ;; \ to Makefile.include1. If it will work properly, f90 might be used instead of f77. -LNO and -IPA should enable better performance. B. A version that will run well on r5000 machines. These are 32-bit machines but will run mips4 code, which should improve modeller4's performance relative to the mips3 code which the existing IRIX n32-bit versions use. A generalized mips4, n32-bit version of modeller4 should be compilable via adding: mips4 ) FC=f77; FFLAGS="-automatic -L/usr/lib32/mips4 -mips4 -n32 -r8 -O2 -GCM:aggressive_speculation=ON -OPT:roundoff=3"; LDFLAGS="-L/usr/lib32/mips4 -Wl,-rpath,/usr/lib32/mips4 -lfastm" ;; \ to Makefile.include1. Again, if it will work properly, f90 might be used instead of f77, and -LNO and -IPA should enable better performance. In both of the above, specialized r5000 and r12000 versions would probably work even better. I don't know if you have either of these types of machines available to you. We are capable of such compilation ourselves but (obviously) don't have the modeller4 source code available to us. Thanks, -Allen -- Allen Smith easmith(a)beatrice.rutgers.edu

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