- modeller_usage - salilab.org

Question about Make_restraints
by Alejandra Leo 08 Jun '04

08 Jun '04

Hi all, I have a problem using Modeller and maybe someone could give a hand. I have my alignment (ecoli-FINAL.pir), my query sequence (Nei1Ecoli_exp), and as structural template I have a trace of C-alpha atoms (E_Coli_Test85) that is very important that do not move from their initial positions. The only thing I want to do is to add the other atoms needed to complete the backbone to my C-alpha trace. I created this script for running modeller: ---------------------------------------------------- READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = 'E_Coli_Test85' MALIGN3D FIT = off SET ADD_SEQUENCE = on READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = ALIGN_CODES 'Nei1Ecoli_exp' CHECK_ALIGNMENT GENERATE_TOPOLOGY SEQUENCE = 'Nei1Ecoli_exp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'Nei1Ecoli-test.ini' MAKE_RESTRAINTS RESTRAINT_TYPE = 'DISTANCE', DYNAMIC_SPHERE = on MAKE_RESTRAINTS DISTANCE_RSR_MODEL = 5 WRITE_RESTRAINTS FILE = 'Nei1Ecoli.rsr' READ_MODEL FILE = 'Nei1Ecoli-test.ini' PICK_RESTRAINTS #OPTIMIZE ENERGY WRITE_MODEL FILE = 'Nei1Ecoli-test_1.final' -------------------------------------------------------------------------- And everything was fine until the make_restraints point. Nei1Ecoli.rsr created file only contains a header line and the rest is empty. I supposse that I am not using this command in the right way, but what I want to do is to tell the program that keep fix the C-alpha coordinates and add the rest, and make the optimization (now in comments), without moving it. Or if it woult be strictly necesary, to get a final structure with a RMS value as low as possible, with respect to my starting C-alpha trace. Any ideas about creating the restraints file and invoke it from the top script? Thanks in advance, any help will be very appreciated! Best, Sandra

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Restricting to Strand
by John Penniston 07 Jun '04

07 Jun '04

I've been trying to restrict portions of my molecule to be alpha helix and other portions beta strand. I did it using the following addition to my special_restraints subroutine: #This one is to put helices & sheets in the PMCA insert SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '254' '274' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '293' '302' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '275' '285' The alpha restraints work fine, but the strand restraint seems to have no effect at all. When I look at a Ramachandran plot of the region which was supposed to be beta strand, the angles are all over the plot. I noticed on looking over the history of this forum that a French group had this same problem in 2002, but I can't find any solution to it. This difficulty has happened in a number of different circumstances. John T. Penniston, Ph.D. Lab of Membrane Biology Massachusetts General Hospital Boston, MA, USA

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objective function
by Gianluca Croce 17 May '04

17 May '04

Hi all, I'm a new user of modeller and I would like to know which it is the measure unit used from mod6v2 for the objective function? It is possible to have a correlation between the unit of objective function and other units (Kcal/mol, KJ/mol etc)? Regards, G. -- Gianluca Croce Ph. D. Student DISTA- Universita' del Piemonte Orientale C.so T. Borsalino 54, Alessandria I-15100 Italy Tel_office: +39 0131 287414 Fax: +39 0131 287416 visit my Web page at the URL: www.mfn.unipmn.it/~gcroce

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different results running mod6v2 on diff OS
by nurul bahiyah 17 May '04

17 May '04

hi all, i tried to run modeller both on SGI IRIX and windows platform and i got different results for both. is this normal? shouldnt it be producing structures with identical coordinates no matter what OS being used? thanks all

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toppar files for Charmm and X-plor
by Han Choe 16 May '04

16 May '04

Dear Modellers, Topology and parameter files for compounds are relatively easy to find for X-plor format rather than for Charmm format that is used for the Modeller program in the websites. What are the major differences of the files between X-plor format and Charmm format? Is there an easy way to convert the X-plor format to the Charmm format? Cheers, Han

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alignment file!
by Yue Yun 07 May '04

07 May '04

Hello everyone, I got the following error message when Modeller reads my alignment file: rdpir___270E> Error reading/processing file: my.ali recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Here's my input file: >P1;1Q4G structureX:1Q4G:32:A:584:A:::: PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK CHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN TKTCPYVSFHVPD* >P1;1EBV sequence -VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK CHPNSIFGESMIEMGAPFXLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN TKTCPYVSFHVP-* Here's my .top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'my.ali' # alignment filename SET KNOWNS = '1Q4G' # codes of the templates SET SEQUENCE = '1EBV' # 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 Can anyone help me to solve this question? I download the 1Q4G.pdb file from the www.pdb.org. Thank you!

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Help!!
by Chaitanya Reddy.A 07 May '04

07 May '04

Dear all, We are modelling a molecule but we are facing a problem to which i am unable to find it. We hope you can help me in this regard. We want to model a map kinase 8 using the map kinase 10 molecule which shows 93% homology. We aligned using clustalx and we submitted to modeller as .ali file. Below is the alignment file we obtained from clustalx >P1;1jnk structureX:1jnk:1 : :346 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30 ------DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLA-----SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN------------- ----------------------------------------------------* >P1;output sequence:output:1 : :427 : :JNK mitogen-activated protein kinase:2.40:-1.00:-1.00 MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLEERTKNGVIRGQ PSPLGAAVINGSQHPSSSSSVNDVSSMSTDPTLASDTDSSLEAAAGPLGCCR* After submitting to modeller, the following is the error.. The error message rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 346 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Please help me in solving this problem. But we manually examined the number of residues in both pdb files and alignment files and we found no difference. Regards Chaitu

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Fwd: homology-based secondary structure modelling
by Amanda Preston 05 May '04

05 May '04

could you please post the attached inquiry on the MODELLER forum? thanks, amanda --- Amanda Preston <amandaraepreston(a)yahoo.com> wrote: > From Amanda Preston Sun Apr 25 19:09:23 2004 > Received: from [4.224.45.52] by web21208.mail.yahoo.com via HTTP; Sun, 25 Apr 2004 19:09:23 PDT > Date: Sun, 25 Apr 2004 19:09:23 -0700 (PDT) > From: Amanda Preston <amandaraepreston(a)yahoo.com> > Subject: homology-based secondary structure modelling > To: sali(a)salilab.org > MIME-Version: 1.0 > Content-Type: text/plain; charset=us-ascii > Content-Length: 446 > > > > i was hoping someone might be able to give me some general information. i'm rather new to > this > > field and i'm having trouble finding resources to obtain computer programs/software for > > homology-based secondary structure modelling. can you give me some advice on where i can > obtain > > such software? in specific, i'm hoping to be able to find a program that can model a rpotein > whose primary structure is unknown. > > > > thanks, > > amanda > > > >

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loop refinement
by Karsten Suhre 05 May '04

05 May '04

Dear Modeller users, I am looking for a simple MODELLER top-script that allows to remodel an already existing loop of a protein while leaving the rest of the molecule unchanged, that is, the input would be a single PDB file and a residue range. The idea is to generate a number of different conformations of that loop and to evaluate them against X-ray crystallographic data (I am trying to model a loop that is only barely visible in a low resolution dataset). Thank you very much in advance, Kind regards, Karsten Suhre, IGS-CNRS, Marseille, France.

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modeller6v2 on apple macitosh G5 machine.
by Wonsuhk Uhm 04 May '04

04 May '04

Hi all. I am trying to use modeller6v2 on my Apple G5 Mac with MacOS 10.3.3 (panther). But whenever I was running modeller, it gave segmentation fault error as follows; /Users/wsum/Desktop/Projects/modeller6v2/bin/mod6v2: line 39: 4504 Segmentation fault ${EXECUTABLE} ${STEERF} >${LOGF} Dose anyone know of the solution for this error ? Thanks in advance Wonsuhk Uhm, PhD.

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