- modeller_usage - salilab.org

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by Jayashankar Selvadurai 22 Jul '14

22 Jul '14

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Protein:Protein complex PIR format
by Parker de Waal 15 Jul '14

15 Jul '14

Hello MODELLER users, After looking through the mailing list I have been able to find numerous discussions about protein:protein complex homology modeling, however I have been unable to find any examples for proper PIR formatting and was wondering if someone would be willing to help. I would like to perform modeling for unknown complex A2:B1 where A1:B1 is known and while holding B1 completely frozen. Would the following PIR snippet below work for such modeling or is more information required on the second line as shown here https://salilab.org/modeller/9v8/manual/node454.html? >P1;Comp1 Known Complex AAABBAAAA/ CCCCCCCCC* >P1;Comp2 Unknown Complex AAADDAAAA/ CCCCCCCCC* Cheers, Parker

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conjugate gradients or molecular dynamics optimizations with automodel.make()
by Li SUN 15 Jul '14

15 Jul '14

Hi everyone, I have a question regarding the usage of automodel.make() for modelling a protein structure from known structures. Does this function include optimization methods e.g. conjugate gradients or molecular dynamics so that it will output a structure close to the native state (lowest-energy state), or do I have to call conjugate_gradients() or molecular_dynamics() explicitly after automodel.make() to do an energy minimization? Thanks in advance. -- Li Sun Department of Physics University of California, San Diego

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Mismatch in the alignment
by Sajeewa Pemasinghe 07 Jul '14

07 Jul '14

Hi everyone, I am trying to fill 11 missing residues in a protein. 5 of them are at the N-terminal and the other 6 are at the C-terminal. Other than that there are 9 non-standard residues and 228 waters in the pdb as well. My alignment file looks as below. >P1;2ABC structureX:2ABC: 6 :A:+402 :A:MOL_ID 1; -----PRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH SKYWRCLQRTTSTAGRSLIEAQTCENE------.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* >P1;2ABC_fill sequence::::::::: GAMTKPRFTTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIRGRKATLEELQTVHSEAHTLLYG TNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRP PGHHAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFYSDPSVLYMSLHRYDDGNFFPGS GAPDEVGTGPGVGFNVNMAFTGGLDPPMGDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLS ARCFGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPEKVLQQRPNANAVRSMEKVMEIH SKYWRCLQRTTSTAGRSLIEAQTCENEEAETVT.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* I get the following error when I run the python script. read_te_290E> Number of residues in the alignment and pdb files are different: 639 402 For alignment entry: 1 2ABC x (mismatch at alignment position 403) Alignment QRTTSTAGRSLIEAQTCENE.........wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww PDB QRTTSTAGRSLIEAQTCENE Match ********************************* I have been trying many modifications for a few hours now but I just cannot figure out what is wrong. I would highly appreciate some advice to get around this problem. Thank you very much Sajeewa Dewage

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Structuropedia
by Amjad Farooq 01 Jul '14

01 Jul '14

Hi everyone, Here is a new web interface that may be of interest to some of you: http://structuropedia.org This is a simply yet powerful and versatile web interface with capabilities for modeling and rendering of proteins alone and in complex with peptides and DNA. Powered by a wide array of engines including Biopython, Blast, Clustal, JSmol, Modeller, RefSense and VMD. Any feedback will be most welcome. With warmest regards, *AMJAD FAROOQ PhD DIC | Associate Professor*Dept of Biochemistry, University of Miami School of Medicine *Location*: Gautier Building, Suite 217 *Address*: 1011 NW 15th Street #217, Miami , FL 33136, USA *Contact*: amjad(a)farooqlab.net | 305-243-2429 *Labpage*: farooqlab.net <http://www.farooqlab.net> | structuropedia.org <http://dalton.med.miami.edu>

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'environ' is not defined error
by Sajeewa Pemasinghe 30 Jun '14

30 Jun '14

Hi everyone, I am working on the tutorial http://salilab.org/modeller/wiki/Missing%20residues I am trying to run the script 1qg8_getseq.py which has # Get the sequence of the 1qg8 PDB file, and write to an alignment file code = '1qg8' e = environ() m = model(e, file=code) aln = alignment(e) aln.append_model(m, align_codes=code) aln.write(file=code+'.seq') I get the following error. File "1qg8_getseq.py", line 4, in <module> e = environ() NameError: name 'environ' is not defined Looks like python is not reading the modeller libraries. Could you please advise how to solve this error? Thank you Sajeewa Dewage

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Heme out in space
by Joel Tyndall 16 Jun '14

16 Jun '14

Hey Ben, I've been generating some models of some cytochrome proteins with heme. I have generated ~6 structures that are all fine but the next two have the heme placed out in space relative to the protein. I have seen this before but have put it down to user error. Now I'm not so sure its me as I have been simply replicating the input files. Any suggestions? (I don't what to post files to bulletin board but can send direct (if needed)). J _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

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Reading density files
by chris.wood＠stfc.ac.uk 09 Jun '14

09 Jun '14

I'm trying to read a density file. The docs (http://salilab.org/modeller/manual/node414.html) suggest that this should work >>> m = modeller.density(modeller.environ(), "file.mrc", 10) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: __init__() takes exactly 2 arguments (4 given) Instead, I've tried: >>> m = modeller.density(modeller.environ()) >>> m.read("file.mrc",10) read_data> Reading electron density of the main map readlinef__W> File: file.mrc, Line: 1 Modeller will only read the first 400 characters of this line. readlinef__W> File: file.mrc, Line: 3 Modeller will only read the first 400 characters of this line. forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Any suggestions what I'm doing wrong? Chris -- Scanned by iCritical.

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Modelling a circular permutated chimera
by James Starlight 30 May '14

30 May '14

Dear Modeller users! I'm looking for the brief tutorial with the description of how I could build model of chimeric protein consisted of A and B constructions fused both from N and C termi in circular manner with cross-section like ---N(A)----C(A) --N(B)--C(B)--N(A)-- assuming that N(A) is shared point in circle. I'll be thankful if you provide me with the example of alignment file for such chimera building based on 2 templates with known pdb structures. TFH, James

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Loop refirement using simulated annealing
by James Starlight 27 May '14

27 May '14

Dear Modeller users! I need to refine some flexible regions (mainly long loop and linker regions) of my models using some enhanced sampling engines implemented in modeller like simulated annealing. In this FAQ salilab.org/modeller/6v2/FAQ.html I've found the same method. Could you suggest me some example of the realization of this method in the modeller python script indicating its differences from the method proposed in the advanced tutorial (listed below). class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('NH1:161:A', 'O1A:336:B'), ('NH2:161:A', 'O1B:336:B'), ('NE2:186:A', 'O2:336:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=3.5, stdev=0.1)) TFH, James

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