- modeller_usage - salilab.org

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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Hydrogen Atom Preservation
by Alexander Parella 23 May '14

23 May '14

Hello! I have been attempting to use Modeller to refine the loops of some generated protein structures. When performing loop refining, Modeller seems to remove all hydrogen atoms from the structure. I have not been able to find any way to change this behavior. Are there any such options? That is, to stop Modeller from removing the Hydrogen atoms from the structures it refines? Thanks for your time, and any help that anyone can provide.

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Should you use multiple pdb files of the same sequence when available for multiple template homology modeling?
by meginir urestal 05 May '14

05 May '14

Hi, Among the proteins exhibiting homology to my sequence of interest is a protein that has been cristallized with three different ligands by the same team. I was wondering if, when faced with this kind of situation, including all three structures in the homology modeling would introduce a bias. Do you think I should pick one of the structures (based on compare.py) or include all of them in my multiple template modeling? meginir,

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Alternate sidechain positions
by meginir urestal 28 Apr '14

28 Apr '14

how does modeller handle alternate sidechain positions in a pdb file?

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Re: [modeller_usage] How do you use MOULDER?
by meginir urestal 28 Apr '14

28 Apr '14

> Hi, > > I was reading the tutorials and one of them cites MOULDER as an iterative > approach to alignment and homology modeling. > The 2003 paper in nucleic acids research says that MOULDER is restricted > to a few users only. > Has MOULDER been implemented in recent MODELLER versions? If not, how can > you use it on the MODWEB server? > > Thanks, > >

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