January 2013 - modeller_usage

Minimize structure energy
by danashah＠post.tau.ac.il 28 Jan '13

28 Jan '13

Hi all, I've only joined this mailing list lately, so pardon me if this question was asked and answered before. We wish to perform energy minimization to a model we created. We were wondering whether we can use your automodel for that, via "use your own initial model": http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel If it's possible, what should be the alignment file, since the sequence we want to use is the same as the model? Thank you, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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leave out termini of a structure
by Ahmet yıldırım 25 Jan '13

25 Jan '13

Dear users, I have four similar structures. They are aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. Unfotunately, the first 15 residues of of all the structures are missing. I modelled the aaa.pdb using aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. When I modelled aaa.pdb, a loop of aaa.pdb goes through the rest of the protein. i.e. occurs knot. My friend said "you should leave out the termini". How will I leave out termini of a structure with Modeller? What do you suggest? Thanks in advance -- Ahmet Yıldırım

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Searching the PDB for similar structures
by nornik 23 Jan '13

23 Jan '13

Hello! I am wondering if MODELLER can be used to search the PDB for entries structurally similar (without taking the sequence into account) to a known target structure. If not, do you know any other software for performing such a search? Thank you Niklas

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moldpdf, DOPE score and GA341 score
by Ahmet yıldırım 23 Jan '13

23 Jan '13

Dear users, I am a new user of Modeller. I have the following results: >> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- qseq1.B99990001.pdb 8602.63281 -113144.73438 1.00000 qseq1.B99990002.pdb 8773.10840 -113346.03125 1.00000 qseq1.B99990003.pdb 8349.71387 -112852.75000 1.00000 qseq1.B99990004.pdb 9365.16406 -111568.75781 1.00000 qseq1.B99990005.pdb 8553.98926 -112664.98438 1.00000 1.) What is "moldpdf", "DOPE score" and "GA341 score"? What is the meaning of them? 2.) how will I determine the best result according to the above table/results? What is the best result? Thanks in advance -- Ahmet Yıldırım

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filtering membrane proteins
by sdimicco 18 Jan '13

18 Jan '13

Dear Modellers, I have built a membrane protein by Modeller. I am aware that none of the Modeller assesment methods are likely to work well on membrane proteins.However, could I use one of the assesment methods to filter the best models among my results, and veluate the selected best models with other methods? Thank you in advance All the best Simone

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membrane protein
by sdimicco 16 Jan '13

16 Jan '13

Dear Modellers, I have built a membrane protein by Modeller. I would like to know if some of the assesment method implemented are ble to evaluate mebrane protein. If not, could you suggest some other method? Thank you in advance All the best Smone

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modeling with water, HETATM
by Krupal Jethava 11 Jan '13

11 Jan '13

Dear, I am trying to make model with Ligand (37 HetAtom) and 3 water molecule. I used the same script as in manual but getting the error that "Number of residue in alignment and pdb are different: 324 288 for alignment entry: tseq.pdb" In My alignment file: 1) query seq = 296 (residues) 2) pdb = 287 (residues) + 3 (water HETATM) + ligand (34 HETATM) align-ligand.ali has >P1;tseq.pdb structureX:tseq.pdb:FIRST:@:END ::@::: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA..... ................................* >P1;qseq sequence:qseq:FIRST:@:END ::@::: AAAAAAAAAAA--AAAAAAAAAAAAAAAAAAA..... ................................* I am using Modeller9v7 and python2.5.1 I will be very thankful for your help.

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Inserting Chain ID Into Model
by David Johnson 07 Jan '13

07 Jan '13

Hello, I am doing a model of a single chain protein. My target model comes out as I expect save for one thing, it is missing a chain ID. How do I get modeller to insert a chain ID into the model, even for single chain proteins. Thank you. DJ

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how to get pdb_95.bin file
by BALA SUBRAMANI G L 07 Jan '13

07 Jan '13

hai friends, can any tell me how to get pdb_95.bin file from modeller website. I need this file to run modeller scripts. please assist me in this regard. -- Thanks & Regards, G.L.Balasubramani (Project Assistant), c/o.Dr.S.Kumaran, Structural & Quatitative Biology Lab, GNRPC, Institute of Microbial Technology (CSIR), Sector 39-A, Chandigarh, India-160036. ph : +91-9041280408/8284860166 off : 0172-6665475 ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202

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Syntax errors in defining model atoms
by doranhen＠post.tau.ac.il 07 Jan '13

07 Jan '13

Dear all, I am trying to create distance restraints in a model based on an example script from the modeller manual named model-addrsr.py . I am following the exact same syntax of this script, yet I need to change the numbering of my residues (since my restraints are for a model that starts at residue 2 and not 1) so I add another restraint to renumber it (self.rename_segments), however, when I try to use my new script (listed at the bottom of this mail), I get an error message that the atom I listed OG1:132A:A does not exist: 'No such atom: OG1:132A:A', does anyone know what am I doing wrong here? Thank you, Doran My script: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ(rand_seed = -500) # create a new MODELLER environment to build this model in env.io.atom_files_directory = './:' # directories for input atom files env.io.hetatm = True # read HETATM records (for Na ions) ################################ # define the modeling parameters class mymodel(automodel): def special_restraints(self, aln): self.rename_segments (segment_ids=('A'),renumber_residues=(2)) rsr = self.restraints at = self.atoms rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['OG1:132A:A'],at['NA:310A:A']),mean=2.4, stdev=0.1)) def user_after_single_model(self): self.rename_segments (segment_ids=('A'),renumber_residues=(2)) a = mymodel(env, alnfile = 'file.pir', # alignment filename knowns = ('No_anis'), # codes of the templates sequence = ('target')) # code of the target in the pir file a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.deviation = 2.0 # Deviation in models #a.md_level = refine.very_slow a.make() # do the actual homology modeling

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