- modeller_usage - salilab.org

Modeller 9.12 release
by Modeller Caretaker 12 Jun '13

12 Jun '13

The new version of Modeller, 9.12, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.12 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.12 is primarily a bugfix release relative to the last public release (9.11). Major user-visible changes include: # Modeller is now only supported on Mac OS X 10.6 or later. If you want to run Modeller on older OS X releases, use Modeller 9.11. # alignment.align(), alignment.salign() and alignment.align2d() now attempt to keep chain breaks aligned when aligning multi-chain sequences. This behavior can be tuned with the break_break_bonus parameter. # alignment.edit() has a new by_chain parameter; if set, overhangs are removed for each chain in multi-chain alignments. # Align codes (identifiers of sequences in alignment objects) can now be of any length. (Codes in profile and sequence_db objects are still limited to 40 characters.) # Modeller now matches residues in PDB files using both name and ATOM/HETATM indicator; previously just the name was used. This allows for correctly reading PDB files containing amino acid ligands, for example (they were previously forcibly mapped to ATOM on output). # Added support for Python 3.3. See the Modeller manual for a full change log: http://salilab.org/modeller/9.12/manual/node39.html If you encounter bugs in Modeller 9.12, please see http://salilab.org/modeller/9.12/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Out-of-range coordinates
by Arjun Ray 04 Jun '13

04 Jun '13

Hi, I am trying to mutate to ARG26 and getting the following error: randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2031 11 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. check_inf__E> Atom 206 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Traceback (most recent call last): File "/Users/arjun/script/mutate_model.py", line 157, in <module> optimize(s, sched) File "/Users/arjun/script/mutate_model.py", line 28, in optimize step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001) File "/Library/modeller-9.11/modlib/modeller/schedule.py", line 71, in optimize return o.optimize(atmsel, schedule_scale=self.scale, **vars) File "/Library/modeller-9.11/modlib/modeller/optimizers/conjugate_gradients.py", line 38, in optimize ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars) OverflowError: check_inf__E> Atom 206 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. It generates the following 2a01.pdbARG26.tmp file. I notice 7 atoms of the ARG have"0" value on the last column. What does that mean? ORIGINAL PDB: ATOM 203 N GLY A 26 84.766 -21.780 101.354 1.00 23.56 N ATOM 204 CA GLY A 26 85.026 -21.762 99.961 1.00 25.16 C ATOM 205 C GLY A 26 86.327 -21.144 99.510 1.00 25.70 C ATOM 206 O GLY A 26 86.994 -21.670 98.600 1.00 26.35 O MUTATED MODEL: ATOM 203 N ARG A 26 84.766 -21.780 101.354 1.00 23.56 N ATOM 204 CA ARG A 26 85.026 -21.762 99.961 1.00 25.16 C ATOM 205 CB ARG A 26 83.792 -21.092 99.292 1.00 0.00 C ATOM 206 CG ARG A 26 83.847 -20.959 97.751 1.00 0.00 C ATOM 207 CD ARG A 26 82.605 -20.290 97.136 1.00 0.00 C ATOM 208 NE ARG A 26 82.821 -20.241 95.649 1.00 0.00 N ATOM 209 CZ ARG A 26 81.927 -19.718 94.798 1.00 0.00 C ATOM 210 NH1 ARG A 26 82.220 -19.725 93.500 1.00 0.00 N ATOM 211 NH2 ARG A 26 80.764 -19.224 95.210 1.00 0.00 N ATOM 212 C ARG A 26 86.327 -21.144 99.510 1.00 25.70 C ATOM 213 O ARG A 26 86.994 -21.670 98.600 1.00 26.35 O The script also gave this error when I am trying to mutate to ARG60. Rest of the ARG and other mutations worked on the model. Would be helpful if someone could explain the error and how may I fix it. Regards Arjun -- **************************************************** The dream is not that you see in sleep , dream is which does not let you sleep. ~Dr. Abdul Kalam (Former President of Republic of India) ***************************************************** Arjun Ray Mobile : +919910497608 Email : arjun(a)ebi.ac.uk / arjun(a)cbr.su.se <arjun.ray(a)cbr.su.se> ***********************************************

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MISSING RESIDUES IN TEMPLATE.
by Priya Chaudhary 03 Jun '13

03 Jun '13

Respected Sir / Mam I have found that in my template coordinates of 16 atoms are missing, still in the modeled structure coordinates for those atoms are present. How have these coordinates calculated when there are no corresponding coordinates for these atoms in template ? Regards Priya

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Mutate script crashing
by Arjun Ray 03 Jun '13

03 Jun '13

Hi, I am trying to mutate a residue on a protein. The residue IS contained in the sequence. Hence, am a little lost about the following error: Traceback (most recent call last): File "/Users/arjun/script/mutate_model.py", line 89, in <module> ali.append_model(mdl1, atom_files=modelname, align_codes=modelname) File "/Library/modeller-9.11/modlib/modeller/alignment.py", line 110, in append_model atom_files, align_codes) ValueError: mod_ali_412E> align code ( /Users/arjun/PDB/APOA1/mutated_models/2a01a.pdb) too long; length 47 is greater than max length 40 This is a sub structure of only the chain 'A' I saved from the original. Regards -- **************************************************** The dream is not that you see in sleep , dream is which does not let you sleep. ~Dr. Abdul Kalam (Former President of Republic of India) ***************************************************** Arjun Ray Mobile : +919910497608 Email : arjun(a)ebi.ac.uk / arjun(a)cbr.su.se <arjun.ray(a)cbr.su.se> ***********************************************

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Question about huge gaps
by Daron Standley 30 May '13

30 May '13

Hi- Although I'm not a very regular user of modeller, I believe it is well known that long gaps, especially terminal gaps, look strange when modeled using default options. I was wondering, would be possible to add an Rg restraint so that such regions at least stay nearby the rest of the (well-modeled) protein? This is not just a problem of aesthetics. When I try to superimpose such structures using structural alignment, sometimes the long gappy regions throw the superpositioning calculation off. I could just write a script to try to cut them out, but it would be nice if I could fix the problem at the source. My suggestion of using an Rg restrain would be basically "if distance of residue x from center is greater than some huge value (2-3x the predicted Rg, based on sequence length), add a bias to the potential for x toward the center of the protein" This kind of restraint should leave the "good" parts of the alone and just pull the "bad" parts closer to the rest of the protein. Any thoughts on whether this can be done? Thanks for your advice and apologies if I have raised a already well-discussed topic. Regards, Daron

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Doubt Regarding multiple X, Y, Z coordinates for same atoms
by Priya Chaudhary 24 May '13

24 May '13

Respected Sir DOUBT REGARDING MULTIPLE X,Y,Z COORDINATES FOR same ATOMS During Modeling via automodel model-full.py script Which coordinates are used while modeling in case multiple coordinates for same atom and residue at a position are mentioned in PDB file ? On what basis are the coordinates for modeling selected if more than one coordinate set is present for same atom? Thanks

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Amount of models
by HERBERT MAX VENTHUR PE¥A 24 May '13

24 May '13

Hello I've read papers where the amount of models generated are not indicated, however, indicate that more than 1 model was obtained. The script of the tutorial of modeller provides 5 models. My question is, Is there any effect in the quality of the model if I generate several models? for example, 200 models versus 5 models? Thank you Best regards Herbert -- *Herbert Venthur Peña Profesor de Estado en Ciencias con Mención en Química* *Estudiante de Doctorado en Ciencias de Recursos Naturales * *Laboratorio de Ecología Química Universidad de La Frontera Temuco, Chile * *08-3104992*

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Urgent Query . Please do reply. Thanks a ton.
by Priya Chaudhary 21 May '13

21 May '13

Using automodel model-full python script, 1. Do we get any changes in side chain conformations or coordinates if the query sequence is perfectly aligned with template sequence at sequence level. Because upon point mutations, there is no change in sequence alignment. Whole query sequence is perfectly aligned with template. I calculated no. of contacts of wild type residues and mutant residues, there is no change at all. I used only distance between C-alpha atoms(CA) while calculating . Is there any change in side chain conformations in the modeled structures by using this script. 2. Can I get to know the details of a.make() and a.auto_align() commands used in this script. I WANT TO KNOW STEP WISE THE INSIDE DETAILS AND WORKING OF THIS SCRIPT. PLEASE HELP. URGENT !!! Please bear up with me as I don't know Python.. *Example: examples/automodel/model-full.py<http://salilab.org/modeller/9.11/examples/automodel/model-full.py> * # A sample script for fully automated comparative modeling from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, # file with template codes and target sequence alnfile = 'alignment.seg', # PDB codes of the templates knowns = ('5fd1', '1fdn', '1fxd', '1iqz'), # code of the target sequence = '1fdx') a.auto_align() # get an automatic alignment a.make() # do homology modeling

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Residues missing !!! How to specify NMR MODEL - 2
by Priya Chaudhary 21 May '13

21 May '13

Sir I used automodel - model-full.py script. I have NMR Structure. Some residues are missing in NMR MODEL no.1. I wish to use NMR Model No 2 as template. How and where to make necessary changes ?

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HETATM modelling query -reg
by venkatesh s 21 May '13

21 May '13

Respected Sir i am trying to add my model one zinc HETATM, but my efforts are failed , *iam getting *ATOM in my file pdb instead HETATM in the template structure Experimentally solved Residues Region *191-609* , protein Total Length: *419* in that Five residue are Missing Residue Here i mentioned Alignment file >P1;2DW0 structureX:2DW0.pdb: 196 :A:+414 :A:MOL_ID 1; MOLECULE CATROCOLLASTATIN; CHAIN A, B; FRAGMENT RESIDUES 191-609; SYNONYM VAP2, VASCULAR APOPTOSIS-INDUCING PROTEIN-2, CATROCOLLASTATIN/VAP2B:MOL_ID 1; ORGANISM_SCIENTIFIC CROTALUS ATROX; ORGANISM_COMMON WESTERN DIAMONDBACK RATTLESNAKE; ORGANISM_TAXID 8730: 2.15: 0.17 PFRFVELVLVVDKAMVTKNNGDLDKIKTRMYEIVNTVNEIYRYMYIHVALVGLEIWSNEDKITVKPEAGYTLNAF GEWRKTDLLTRKKHDNAQLLTAIDLD-RVIGLAYVGSMCHPKRSTGIIQDYSEINLVVAVIMAHEMGHNLGINHD SGYCSCGDYACIMRPEISPEPSTFFSNCSYFECWDFIMNHNPECILNEPLGTDIISPPVCGNELLEVGEECDCGT PENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDN YGYCYNGNCPIMYHQCYDLFGADVYEAEDSCFERNQKGNYYGYCRKENGNKIPCAPEDVKCGRLYCKDNSPGQNN PCKMFYSNEDEHKGMVLPGTKCADGKVCSNGHCVDVATAY.* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 P-RYIELVIVADRAMVTKNNGDLTAIRTWVHQIVNDMTVMYRDLNIHITLAAVVIWNKRDLITVTSSAEDTLNLF GTWRETKYLKHRKHDNAQLLTGIILDDDTIGLAYVGGMCDPKKSVGIIEDHSTEHLLVAATMAHEMGHNLGMNHD ANQCNCGANGCVMSATLTEQTSYQFSDCSKDEYQNYLTDHNPQCILNQPLRTD-T-P-VSRNELLQ-NSAHPC-- --------CDPVTCQPK--RFCVSGPCCENCQFVRAGTVCNPAKGD-WMDDYCTGISSDCPRNPL---------- -----NGFR------------------------------------------------------------------ ----------------------------------------.* and Model Ligand python script which i used as followed # Homology modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile = 'TvLDH-2DW0A.ali', # alignment filename knowns = '2DW0', # codes of the templates sequence = 'TvLDH') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling kindly give provide your valuable suggestion regarding error -- Regards,* *S.VENKATESH,

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