June 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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headache with alignment
by Francesco Pietra 30 Jun '13

30 Jun '13

Hello: Could a nice person help correcting the mismatch described by mod9.11 for missing residues with a trimer? read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 551) Alignment .....VVWALCFMGSLALLALVCTNRIQYYFLYPHVTKLDEVAATRLTFPAVTFCNLNEFR PDB DFKVVFTRYGKCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEA Match ***** * Alignment residue type 18 (V, VAL) does not match pdb residue type 5 (F, PHE), for align code XYZ_pure (atom file XYZ_pure), pdb residue number "189", chain "B" alignment.ali: >P1;XYZ0_pure structureX:XYZ_pure: 50 :A:+1221:C:::-1.00:-1.00 ------------------------------------CFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFD---------.............................. ............................................................ ......................................................./ -------------------------------VVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVL-------------.............................. ............................................................ ......................................................./ ----------------------------LKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLE------------.............................. ............................................................ ....................................................... * >P1; XYZ_pure_fill sequence::::::::: GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ......................................................./ GQPVSIQAFASSSTLHGISHIFSYERLSLKRVVWALCFMGSLALLALVCTNRIQYYFLYP HVTKLDEVAATRLTFPAVTFCNLNEFRFSRVTKNDLYHAGELLALLNNRYEIPDTQTADE KQLEILQDKANFRNFKPKPFNMLEFYDRAGHDIREMLLSCFFRGEQCSPEDFKVVFTRYG KCYTFNAGQDGKPRLITMKGGTGNGLEIMLDIQQDEYLPVWGETDETSFEAGIKVQIHSQ DEPPLIDQLGFGVAPGFQTFVSCQEQRLIYLPPPWGDCKATTGDSEFYDTYSITACRIDC ETRYLVENCNCRMVHMPGDAPYCTPEQYKECADPALDFLVEKDNEYCVCEMPCNVTRYGK ELSMVKIPSKASAKYLAKKYNKSEQYIGENILVLDIFFEALNYETIEQKKAYEVAGLLGD IGGQMGLFIGASILTVLELFDYAYEVIKHR.............................. ............................................................ ....................................................... * As the pasted alignment.ali is misreproduced here, even with plain text, the file is also attached. Dots stand for chloride ions and water. Thanks a lot francesco pietra

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Denovo loop remodeling
by Ramin Ekhteiari 28 Jun '13

28 Jun '13

Hi, Is there any Denovo loop remodeling on the base of the fragment data base in MODELLER? Cheers, Berk

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Long loop omitting
by Ramin Ekhteiari 25 Jun '13

25 Jun '13

Hi, I am predicting a protein by homology method, this protein has a long loop (i.e., 40 resides) and there is no any residues in template for modeling, I don't want modeler to model this loop site by energy minimizing method and leave it. So how can I arrange this in build script. Cheers, Ramin

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Model of the GFP
by James Starlight 25 Jun '13

25 Jun '13

Dear Modeller Users! I've forced with the problem during preparation of the model of my Green Fluorescent protein. In particular this model consist of heteroatomic chromophore group which is the part of the protein polypeptide chain. Because my initial pdb file have missed N term (first 1-10 residues) I'd like to build full-residue model including chromophore group which present in the pdb file as the HETATM. below you can see my alignment file as well as script >P1;input structureX:input:6: ::225 : ::-1.00:-1.00 -----NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL* >P1;seq sequence:seq: : : : ::: 0.00: 0.00 MRSSKNVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL* # Homology modeling with multiple templates 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 # Read in HETATM records from template PDBs env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] allow_alternates=True a = automodel(env, alnfile = 'align-multiple_new.ali', # alignment filename knowns = 'input', # codes of the templates sequence = 'seq') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 30 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling Here in both sequences dot (.) in the SPQ.SK motif correspond to the chromophore group (env.io.hetatm = True). Unfortunatelly I have error after processing this _modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found in PDB file: 1 ./input.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q). How I could fix it ? Thanks for help, James

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Missing atoms
by Francesco Pietra 25 Jun '13

25 Jun '13

Hi Ben: I already modeled in the past, using modeller, this trimer from chicken to humans. Now, from new, low-resolution x-ray diffraction data for that trimer in complex with a small molecule, I merely want to reconstruct the missing side chains (many of them) while omitting the missing residues (these are at the beginning and final portion, i.e. protruding from the pore into the intracellular). The lacking residues are many and for a flexible region that resists any modeling, and I am not interested in that part of the transmembrane protein. My question is whether <http://salilab.org/modeller/wiki/Missing%20residues> can be adapted to do that for the trimer. Unless I did something wrong, I got the answer "no missing residue', in fact I had eliminated the flexible portions. In other words, what I would like to do, is reconstructing the missing atoms (side chains) in the context of the trimer, not each chain at a time. Thanks francesco pietra On Jun 23, 2013, at 7:00 PM, Ben Webb <ben(a)salilab.org> wrote: > On 6/22/13 10:17 PM, Francesco Pietra wrote: >> Modeling a trimer (all three chains present, though missing residues and >> atoms) with chimera and modeller installed locally. >> >> The default is modeling each chain, one at a time. The chains are >> identical in sequence but the X-ray structure shows different localized >> conformations. Question: is modeller modeling by taking the other two >> chains into account? > > The Modeller mailing list would be more appropriate for such a question (unless it's specific to the Chimera Modeller interface). If you want to model a trimer using a trimer template, you don't need to do anything special (just include the entire sequence of each trimer, with '/' chain break characters where appropriate). Modeller will consider all interatomic distances. (If the Chimera Modeller interface isn't doing this, the Chimera people may want to comment further.) > > If you want Modeller to model (e.g.) chain A using structural information from each of chains A, B, and C, that's just multiple template modeling (using A, B, and C as templates for A). > > Ben

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MUTATE_MODEL.py QUERIES....
by Priya Chaudhary 24 Jun '13

24 Jun '13

Respected Sir 1. Can I get any detailed documentation explaining mutate_model python script. Since, I am a beginner both in Python and MD Simulations, I am finding it tricky to understand this script.. The link is as follows. http://salilab.org/modeller/wiki/Mutate%20model 2. My second doubt is " How and where can I specify the mutation. Is 1699 mentioned in this script "RESIDUE POSITION " and LEU as "MUTANT RESIDUE" ? 3. My third doubt is how much time will it take for this script to run ? 4. My Fourth doubt is at the end, will I get single or multiple models ? If the output is multiple model, how shall I select the best one ? Please send some detailed documentation for this script. I am unable to understand the basic logic behind this script.. I will be highly obliged. Thanks Priya

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constant starting molecule for models
by Dermot Mallon 15 Jun '13

15 Jun '13

I am trying to model difference versions of a protein; each differing by one or two amino acids. I am then looking at differences in electrostatics. The effect size I am looking at is quite small and there is considerable difference simply from differences in modeller - I believe this is because it starts at a different amino acid. Between models with identical sequence the RMSD is ~0.2, which although small is abolishing any meaningful difference I could expect to see form the one or two amino acid change. Therefore, I wonder if there is a way to ask modeller to start at the same point in these molecules? I tried a.rand_model = None, but that doesn't appear to be the correct option. Does anyone know how I can achieve this? Many thanks for your help. -- D Mallon Clinical Research Fellow e: dhm31(a)cam.ac.uk m: 07879 200800 t: 01223 336975

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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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