- modeller_usage - salilab.org

R: R: question for a (putative?) disulfide bridge
by Anna Marabotti 26 Nov '08

26 Nov '08

Dear Ben, I'm re-sending the message below because it seems to me that you did not receive it. Sorry for duplication. Best regards Anna Marabotti -----Messaggio originale----- Da: Anna Marabotti [mailto:anna.marabotti@isa.cnr.it] Inviato: lunedì 24 novembre 2008 13.47 A: 'Modeller Caretaker' Oggetto: R: R: [modeller_usage] question for a (putative?) disulfide bridge Dear Ben, thank you for your continuous support. I'm attaching here the pdb file of the model in which I would like to create the disulfide bridge, and the scripts I used to do it. My knowledge of Python language is very very poor and so I'm doing a trial&error procedure, but at present I obtain only errors... If I understand well, I should only provide the PDB file to Modeller, since I don't see any request of alignment. The sequence then should be read from the PDB file, right? The PDB file I have attached is the one that I obtained using mutate_model: residue 55 was previously a Gly, and now is a Cys in both subunits.So, the number of the residue should be correct. I tried to model a disulfide bridge between Cys55 of the subunit A and Cys180 of the subunit B, and I tried: 1) model-patch_1.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_1.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_1.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['55:'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 55:' 2) model-patch_2.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_2.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_2.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 180:B' 3) model-patch_3.py (see attachment): here the error message: Traceback (most recent call last): File "model-patch_3.py", line 19, in ? mdl = complete_pdb(env, code, special_patches=patches) File "C:\Programmi\Modeller9v5\modlib\modeller\scripts\complete_pdb.py", line 37, in complete_pdb special_patches(mdl) File "model-patch_3.py", line 15, in patches mdl.patch(residue_type='DISU', residues=(mdl.residues['A:55'], File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 226, in _ _getitem__ (self.offset, self.length, self.suffix)) File "C:\Programmi\Modeller9v5\modlib\modeller\util\modutil.py", line 19, in h andle_seq_indx int_indx = lookup_func(*args) File "C:\Programmi\Modeller9v5\modlib\modeller\coordinates.py", line 283, in _ indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: A:55' I also obtained the .log file, that I'm attaching here. I don't understand if there is only a problem in identifying the numbers of the residues or there are other supplementary problems, anyway the disulfide bridge is not forming, and I don't see any trivial error to correct. Thank you for your help and best regards. Anna Marabotti -----Messaggio originale----- Da: Modeller Caretaker [mailto:modeller-care@salilab.org] Inviato: venerdì 21 novembre 2008 19.02 A: Anna Marabotti Cc: modeller_usage(a)salilab.org Oggetto: Re: R: [modeller_usage] question for a (putative?) disulfide bridge Anna Marabotti wrote: > thank you for your message, and sorry to bother you again. I tried to > use model.patch() to add the disulfide > bridge to my model, but I have a supplementary problem. In fact, my > protein is a homodimer and the disulfide > bridge should link two Cys residues in the two different subunits. I > tried to indicate "A" and "B" in the > script in this way: > > # Create the disulfide bond: > def patches(mdl): > mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A.'], > mdl.residues['180:B'])) > > but it doesn't work. What do you mean by "it doesn't work"? You get an error message (what is it?) or everything runs but the disulfide isn't created? In the latter case, I'd need to see the full script. In the former case, you probably have the wrong residue numbers and/or chains for your two Cys residues. The first residue should probably be '55:A' rather than '55:A.' but one way to check the numbers is to run modeling first without the patch, and look at the numbers in the generated model. 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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how to build a model from a template with only CA atoms?
by Lixia Jin Day 25 Nov '08

25 Nov '08

Hi, I have a protein conformation with only alpha carbon (CA) atoms. And I want to build up the full structure without moving the position of the CA atoms. Can I do it with MODELLER? How to do it? Thanks! Lixia

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question for a (putative?) disulfide bridge
by Anna Marabotti 21 Nov '08

21 Nov '08

Dear Modeller caretaker, using mutate_model I replaced a residue in a protein with Cys. Looking at the mutant protein, I saw that this new Cys residue is near to another Cys residue that was previously in the protein. The two sulphur moieties are not facing each others as in a disulfide bridge, but are rotated away. However, manually rotating the side chains, they can approach their sulphur moieties until less than 3A of distance, so in my opinion a disulfide bridge could be formed. At present I have not experimental data to confirm if a disulfide bridge is forming or not in this mutant. How can I check with MODELLER if this newly introduced mutation is really able to form a new disulfide bridge into my protein? How can I model this new disulfide bridge? Many thanks and best regards Anna Marabotti ______________________________________________ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti(a)isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm Coming soon: BBCC2008: http://bioinformatica.isa.cnr.it/BBCC/BBCC2008 ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

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normalized DOPE - expected values vs quality of template?
by Daniel Rigden 20 Nov '08

20 Nov '08

Dear all I expect this is more a question for the developers, but perhaps other users have relevant experiences to share. With 9v5 we have the very useful Z scores from a normalized DOPE assessment. The manual says that +ve scores are bad, and that anything less than -1 or so is 'native-like'. Presumably the best achievable Z score will depend very much on the available templates - we should be able to do much better with 70% identical templates than with 30% identical templates. Has anyone got a feel for what kind of figures we should be happy with (and be able to quote in a paper as supporting the quality of our model) in different ranges of template % sequence identity? Thanks in advance Dan -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.

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Loop model refinement level
by Mauricio Carrillo Tripp 17 Nov '08

17 Nov '08

In the example taken from http://salilab.org/modeller/manual/node32.html, the loop refinement level is set to "fast" a.loop.md_level = refine.fast # Loop model refinement level What other levels of refinement do I have access to? I've seen in other examples something like the following for complete models: # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e8 Would this also apply for loops? Would it make much difference in terms of final model/loop quality (DOPE score maybe)? Thanks again for all your help. -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | 0 |

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dopehr_loopmodel crashed
by Mauricio Carrillo Tripp 17 Nov '08

17 Nov '08

I'm trying to do a loop refinement calculation with the dopehr_loopmodelclass, modeller 9v4. Here's the python script I'm using: from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # directories for input atom files env.io.atom_files_directory = ['./', 'PDB/'] a = dopehr_loopmodel(env, alnfile='TTN.ali', knowns='2g8gOligo', sequence='1s58', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 a.loop.ending_model = 1 a.loop.md_level = refine.fast a.make() After a few hours of running, it stop. Here's the last part of the log: ... randomi_498_> Atoms,selected atoms,random_seed,amplitude: 36972 36056 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 327553569 319876.531 312.379 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 554709537 541708.562 529.012 preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. >> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- 1s58.B99990001.pdb 75059.09375 -361379.46875 0.78559 >> Summary of failed loop models: 1s58.BL00010001.pdb check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Dynamically allocated memory at finish [B,KiB,MiB]: 549216697 536344.438 523.774 Starting time : 2008/10/24 10:37:24 Closing time : 2008/10/24 12:51:48 Total CPU time [seconds] : 8018.72 The model part went OK, but when it tried to do the loop refinement it went crazy (the coordinates in1s58.BL00010001.pdb are all messed up). I'm also testing the other two classes (loopmodel and dope_loopmodel) and they've been running for a long while now, so I don't know if they'll work or not. I'd just like to know if I'm doing something wrong or I just ran into some kind of glitch or bug in the dopehr algorithm. Thanks! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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Visuvalise
by nagaraju ngaraju 17 Nov '08

17 Nov '08

Dear caretaker I want to know how to visulized the protein structrue after completing the "plotprofile.py" . Thank you I.Nagaraju Sugen Life Sciences Tirupati 9949860196 Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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model a peptide without moving a part of it
by Omar Piña 14 Nov '08

14 Nov '08

I need to bound two peptides and mantain one of them without moving. I looked for restraint but I don´t find how to do it. Sorry If my cuestion is too basic. Omar

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Heme
by Bo Yang 12 Nov '08

12 Nov '08

Dear Modeller: I have heme modeled into my target using Modeller. When I try to visualize the model, the Fe is not shown. I check the pdb file of the model, Fe is there. I couldn't understand what could be wrong. Why can't "Fe" be visuallized? I use Modeller 8v1. The program used for structure visuallization are Chimera and VMD. Thank you for your advice. Bo

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How to install pylab in modeller?
by vidhya ganesh 12 Nov '08

12 Nov '08

Hi, In Model evaluation, I installed matplotlib inorder to build the plot between my template and model , but I can't find pylab, which I think is a submodule under matplotlib. All of the documentation for matplotlib starts with "from pylab import *", but this of course doesn't work. Is pylab included in the distribution? If not, is there a use for matplotlib _without_ pylab? Thanks Vidhya

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