November 2008 - modeller_usage

Residues in disallowed region
by Bo Yang 01 Dec '08

01 Dec '08

Hello, Modeller: The models built from Modeller 8v1 contain some residues (non-Gly and non-Pro) in the disallowed region based on Ramachandran plot. I wonder how this could happen? How to change these residues back to allowed region? I try to use energy minimization such as NAMD and Amber. After all, the minimized models had increased numbers of residues in the disallowed region. Thank you for your advice Bo

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Transfer_xyz or other methods?
by plmallip＠mail.uh.edu 01 Dec '08

01 Dec '08

Hi, I am trying to obtain a model by transfer_xyz method, using a template which have less than 30% homology. I want to copy the coordinates of the template and if there is a gap, then obtain coordinates for those regions using model.build(). But, I end up with a model in pieces i.e. Some regions are displaced and built elsewhere. Even for some of the residues for which there is template structure, I get long linear chains built. May be the .ali file is not being used in getting the model! If transfer.xyz will not work if my the alignement has gaps in between, is there any other way to achieve this? I cannot exclude the gaps because, this will not serve the pupose of getting the template coordinates at equivalent regions where my model should have. The .ali file is >P1;1UW6 structureX:1UW6.pdb: 0 :E:215:E:undefined:undefined:-1.00:-1.00 EFDRADILYNIRQTSRPDVIPTQRD-RPVAVSVSLKFINILEVNEITNEVDVVFWQQTTWSDRTL AWNSSHS--PDQVSVPISSLWVPDLAAYN-AISKPEVLTPQLARVVSDGEVLYMPSIRQRFS CDVSGVDTESG-ATCRIKIGSWTHHSREISVDPTTE---------NSDDSEYFSQYSRFEIL DVTQKKNSVTYSCCPEA-YEDVEVSLNFR* >P1;NRmiss_210testb sequence:NRmiss_210testb:0 :E:215 :E:::-1.00:-1.00 SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAWTDYRL QWDPAAYEGIKKLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQPSAIYRSS CTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAFTENGQWSIE HKPSRKNWR--SDDP--SYEDVTFYLIIQ* .py file is from modeller import * from modeller.automodel import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env, file='NRmiss_210anti_1UW6.ali', align_codes=('1UW6')) aln.malign3d(fit=False) aln.append(file='NRmiss_210anti_1UW6.ali', align_codes= 'NRmiss_210testb') md1=model(env) md1.generate_topology(aln['NRmiss_210testb']) md1.transfer_xyz(aln) md1.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') md1.write(file='NRmiss_210testb.ini') Any suggestions in this regard is appreciated. Thanks & regards, Latha, Graduate student.

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dope batch processing
by jinlian 01 Dec '08

01 Dec '08

Hi all I want to use the 'DOPE' to do the filtering the docking structure of thousands of proteins, and I want to do batch possessing, but the script can only calculate one structure: from modeller import * from modeller.scripts import complete_pdb env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Read a model previously generated by Modeller's automodel class mdl = complete_pdb(env, '1acb.pdb') # Select all atoms in the first chain atmsel = selection(mdl.chains[0]) score = atmsel.assess_dope() I am not familiar with python, Could you tell me how to do the batch processing in the above script? Thank you very much!

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dope batch processing
by Mauricio Carrillo Tripp 28 Nov '08

28 Nov '08

This is not a python solution, perhaps there is one, but what I did was to write a bash shell script to modify the python script changing the name of the model consecutively (might have to be modified for other shells): # DOPE for c in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15; do sed 's/NAME/Model_'${c}'/g' model-DOPE.py > tmp.py; mod9v4 tmp.py ; echo "Model "${c}": ";grep 'DOPE' tmp.log >> Models_DOPE.dat; done In the python script (model-DOPE.py in my case) replace the line mdl = complete_pdb(env, '1acb.pdb') with mdl = complete_pdb(env, 'NAME.pdb') your previously built models should be named sequentially Model_01 to Model_15 (or the last one in your case), or change the regexp in the sed command above according to your file naming. At the end you'll have a list of DOPE values in the file Models_DOPE.dat. Hope this helps... Message: 1 > Date: Thu, 27 Nov 2008 10:03:30 +0800 > From: "jinlian" <jinlian05(a)lzu.cn> > Subject: [modeller_usage] dope batch processing > To: <modeller_usage(a)salilab.org> > Message-ID: <427750030.20199(a)lzu.cn> > Content-Type: text/plain; charset="us-ascii" > > Hi all > > I want to use the 'DOPE' to do the filtering the docking structure of > thousands of proteins, and I want to do batch possessing, but the script > can > only calculate one structure: > > > from modeller import * > from modeller.scripts import complete_pdb > > env = environ() > env.libs.topology.read(file='$(LIB)/top_heav.lib') > env.libs.parameters.read(file='$(LIB)/par.lib') > > # Read a model previously generated by Modeller's automodel class > mdl = complete_pdb(env, '1acb.pdb') > > # Select all atoms in the first chain > atmsel = selection(mdl.chains[0]) > > score = atmsel.assess_dope() > > I am not familiar with python, Could you tell me how to do the batch > processing in the above script? > Thank you very much! > -- 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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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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