- modeller_usage - salilab.org

query about chimeric protein
by Sana Bilal 15 May '07

15 May '07

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query
by ajeeta kaushiki 15 May '07

15 May '07

Hi.. I am doing advance modelling with multiple template . I have to add ATP ang Mg in my structure . I am trying to add @ , $ for the purpose ,ATP hetero atom is present in the template even though its giving error . Can I add ATP in 1 of the template only . The error is - File "model_mult.py", line 9, in ? a.make() File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 108, in make self.homcsr(exit_stage) File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 416, in homcsr aln.check() File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/alignment.py", line 154, in check libs=self.env.libs.modpt) _modeller.error: rdabrk__337E> Structure not read in... The log file is - runcmd______> alignment.append(align_codes=['2FFAA', '1XEFA', '2FFBA', 'CaNBD'], atom_files=[], file='CaNBD-mult.ali', (def)remove_gaps=True, (def)alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) read_te_290E> Number of residues in the alignment and pdb files are different: 242 241 For alignment entry: 2 1XEFA x (mismatch at alignment position 242) Alignment KELLSEPESLYSYLYQLQSD@ PDB KELLSEPESLYSYLYQLQSD Match ******************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 2 1XEFA rdabrk__337E> Structure not read in (please consult the log file for more details): Please help. Thanks and Regards Ajeeta kaushiki JNU

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Optimizing the Helix strain in the model?
by Ngo Duc Tri 14 May '07

14 May '07

Dear Modeller users, I can learn from the Interative Example (Modeller Tutorial) that I can increase the accuracy of the helix strain by removing or transfering the gap to the begining or ending ot the helix. However If my alignment don't have the gap in the helix region and the alignment score seem maximum. I would like to know how I can do in this situation because optimizing the loop cannot be applied in this. This region is in the transmembrane of a membrane protein. Thank you very much for all of your advices, My best regards, TriNgo

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loop to connect two domain
by Jayapal, Prabha 14 May '07

14 May '07

Dear Modeller: I am new to protein modelling. I want to connect two domains by a loop containing 16 residues. I am having templates for both the domains and not for the loop. I have tried some of the loop modelling techniques but unsuccessful. Can anybody help me with this situation? Thanks in advance. Cheers J.Prabha

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getting pdb's but not fit.pdb's
by roac0030＠flinders.edu.au 09 May '07

09 May '07

hey, i'm new to modeller. I can use modeller and and get homology models of proteins but when it comes to writing the superposed pdb's (the x_fit.pdb's) it comes up with an error and doesn't... i've included the .top, .ali, and .pdb as well as a screenie of the error. any help would be greatly appreciated. thanks heaps -mike

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Modeller as webservice (WSDL)
by Francoijs, Kees-Jan 09 May '07

09 May '07

L.S, I'm currently using modeller as standalone application but 'm planning to set up a more automated setup. To do this i wanted to use modeller as a webservice (WSDL) in Taverna. Has any body ever created a wrapper for this? In the archives no reference to wsdl found :-( Thanx in advance Kees-Jan

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[Fwd: Cannot generate the plot of DOPE?]
by Modeller Caretaker 08 May '07

08 May '07

-------- Original Message -------- Subject: Cannot generate the plot of DOPE? Date: Wed, 9 May 2007 02:03:18 +0900 From: Ngo Duc Tri <ngoductri(a)gmail.com> To: modeller-care(a)salilab.org Dear Modeller users, I finished modelling my protein and doing the evaluation step. I run the file evaluate_model.py to calculate the DOPE score of my model. I got DOPE score : -39521.605469 and there was no error in the log file. I use this profile file to generate the DOPE plot using GNUPLOT but this program show a strange line. Actually It just show the position of my aminoacid but no DOPE score for each. I run the GNUPLOT and used the command: plot ' myprotein.profile' I want to ask you If it's the error of GNUPLOT or my profile file? And how can i fix it to show the actual DOPE score for each residues. Thank you very much for your comments, Best regards, TriNgo Sungkyunkwan University

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Ubuntu installation issue
by Christian Meesters 07 May '07

07 May '07

Hi, I just installed Ubuntu 7.04 on one machine and tried to get modeller running. I tried an installation from source as well as using the rpm. Actually modeller itself is installed, but the python module is not available. The only python-installation I have is 2.5 and I would rather not work with 2.3. Last time I installed modeller I had the module running with python 2.4, so I guess running with 2.5 should be possible, too. (There are no .so-files I could get into the python path manually.) Did anyone try to install modeller on Ubuntu/Debian or alike and has a hint for me? TIA Christian

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CONECT record in MODELLER?
by Ngo Duc Tri 03 May '07

03 May '07

Dear Modeller users, I used Modeller to model one protein and I want to modify some part using BIOPOLYMER (Sybyl software). However, the pdb file don't have the CONECT record. The structure cannot be viewed in BIOPOLYMER. Can you tell me how to add the CONECT record to the model structure? Thank you very much for your advices. Best regards, TriNgo Sungkyunkwan University, Korea

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Unpick restraints and partial optimization.
by Gregoire Depret 26 Apr '07

26 Apr '07

Dear Modeller users, I am trying to unselect some restraints of the restraint file coming from my homology model in order to perform some optimization. Following the recommandations, I have tried the unpick method like this. mdl = complete_pdb(env, 'homo_model.pdb') mdl.restraints.append(file='./original_restraints.rsr') mdl.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) allrest = selection(mdl) mdl.restraints.pick(allrest) mdl.restraints.unpick(mdl.residue_range('706:B', '736:B')) mdl.restraints.condense() I get the following logfile runcmd______> restraints.append(file='./original_restraints.rsr') runcmd______> model.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) runcmd______> restraints.pick((def)residue_span_range=(0, 99999), (def)restraint_sel_atoms=1, (def)restraints_filter={'default':-999 .000000}) runcmd______> restraints.unpick() unpick__441_> Number of restraints unselected: 0 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 101301 101301 None of the restraints were removed. Since I renumber my model I have tried the restraint.reindex command but I didn't make it through either. I know I can edit my restraint file and remove the unwanted restraints but I can't find my residues back in the homology generated restraint file, I only read atom index. Another question. I want to perform an optimization on some parts of my model only. I have tried to add residue ranges to a selection and then optimize this selection, but in this case modeller don't take into account the unselected parts of my model and I get overlapping helices. I understand why It is happpening nevertheless is there still a way to achieve partial optimization without overlapping ? Many thanks for your answers. -- Depret Grégoire Graduate Student gdepret(a)ulb.ac.be Service de Structure et Fonction des Membranes Biologiques Centre de Biologie Structurale et de Bioinformatique Université Libre de Bruxelles Boulevard du Triomphe CP 206/2 B-1050 Bruxelles Belgium

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