- modeller_usage - salilab.org

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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using multiple template in Modeller9v1
by jinlian05＠lzu.cn 19 Apr '07

19 Apr '07

Hi, I am new to modeller and I have trouble creating a homology model of a protein using multiple template. During making model,it appares model error, structure not read in.I would appreciate it if any one can give me any suggestion. Thanks! log file: runcmd______> alignment.append(align_codes=['1u19', '1PFC', '1BGY', '1AVQ', '1ARP', 'ccr'], atom_files=[], file='multiccr.ali', (def)remove_gaps=True, (def)alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) readlinef__W> File: 1u19.pdb, Line: 1371 Modeller will only read the first 80 characters of this line. readlinef__W> File: 1u19.pdb, Line: 1371 Modeller will only read the first 80 characters of this line. read_pd_702E> File: 1u19.pdb, Line 1371 Could not parse data from file; file is probably corrupt. read_te_288W> Protein not accepted: 1 1u19 rdabrk__337E> Structure not read in (please consult the log file for more details):

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Rigid bodies on the backbone only.
by Gregoire Depret 18 Apr '07

18 Apr '07

Hello, I would like to apply rigid bodies only on the mainchain of my model in order to run molecular dynamics and conjuguate gradients. I have already tried to do it with : mdl.restraints.rigid_bodies.append(rigid_body(mdl.residue_range('56:A', '48:A'))) and just before the optimization start : atmselall = selection(mdl) atmsel = selection.only_mainchain(atmselall) and then : cg.optimize(atmsel, max_iterations=50, actions=actions.trace(5, trcfil)) But my model is destroyed by CG and MD which is not the case when rigid body is applied on the whole chain. Maybe I can define "rigid_body" with "atom_range" in place of "residue_range" and selecting all the atoms of the backbone (Ca, CO, N) for my residue range, but I think there must be a better way to achieve this. Many Thanks for any suggestion. 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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stuck even before begining - how to create the .ali file
by Ariel Bensimon 18 Apr '07

18 Apr '07

I would like to use MODELLER to structurally align a protein domain with a known PDB. But I am stuck. I could even create the basic .ali file. Trying using the manual. Couldn't find the basic start of things Thanx , A.

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