- modeller_usage - salilab.org

Parallel job
by Francesco Musiani 17 Jun '08

17 Jun '08

Hi, I would like to run a job on a QuadCore PC running linux, but I do not have any experience of parallel programming. Can you tell me how to parallelize a script like this? ---------- (script) from modeller import * from modeller.automodel import * from modeller.scripts import complete_pdb log.verbose() class mymodel(allhmodel): def special_restraints(self, aln): s1 = selection(self.chains['A']) s2 = selection(self.chains['B']) self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = environ() env.io_atom_files_directory = './' a = mymodel(env, alnfile = 'HpUreE.ali', knowns = 'dimerBp', sequence = 'HpUreE', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 25 a.make() # Output data ok_models = filter(lambda x: x['failure'] is None, a.outputs) key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # read model file mdl = complete_pdb(env, m['name']) # Assess with DOPE: s = selection(mdl) s.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='HpUreE.best.profile', normalize_profile=True, smoothing_window=15) ---------- (end script) Thanks Francesco --- Francesco Musiani francesco.musiani(a)unibo.it ---

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Problem with running Flex-em
by Hua Li 13 Jun '08

13 Jun '08

Hi, I am very new to the program Modeller. I got a problem as I tried to run the program Modeller 9v4 on Linux. Is there anybody that can enlighten me on how to solve this problem? Any advice gratefully received. Error message: 'import site' failed; use -v for traceback Traceback (most recent call last): File "flex-em.py", line 10, in ? import shutil ImportError: No module named shutil In fact the module "shutil" is available at python library and I have added "setenv PYTHONHOME /usr/lib64/python2.4" to my .cshrc file. Thank you. Hua

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PIR format clarification
by Thomas Juettemann 01 Jun '08

01 Jun '08

Dear all, a question about the PIR format in the align input file. I could not find the answer in the manual or the archives, apologies if I overead it. I created some PIR alignments with comment lines like these (2 different files): >cdk-cyclin;1W98.core >CDK2HUMANaCGA2HUMAN;1FIN both times MODELLER crashed and I got these error messages: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1W98.core read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1FIN.core changing the comment lines to: >P1;1W98.core >P1;1FIN solved the problem. Must the comment line always start with ">P1"? If not, what are the limitations length and/or alphabet-wise? Many thanks, Thomas

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multiple templates
by Petr Danecek 30 May '08

30 May '08

Hello, I am attempting to build a model from multiple templates, but I am getting very bad results. After doing some tests I have discovered that the problem lies most probably in the unwanted 3D orientation of the blocks which the model is built from. To test this, I took a single PDB file and splitted it into three chunks aligned as: aaaaaaaaa------------------------- ------aaaaaaaaaaa----------------- --------------aaaaaaaaaaaaaaaaaaaa aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa In this test, I would like to reconstruct the original structure. Is it possible? I tried to set the variable a.initial_malign3d=1, but the modeller ends with the error "_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0" Any help would be greatly appreciated. Best regards, Petr Danecek

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Post - problem with modelling a chain using another chain as template
by plmallip＠mail.uh.edu 29 May '08

29 May '08

Is it possible to re-orient chains in a pentameric way after using one of those chains as template to build others? I have a pentameric protein. The protein and the nearest template miss some residues at a particular position in all the chains, except one chain. So, I carried out homology modeling using modeller9v3 as follows: 1. I modelled the pentamer at a time using the nearest available pdb file as template (~85% similarity). 2. Each of the chains are about 70% similar to each other. I built a model of chain C Using chain A of available pdb file 3. Then, I overlapped chain C from step 3 and step 1, using VMD "RMSD tool". Saved both pdb's in this orientation. Copied the "region of missing residues (14) only" to chain C of step 1. 4. Similarly I did for chain B. 5. When, I reassembled chains B and C with other 3 subunits from step 1, Chains B and C are overlapping with chain A. Imagine, its like a trimer now, with 3 chains overlapping at one place. I tried both VMD, InsightII using Chains from the pentamer as reference and overlay the modelled chains. But, there is no change in orientation. Is there any way I can do this? Is this a plausible way to build missing residues, when there is not at all any template available for that region in the entire family of this protein? I would be grateful for your suggestions in this regard. warm regards, Prema, plmallip(a)mail.uh.edu

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Searching the PDB for sequence with structure
by Florian Odronitz 28 May '08

28 May '08

Hi Modelleros, I am in the process of modeling ~100 similar structures. I have a bunch of templates that cover most of the sequence of the targets. However, there are some gaps. Most gaps are loop regions or contain loops, sometimes comprising ~30 aas, so ab initio modeling is not an option. So I go to the PDB and BLAST with my missing sequence as a query. I get a great number of hits but for most of the PDBs, the large parts of the sequence have no _structure_. Downloading each of those PDBs and looking at them is not an option since its hundreds. I am looking for a tool to BLAST (or otherwise search) the sequences in the PDB that have _structure_. The people at the PDB told me there is no such option and they are not aware of such an resource. I figure I am not the first person to encounter such a difficulty. How would you handle this? Is there such a resource? Thanks and best regards, Florian

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how add sidechains
by matziast＠med.uth.gr 28 May '08

28 May '08

Hi, I have a problem with the model building. Specifically, I have the coordinates of the backbone and I want to add its sidechains but I can't find the appropriate script. If someone knows the name of the script, tell me. Thank you in advance, Maria.

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Re: [modeller_usage] Searching the PDB for sequence with structure
by Florian Odronitz 28 May '08

28 May '08

Hi Christian, > If no one will come up with a better solution, you might want to build > this tool yourself: That sounds like fun! > > All you need to do is to download the PDB files and check whether the > sequences in question are contained. The thing is that the sequence might be there but with gaps. It would be nice to have that be matched by BLAST, since regular expressions are not suited for this. If I am not the only one who has this problem I might do something like: - Download all PDB Structures. - Extract the sequences of the proteins as well as the sequences that have ATOM records. - Make a quick alignment between each of those two sequences. - Put the two sequences and the PDB ID in a database. - Make a BLAST database file witch the full sequences. - Make BLAST accessible on a web server. The search results could be presented as an alignment of the sequence that was searched for and the sequence that actually has structure. It would be easy to implement queries like "search for sequence X and return only results where more than 30% has structure". > checks) is contained in the biopython project ( http:// > biopython.org/ ). I would prefer to do it in ruby, but same same. > MD is not an option for you? I think the stretches are too long (several dozen aas) and to numerous (~100 structures * several gabs/structure). I would also feel better if I could use experimental data. Cheers, Florian

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one question,please answer
by Maryam Nikoosaleh 27 May '08

27 May '08

Hi all! My question is about Modeller restraints. Have you ever used of special_restraints or add_rsr to add your own restraints? Or to build conserved part of your target protein (such as ligand binding site or binding state of ligand)?Did Modeller build a model without any violation of your restraints? My target protein has a conserved ligand binding site.But even when I give it the restraints ,it doesn't work exactly.(e.g. I gave it distance restraints with mean=2.3 Åand std=0.03 Åand one of pair_atom were in 3.7 Å from each other) Is it common?Even about conserved parts of structure? Thanks Maryam

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PDB gap fill
by Anna Marabotti 23 May '08

23 May '08

Dear all, I tried to use the script shown in Wiki "Missing residue" section to automatically fill a gap of 12 residues in a file PDB. However, the application stops with the error message: "No loops detected for refinement: you must redefine select_loop_atoms". I had a look at the archive and found that 12 residues is the upper limit for loop detection and refinement, therefore I don't know why Modeller 9v4 does not work in my case. Does anyone have suggestions? Many thanks and best regards Anna ______________________________________________ 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.htm ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"

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