- modeller_usage - salilab.org

Using unpublished structures for template to create models?
by Geoffrey Lippa 10 Dec '14

10 Dec '14

Hi all, I was hoping to get some help on the modeling of a protein target by sequence alignment using a 41% similar structure template I recently solved, in place of a published structure on the PDB. The resolution has changed and may help create a more accurate model for ligand docking. Thanks. Geoff Dr. Geoffrey Lippa Post-doctoral Research Associate Laboratory of Dr. Andrew Gulick Hauptman Woodward Medical Research Institute 700 Ellicott St., Buffalo, NY 14203 Phone: 585-690-0850 Email: glippa(a)hwi.buffalo.edu

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alpha-helix
by Juan Munoz-Garcia 24 Nov '14

24 Nov '14

Dear Modeller users, I’ve tried to make an alpha helix from the peptide sequence (21 amino acids) using the script shown in the website (http://www.salilab.org/modeller/wiki/Make%20alpha%20helix) i.e., imposing restraints to force the alpha helical structure. I’ve tried with conjugate_gradients, molecular_dynamics and quasi_newton methods, but the output just showed a helix for a small part of the peptide, showing a coil for the rest of it. Although this is providing some information itself, and it roughly agrees with experimental data, I do want to force an alpha helical structure for the whole peptide. Do you know how this can be done? I was wondering if there is any method to grow an alpha helix just based on the backbone and once formed growing the side chains from it, thus avoiding possible highly destabilising side chain - side chain interactions precluding the helix formation. Regards. Juan C.

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Modelling loop region in homodimer
by aneesh cna 14 Nov '14

14 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

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Modelling loop region in homodimer
by aneesh cna 11 Nov '14

11 Nov '14

Drear members, I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.? I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here? Many thanks in advance Regards Anu

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Physical.values
by chris.wood＠stfc.ac.uk 30 Oct '14

30 Oct '14

In the modeller.physical module, is there a way to select to select the physical types given the index? Something like: >> import modeller >> print modeller.physical.types[1] physical.bond I see that each modeller.physical.<restraint type> has a _num method which returns the index, but I'd like to avoid looping through all the object types if possible! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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Compatability with Anaconda
by R. Michael Sivley 30 Oct '14

30 Oct '14

I’ve installed Modeller-9.14 on a Mac (Mavericks). If I launch the system python2.7, I can import modeller successfully. However, I use the anaconda python distribution. I have tried creating a symbolic link from /Library/modeller-9.14/modlib/modeller to anaconda/lib/python2.7/site-packages/modeller, but I get the following import error: >>> import modeller Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/mikesivley/anaconda/lib/python2.7/site-packages/modeller/__init__.py", line 93, in <module> import _modeller ImportError: No module named _modeller I wasn’t able to find any mention of Anaconda on Modeller’s installation or FAQ pages. Has anyone successfully installed Modeller and imported from anaconda python? Thanks! Mike Sivley PhD Student Department of Biomedical Informatics Vanderbilt University Medical Center

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Newbie question - Selecting chains and plotting DOPE profiles
by Justin Havird 22 Oct '14

22 Oct '14

Hi, I have just been using MODELLER for a couple weeks now and have a question that is hopefully an easy one. I am trying to model proteins of the cytochrome oxidase (COX) complex from a variety of organisms. I followed the "basic tutorial" online and got great results for the first subunit in the complex (COX1). But, when I tried the same thing for COX2, the align2d.py script aligns my sequence against ChainA in the complex instead of ChainB, so I end up with something that looks like COX1 instead of COX2. This happens even though I change the "aln.append_model" line in align2d.py to align_codes='1v54B', instead of 1v54A. I was able to work around this by following the advanced tutorial and using the multiple templates scripts (even though there is sometimes only a single template to compare the sequence to). However, I am not able to compare the correct DOPE profiles when trying plot_profiles.py; ChainA's profile is being used when comparing to the model instead of ChainB. I would like to be able to get an idea of how good the model is and identify areas of weak reliability, so the DOPE profiles seem like a good tool. Any help would be appreciated, as I really like the MODELLER software so far and hope to be able to make use of it. Thanks, Justin ************************************************************ Justin C. Havird, PhD Department of Biology Colorado State University Room E106 Anatomy/Zoology Building Fort Collins, CO 80523 Lab telephone: 970-491-2058 Fax: 970-491-0649 Email: Justin.Havird(a)colostate.edu Justin's Research Website: http://jchavird.wix.com/jchavird Sloan Lab Website: https://sites.google.com/site/danielbsloan/ ************************************************************

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selection of loop
by Yixin Ai 09 Oct '14

09 Oct '14

Dear everyone, i have a question and i need your help. i want to refine loops (50-60 and 90-100) of my model after building model by modeller9.14. however, i don't know how to set the two regions. the part codes of my script is: return selection(self.residue_range('50:', '60:'), self.residue_range('90:', '100:'), selection_status='INITIALIZE') is right or not? And what's the difference between self.residue_range('90:', '100:') and self.residue_range('90', '100')? thank you very much! ai yixin

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modeller parallel
by Yixin Ai 08 Oct '14

08 Oct '14

Dear everyone, i have a question and i need your help. when i use the command 'modpy.sh python model-parallel.py' to perform parallel computation. but i got the empty modelparallel.log file which not contain the molpdf, dope and ga341 score. how can i get the score functions in the log file? thank you very much ai yixin

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Modeller for alignment and modeling
by Michael Meyer 02 Oct '14

02 Oct '14

Hi everyone, I'm relatively new to Modeller, so please bear with me. I have specific applications in-mind for the future, but for now as an exercise I'm trying to accomplish basic tasks. Right now, I'm trying to accomplish some basic multi-chain modeling. Let's say I have two target protein sequences, and I have found a PDB template that is appropriate for modeling them via PSI-BLAST. However, unlike the 2-chain example here: http://salilab.org/modeller/manual/node29.html the two chains that are homologous to my target sequences are not A and B in a two-chain PDB. They are C and E, or worse, F and B. My question: Is there any way to use the PIR format en route to automodel.make() to specify two chains that aren't contiguous in a template? The example given below assumes that the two chains in 2abx are the first two, but what if they were chains C and A?. I could flip their order to get them to be in the order they appear in the PDB file, but there's still the issue that chain B doesn't factor into my modeling step, and so I would like modeller to ignore it? Is there any way to not use chain B without altering the original PDB file to only include the two chains I want to use for modeling? >P1;2abx structureX:2abx: 1 :A:74 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;1hc9 sequence:1hc9: 1 :A:148:B:undefined:undefined:-1.00:-1.00 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG/ IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG* Furthermore, is there any way to use align2d to perform the two sequence-two chain alignment in one step to create the appropriate PIR file for multi-chain modeling. Right now, I'm doing two align2d commands to create two separate PIR files, and then mashing them together afterward. Thanks! Michael

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