October 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11
by listek_wfrp＠interia.pl 30 Oct '13

30 Oct '13

Hello everybody ! I am new to modeller, so please excuse me if my question seems trivial. I have a problem building a model from multiple templates. When i try to run build model script I get an error: "Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11" I followed all the previous steps from advanced modeling tutorial and all of them worked fine. Now I am stuck, and all solutions I`ve tried dont work. I attatch my script and alignment file. Thank you for your help in advance !

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Fwd: Extract Chain ID
by Amjad Farooq 28 Oct '13

28 Oct '13

I am not scanning against PDB95 but rather working on multi-chain PDBs locally. For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested in extracting the chain ID of the second segment (D) that best aligns with my query sequence, I do not believe you can extract that from PIR alignment file, which only provides chain IDs of the first (A) and the last chain (P). Also, how would I know if my query sequence aligned up against chain D unless I look at the alignment file manually. I want to automate this procedure. In other words, have a python script extract the chain ID of the aligned segment in a multi-chain PDB and automatically proceed to next step for homology modeling--that is I only want to use segment D as a template during homology modeling rather than the whole multi-chain PDB, which compromises the quality of the alignment and hence the model. Thanks! On Mon, Oct 28, 2013 at 2:36 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 10/27/2013 11:08 AM, Amjad Farooq wrote: > >> Is it possible to perform an automatic search of a multi-chain PDB >> template with a known protein sequence that is to be modeled (say >> 100-200 residues in length) and then extract the chain ID of the segment >> of the PDB template that best matches with the query sequence. >> > > If I understand you correctly, this is straightforward. If you're scanning > against our PDB95 database, for example, all the templates are single > chain, and the chain ID is simply the last character in the align code. > > If you're trying to align against a multi-chain template (presumably a > local alignment) you could extract the chain ID trivially from the > alignment object. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/**modeller/<http://www.salilab.org/modeller/> > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usage<https://salilab.org/mailman/listinfo/modeller_usage> >

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Extract Chain ID
by Amjad Farooq 28 Oct '13

28 Oct '13

Hi everyone, Is it possible to perform an automatic search of a multi-chain PDB template with a known protein sequence that is to be modeled (say 100-200 residues in length) and then extract the chain ID of the segment of the PDB template that best matches with the query sequence. As far as I understand, if you align a protein sequence against a multi-chain PDB template in MODELLER, it generates an alignment file (PIR/PAP) that does not automatically give you the chain ID of the PDB segment against which the alignment has been performed. Of course, this is a non-issue if you work manually but I would like to automate modeling for a large number of sequences. Any insights would be greatly appreciated. Thank you! Amjad *************************************************************************************************************************************************** *AMJAD FAROOQ PhD DIC | Associate Professor* Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad(a)farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net ***************************************************************************************************************************************************

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Check out my profile on LinkedIn
by Sako Mirzaie 28 Oct '13

28 Oct '13

LinkedIn ------------ I'd like to include you in my network to share updates and stay in touch. - Sako Sako Mirzaie assistant professor at university Iran Confirm that you know Sako Mirzaie: https://www.linkedin.com/e/-xaf1me-hnbd4jjr-2e/isd/17610846466/X2KwjCWW/?hs… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-xaf1me-hnbd4jjr-2e/3GpqQCFu9Ujj9Gys3027RLVJQStjD… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Re: [modeller_usage] missing sc atoms and rotamers
by micheal j twin 25 Oct '13

25 Oct '13

Dear Ben, thank you very much for your quick reply, I will try your suggestions. Regards Micheal > 1. Use complete_pdb() to make a complete structure for the second PDB (just with "wrong" sidechains). > > 2. Make an alignment using the two PDB structures as templates (presumably this a simple 1:1:1 100% identical alignment). Use the output structure from step 1 as the initial model. > > 3. Override automodel's select_atoms() to select only the missing sidechains, and then build ?> comparative models as per usual. Those sidechains should inherit the dihedral preferences from the first PDB. Dear Lalith, As I said, I'm really new to modeller but I will help you with this when I figure out how to perform Ben's suggestions. Regards Micheal > Dear Michael. > I am also working and facing with the same kind of issue through Modeller. I mean I have to copy residues selectively from two different templates for my homology model and have to follow exactly the same steps as Ben suggested to you in the last reply. Here, I am unable to use the initial model for my second strep model generation. I am facing the usual error (saying 'No atoms are specified from input file) as reported earlier by others. Please let me know if you could successfully execute this step. > Thank you in Advance > > Regards, > Lalith

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missing sc atoms and rotamers
by micheal j twin 24 Oct '13

24 Oct '13

Dear all, I'm new to modeller and I hope you can help me to solve this simple problem. I have 2 pdb structures of the same protein but with two different ligands. The first pdb is complete while in the second structure some sidechainsatoms are missing. What I need is to simply complete the missing sidechains in the second pdbon the basis of the rotamers they have in the first structure. Please, excuse me if this subject has been already addressed elsewhere Thank you Micheal

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cryo-EM maps
by Leonardo Herrera 22 Oct '13

22 Oct '13

* Hi all I am building a model and i am using a cryo-EM data. I want to make my own TvLDH.10A.mrc map to my protein , but i i don't know how can i do this ? anybody can help me or can explain me how can i do it ? thanks in advance * -- MenB Leonardo David Herrera Zúñiga POSGRADO EN QUÍMICA UAMI Biofisicoquímica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674

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Scattered homology model based on multiple temlpates
by Lalith Kumar 21 Oct '13

21 Oct '13

Hi all, Last week, based on my Query regarding '*Modelling with Side Chain Restraints*', I have prepared my script (see attachment) and built a homology model of a heterotrimer. Eventhough, I restrained the movement of side chains of those copied residues, I failed in keeping my model intact. I mean, my model has got gaps equal to the number of templates. I can say that the templates are not superposed (default by MODELLER) and therefore residues copied from each template have fallen apart with out getting joined to each other. Hope so I have gave a clear idea about the situation. Please let me know if anything more to be provided from my side. Thanks in Advance Regards, Lalith -- Lalith Kumar K Research Associate, CADD Division, Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of Life Sciences) University of Hyderabad Campus Gachibowli, Hyderabad 500046, India Tel: +91 9502074040

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Problem importing modeller and _modeller modules
by Gustavo Machado Alvares de Lima 18 Oct '13

18 Oct '13

Hi, I'm trying to import modeller modules to python in order to create custom scripts for my needs. When I used the 32bit version of ubuntu (or debian), it works perfectly. When I try to run the same script in a 64bit OS, python cant find modeller. I added /usr/lib/modeller9.12/modlib/ to python path, and python can import modeller, but in the /usr/lib/modeller9.12/modlib/modeller/__init__.py it tries to import _modeller module, and that one I cant find/add. I also added LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/modeller9.12/modlib", with no success. I'm using ubuntu 13.04 64bit, but I have this same problem in some other distros, like Mint linux (even 32bit on this one). How can I locate and add the _modeller module to my pythonpath? Thanks in advance

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