modeller_usage

modeller_usage@salilab.org

3151 discussions

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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Fwd: [ModPipe-users] Installation Issues
by Amjad Farooq 18 Oct '13

18 Oct '13

Hi Ben, That worked. I was able to generate the "mod9.12" script inside /bin directory of modeller 9.12 under $MODPIPE/ext/mod/. However, when I run a test under /tests, I get the following error: > make ************************************************************************** cd unit && ../../int/runscript.sh python run-all-tests.py -v > /dev/null /bin/sh: ../../int/runscript.sh: No such file or directory make: *** [unit] Error 127 ************************************************************************** Where is this ../../int/runscript.sh script? The /int directory is empty! Also, when I run a demo under /demo, I get this error: ************************************************************************** Traceback (most recent call last): File "AddSeqMP.py", line 17, in <module> import modpipe.version ImportError: No module named modpipe.version ************************************************************************** Any thoughts on what I may be doing wrong? I have tried to follow installation instructions for MODPIPE as closely as possible: http://salilab.org/modpipe/doc/intro.html#getting-modpipe Thanks very much, Amjad ---------- Forwarded message ---------- From: Ben Webb <ben(a)salilab.org> Date: Fri, Oct 18, 2013 at 12:15 PM Subject: Re: [ModPipe-users] Installation Issues To: Help and discussion for users of ModPipe <modpipe-users(a)salilab.org> Cc: Amjad Farooq <amjad(a)farooqlab.net> On 10/17/13 7:50 PM, Amjad Farooq wrote: > How does one install MODELLER 9.12 inside ModPipe? I have MODELLER 9.12 > installed on a linux machine and it runs fine. But, I am having some > issues with installing MODELLER 9.12 inside ModPipe. > Download the Modeller .tar.gz installer, run the Install script, and tell it to install in $MODPIPE/ext/mod/. Once that's done, there should be a mod9.12 script in the bin subdirectory. Is there a way to tell ModPipe to read in automatically pre-installed > MODELLER 9.12 at another location > No, but you could probably make it work with some symlinks if you really don't want to have two copies of Modeller. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Fwd: Installation Issues
by Amjad Farooq 18 Oct '13

18 Oct '13

Dear Ben, How does one install MODELLER 9.12 inside ModPipe? I have MODELLER 9.12 installed on a linux machine and it runs fine. But, I am having some issues with installing MODELLER 9.12 inside ModPipe. According to the instructions, one should make changes to the $MODPIPE/ext/mod/bin/modXXX executable: http://salilab.org/modpipe/doc/install-ext.html#install-ext But, I do not see modXXX under the bin/ directory in MODELLER 9.12? The only scripts available under the bin/ in MODELLER 9.12 appear to be: mod9.12_i386-intel8 modpy.sh.in modslave.py Is there a way to tell ModPipe to read in automatically pre-installed MODELLER 9.12 at another location instead of installing it again under $MODPIPE/ext/mod/ on the same machine? Can you please help?! Thanks very much, 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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modeller_usage