- modeller_usage - salilab.org

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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extended conformations
by fantasticqhl 16 Oct '13

16 Oct '13

Dear all, I am trying to construct a model with two chains, the conformation of the template is extended helix, However, the conformations of the model I got were folded, the C-terminal is very close to the N-terminal. It is not extended which is what I want. How can I do to make sure that the conformation of the models are extended? All the best, Qinghua

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channel-like structure
by fantasticqhl 15 Oct '13

15 Oct '13

Hi all, I want to construct a model of channel-like hexamer based on a monomer peptide, is that possible with modeller? If yes, is there some similar tutorials, or could you please give me some suggestions? Thanks in advance! All the best, Qinghua

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constraints failed
by fantasticqhl 14 Oct '13

14 Oct '13

Dear all, I am trying to construct a model with four HIS binding to a copper. I set the distance constraints for ND1--CU as 2.0 angstrom, but the distances between ND1 and CU of the constructed models are around 2.5 angstrom, it seems that the constraints failed. Acctually, when I checked the model, I found that the distances could be around 2.0 angstrom if CU was just moved a little bit. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['ND1:13:X'],at['CU:43:Y']), mean=2.00, stdev=0.05)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['ND1:14:X'],at['CU:43:Y']), mean=2.00, stdev=0.05)) Could someone tell me what kinds of reasons could result in restraints failure? Thanks very much! All the best, Qinghua

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problem in using mutate_model.py
by Anna Marabotti 10 Oct '13

10 Oct '13

Dear Modeller users, I created several mutants of my protein (which is a homodimeric protein) using the script mutate_model.py.and all has gone perfectly, but I have a problem in introducing a mutation. I want to introduce mutation in position 321 of both chains. So, I started introducing mutation in chain A using the command: mod9.11 - myprot 321 TYR A <mutate_model.py> myprotTYR321.log and all went OK. When I introduced the mutation in chain B starting from the mutant obtained in the previous step, using the command: mod9.11 - myprotTYR321 321 TYR B <mutate_model.py> myprotTYR321TYR321.log MODELLER gave me the following error message: OverflowError:check_inf__E> Atom 5347 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. The strange thing is that if I start introducing the mutation from chain B using the command: mod9.11 - myprot 321 TYR B <mutate_model.py> myprotTYR321-B.log MODELLER stops with the following error: OverflowError:check_inf__E> Atom 5345 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. I had a look at the original structure; atoms 5345 and 5347 are, respectively, atoms CB and O of the residue preceding the mutant one, and no apparent problems are present in the protein structure (no distortions, no aberrant structures - the residue is inserted into a beta sheet). But assuming that I have a problem on my structure, why the problem is not in the same atom when I start mutating from chain A or from chain B, considering that the procedure involves exactly the same residue? Thanks a lot for your help, best regards Anna -- ______________________________________________ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabotti(a)unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index "Indifference is the eighth deadly sin" (don Andrea Gallo)

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