- modeller_usage - salilab.org

pdb code
by si yang 21 Dec '11

21 Dec '11

Good day to all, I have encountered a small problem during model.evaluation, the normalized dope.py requires to load a built model as indicated below: # Read a model previously generated by Modeller's automodel class mdl = complete_pdb(env, '../atom_files/xxx.pdb' right now the xxx should be replaced by the pdb code such as 1fdx, however my protein sequence is not yet deposited into PDB, thus it does not has pdb code, i just name it as MBL.B99990003.pdb (for example) after the atom_files: mdl = complete_pdb(env, '../atom_files/MBL.B99990001.pdb' However, the error stated that the pdb file is not a valid file, so do any expert provide suggestion to solve this problem?? Your response is appreciated.... Regards, Zhao Yang Institute of Bioscience UPM, 43400, Serdang Selangor, Malaysia

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Re: [modeller_usage] Who is best among these to search templates?
by Mensur Dlakic 19 Dec '11

19 Dec '11

First, as to the differences between CS-Blast and HHpred, please consult the two links below: http://lmgtfy.com/?q=hhpred+wiki&l=1 http://lmgtfy.com/?q=cs-blast+wiki&l=1 There is no absolute way to answer your second question. CS-BLAST provides only a starting (and context-dependent) checkpoint for BLAST or PSI-BLAST, from which those programs usually find more homologues than when they start from a single protein sequence. HHpred, however, further uses all sequences found by PSI-BLAST, aligns them and makes hidden Markov models, and then performs HMM-HMM search which is at present the most sensitive way to detect homology. The problem with HHpred is that even though it is most sensitive, it doesn't contain all PDBs in its library, so PSI-BLAST jump-started by CS-BLAST may still end up finding a better alignment simply because, unlike HHpred, it searches against all PDB sequences out there. Publications about both methods and their respective web pages offer clear descriptions of what each approach can do. Shouldn't be too hard to find them using PubMed. Take care, Mensur At 03:37 AM 12/19/2011, you wrote: >Respected Sir, >First of all sorry for a bit unrelated question to MODELLER, but please >tell me, what is the difference between >1. CS-BLAST >2. HHpred > >Who is the best of these two at searching most reliable homologoua >templates (PDBs) for a target sequence? I am not able to find differences >between these two. > >Thank you Sir and Sincerely, >Ashish > > > >Ashish Runthala, >Lecturer, Structural Biology Cell, >Biological Sciences Group, >BITS, Pilani >Rajasthan, INDIA >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >https://salilab.org/mailman/listinfo/modeller_usage ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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Who is best among these to search templates?
by Ashish Runthala 19 Dec '11

19 Dec '11

Respected Sir, First of all sorry for a bit unrelated question to MODELLER, but please tell me, what is the difference between 1. CS-BLAST 2. HHpred Who is the best of these two at searching most reliable homologoua templates (PDBs) for a target sequence? I am not able to find differences between these two. Thank you Sir and Sincerely, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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What is the difference in salign_multiple_struc among these 2 conditions
by Ashish Runthala 14 Dec '11

14 Dec '11

Dear Modellers, I am a bit confused about the utility of auto_overhang=true usage in salign_multiple_struc.py for MSA computation. Even if i don't use this line, result comes the same as _fit files are generated. Same is the case when i don't use this line before computing the alignment writing the result. Alignment files generated are also same in both these cases, both including the sub-optimal alignments. Please explain me this difference. Is it that auto_overhang option is integrated in salign_multiple_struc.py and is employed automatically without being called for it. Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] windows 7, modeller 9.10 and python 2.6.6
by Modeller Caretaker 09 Dec '11

09 Dec '11

On 12/09/2011 03:46 PM, Ludovic Autin wrote: > the installation didn't change the environment variable in the > Computer properties even if I launch the installation as administrator Right, but it doesn't need to for it to work with Python. What environment variables did you set? You could try removing them and see if that fixes the problem. > I have a totally different question, did you plan to support > python3.2 universal binary for Mac os 10.6 and +? No, we only support the standard version of Python (/usr/bin/python) shipped with OS X. > I currently use it, and I cant import modeller We distribute all the SWIG inputs to build the Modeller Python extension, in src/swig/, so in principle you can build it for a newer version of Python if you like (the rest of the Modeller Python code will already work with Python 3). Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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windows 7, modeller 9.10 and python 2.6.6
by Ludovic Autin 09 Dec '11

09 Dec '11

Hi, until I never add any problem with MODELLER, which is a really nice software. I recently encounter a problem on windows 7-64bits. Python2.6.6 32bits is installed as well as a python2.7 64bits version. Modeller 9v10 is installed and seem to work. The problem is accessing modeller from Python 2.6.6. After setting all the environment properly for modeller, inside python I got this error : import _modeller ImportError : DLL load failed: La procedure specifie est introuvable (sorry for the french, ie file not found) Its seems that there is some library that cant be found. I used dependancy walker to see what was the dependancy of _modlib.so in modlib/python2.6/ and it appear to be libmodlib.dll that is in the bin directory... I try to add the bin directory ion the path but didnt solve the problem... Any idea what could cause this confusion/problem ?? what should I do ?? Thanks a lot in advance, any help is welcome Ludovic

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have problem running modeller 9.10
by Yu Li 04 Dec '11

04 Dec '11

Hi, I am trying to use modeller to model a chimera protein. I am going through the online tutorial and documentations. However I found that I cannot run modeller on my computer. I have a windows 7 machine with python 2.7 installed. The error message I got when I type mod9.10 model-default.py in command window is: 'import site' failed; use -v for traceback Cannot open logfile model-default.log: Permission denied. I am in the same fold as the model-default.py file. Anyone know what is going on? Many many thanks.

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Enc: Error with import os
by Bruno Madio 30 Nov '11

30 Nov '11

Dear Modeller, When I try to do anything with modeller9.10, an error menssage occurs with "C:\Program Files (x86)\Modeller9.10\modlib\modeller\__init__.py" line 51 and I can´t import "os" from "C:\Program Files (x86)\lib\os.py" line 106. Please, could you help me fix this bug? I have read the release notes, but I still could not fix the error. Could you teach me step by step? All the best, Bruno Madio

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 148
by Ashish Runthala 30 Nov '11

30 Nov '11

Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!) Sorry to say sir benn, but MODELLER do refine the models to some extent if the mutual orientation of individual domains in a multi-domain structure or the initial models's topology is correct and parallel to the actual native structure. But all this fun of pulling the models closer to native state works well only when the correct model decoy is correctly selected for. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, November 30, 2011 7:32:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 148 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Refine part of an existing model (Modeller Caretaker) 2. Is there any Modeller Script to refine unaligned loop chunks (Ashish Runthala) 3. Enc: Error with import os (Bruno Madio) ---------------------------------------------------------------------- Message: 1 Date: Tue, 29 Nov 2011 12:22:25 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Refine part of an existing model To: flavio seixas <oivalf_nix(a)yahoo.com>, Modeller Queries <modeller_usage(a)salilab.org> Message-ID: <4ED53F01.2020907(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 11/29/2011 03:03 AM, flavio seixas wrote: > I was studing Modeller manual and I am not sure if there is a routine > in modeller that can refine only part of an existin model, like loop > refinement do. Just build a new comparative model using the regular automodel class, using your original model as the template. Use a simple alignment containing two copies of the model sequence. Override select_atoms() as per the example at http://salilab.org/modeller/9.10/manual/node23.html to define the region to refine. Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!) > However, the region that I am interested to refine is > not a loop. Because of this, I can not use loop refinement in helical > segments, even though a region of three residues. Loop refinement can be used for any region without a template. The protein can adopt any secondary structure, including an alpha helix. But yes, typically loop refinement will give you coil structures. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Wed, 30 Nov 2011 15:02:09 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] Is there any Modeller Script to refine unaligned loop chunks To: modeller <modeller_usage(a)salilab.org> Message-ID: <10902351.27461322645529168.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem. Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region. SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE. Thanks a lot, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 3 Date: Wed, 30 Nov 2011 05:48:11 -0800 (PST) From: Bruno Madio <brunomadio(a)yahoo.com.br> Subject: [modeller_usage] Enc: Error with import os To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Message-ID: <1322660891.50858.YahooMailNeo(a)web45310.mail.sp1.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear Modeller, When I try to do anything with modeller9.10, an error menssage occurs with "C:\Program Files (x86)\Modeller9.10\modlib\modeller\__init__.py" line 51 and?I can?t ?import "os" from "C:\Program Files (x86)\lib\os.py" line 106. Please, could you help me fix this bug? I have read the release notes, but I still could not fix the error. Could you teach me step by step? All the best, Bruno Madio

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Is there any Modeller Script to refine unaligned loop chunks
by Ashish Runthala 30 Nov '11

30 Nov '11

Dear Modellers, Though there are many problems in modeling the loop regions, but even when there is no insertion in the loop region and is devoid of any higher order localized structural topology, the loop residues are just connectors. Here also i am seeing some problem. Even when the periphery is at a minimal distance threshold to native state making the GDT_TS or even GDT_HA very high, the RMSD i found was much more than expectation. So the model scrutiny revealed the complexity in the loop region. SO IS THERE ANY SCRIPT IN MODELLER WHICH REFINES ALL LOOP CONNECTORS THROUGH MD CONJUGATED GRADIENT, MAKING THE RMSD ALSO DROOP DOWN AS IS THE CASE FOR GDT OR TM-SCORE. Thanks a lot, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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