- modeller_usage - salilab.org

Is there a way to it?
by Ashish Runthala 10 Jan '12

10 Jan '12

Dear Modellers, Is there a key to increase gap penalty scheme for different factors, like residue compatibility, Solvent Accessible Surface Area, depth of residue center from the molecular surface etc. Your help is appreciated. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] What is Modeller v9.10 , can you explain to me?
by Modeller Caretaker 06 Jan '12

06 Jan '12

On 01/06/2012 09:18 AM, Reincarnation Mourir wrote: > If I use 'Modeller v9.10'. Do I necessary/need to use 'Modeller > v9.10' with 'Sybyl Program' or not? No, you do not need Sybyl to use Modeller. Modeller is fully functional by itself. (In fact, to the best of my knowledge Sybyl only works with extremely old versions of Modeller anyway - these days Sybyl has been replaced with Discovery Studio.) > Can I use 'Modeller v9.10' with 'Python' or not? Yes, Modeller works with any version of Python between 2.4 and 3.2. > What is difference between use Modeller v9.10 with 'Python' *on > **Linux *and use Modeller v9.10 > with 'Python' *on **Windows Xp and **Windows 7*. Modeller will work in the same way on Linux and Windows. However, if you want to use other Python modules in combination with Modeller, you may find it easier to use Linux. 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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Plot profile of All or selected assessment methods
by junior 06 Jan '12

06 Jan '12

Dear Sir, I have a question. What commands are required in a Python script, 'evaluate_model.py', to, edit/prepare, 'plot_profiles.py', to, run linear plots of, selected assessment methods (assess.methods) or All , .i.e., GA341 scores' , DOPE-HR scores, normalized DOPE scores, apart from default, DOPE scores and MOLPDF graph plots? Sam Kauba (Mr.) Post-Grad Honors candidate c/- Chemistry Department School of Natural & Physical Science University of Papua New Guinea P.O Box 320 UNIVERSITY P.O Waigani, NCD 131 Port Moresby Papua New Guinea

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CSA incorporation in salign
by Ashish Runthala 05 Jan '12

05 Jan '12

Dear Modellers, Is there any way to incorporate CSA (Conformational Space Annealing)alignment approach in Salign_multiple_struc.py? Or is there any similar script in MODELlER which computes such alignments? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Error in opening log file.
by Prija Ponnan 03 Jan '12

03 Jan '12

Hello I am using Modeller 9v8 and while executing model-disulfide.py, I am encountering the following error. *C:\Program Files\Modeller9v8\examples\crmodel>mod9v8 model-disulfide.py 'import site' failed; use -v for traceback Cannot open logfile model-disulfide.log: Permission denied* Please Help me to find a solution to this problem. Thank you Dr. Prija Ponnan Dept. of Chemistry University of Delhi,Delhi,India

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Is it possible to change the output file directory?
by 조윤성 03 Jan '12

03 Jan '12

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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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