- modeller_usage - salilab.org

how to analyse the output file of align2d.py
by Naresh 30 Jan '12

30 Jan '12

mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. I checked for the template sequence in the pdb_95.pir. but unfortunately I could not find any template sequence for the templates which I selected from the blast result.

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modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 3O96
by Naresh 29 Jan '12

29 Jan '12

I am getting this error when I run model-single.py I am using windows 7 OS, modeller9.10, python3 The other commands (build_profile, align2d, compare) run successfully .. C:\Program Files\Modeller9.10\bin\akt3>mod9.10 model-single.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-single.py", line 9, in ? a.make() File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 96, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 408, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller9.10\modlib\modeller\automodel\automodel.py", l ine 398, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller9.10\modlib\modeller\alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was n ot found in the alignment file; ALIGN_CODES( 1) = 3O96

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Import Error: No module named _modeler
by Naresh 28 Jan '12

28 Jan '12

Hi, I am new to modeller, I followed the tutorial and ran this command model-default.py I got the following error, Import Error: No module named _modeller Could you please suggest me with some best solution

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Re: [modeller_usage] Is there a way to it?
by Modeller Caretaker 11 Jan '12

11 Jan '12

On 1/10/12 7:34 PM, Ashish Runthala wrote: > Respected Sir, > Are you saying about this line? > for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), > ((1., 0.5, 1., 1., 1., 0.), False, True), > ((1., 1., 1., 1., 1., 0.), True, False)): That looks like a loop from one of the SALIGN example scripts, which simply calls SALIGN three times. If you look further down in the script you will see this: aln.salign(..., feature_weights=weights) i.e. SALIGN is being called with the weights given by the first argument in that 'for' statement above. > What do each of the 6 float constants represent? They're weights - just numbers that multiply each feature's distance matrix. The distance matrix used by SALIGN is simply a linear combination of these. > Also tell me What you exactly mean by feature_weights=[0]*6. I mean exactly what it says - that's elementary Python syntax. [0]*6 is the same as saying [0,0,0,0,0,0]. In other words, all of the features will have zero weight, so SALIGN won't calculate any of them. 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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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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