- modeller_usage - salilab.org

How can I get MolPDF of an existed PDB file of an model
by Yun He 07 Jun '06

07 Jun '06

When I use automodel class to generate N models, the energy MolPDF of every model will be displayed in the log file, e.g. =========================================== >> Summary of successfully produced models: Filename molpdf ---------------------------------------- T0291.B99990001.pdb 2029.54651 T0291.B99990002.pdb 2719.03467 T0291.B99990003.pdb 2009.53479 T0291.B99990004.pdb 2688.20435 T0291.B99990005.pdb 2311.00342 =========================================== But, sometimes, after the models got be refined by some other means, how can I get those changed molpdf by handling the existed PDB files, rather than to involve the automodel class again to rebuild such models? I think "examples/commands/energy.py" in node151.html of the manual may help me, but I wonder whether the molpdf got by this method is identical to that recorded in log file.

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Re: [modeller_usage] loop optimization problem
by Agnieszka Szarecka 07 Jun '06

07 Jun '06

Hello Modeller Users, I am trying to run the loop structure refinement using loop_refine.py. I have several 3-5 residue long gaps in my pdb structure and I am trying to get them "patched". The program crashes with "..... ddihedr_262E> Central bond too short: 0.000" I checked the structures (they seem fine) and actually tried running three different loops and the same error pops up. Would anyone have an idea what the problem is and how I should fix it? Also: I ran the same time type of calcs with mod8v1 and had no such problems. The only difference is that I switched from Linux to Windows for this run. tons of thanks for help, Agnieszka

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Save y0ur budget, p0werful medicine for a l0w price.
by Juanita 02 Jun '06

02 Jun '06

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Averaged RMSD for 100 models
by Robert Selwyne 01 Jun '06

01 Jun '06

Dear Benn Good Day !!!!!!!!!!!!! I had run MODELLER to produced model 1-100.pdb (100 models) of same acid sequence but different energy values. Now, i want to calculate the RMSD values for the models. I know that SUPERPOSE will do for me. But i couldnot correlate and implement the results. Say in VMD 1.8.4 in the RMSD calculator option, if Average is selected, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure. By the same manner, my first model is model1.pdb and now is superpose my model2.pdb and calculate an averaged RMSD. And on the next step i have to superpose my model3.pdb to the averaged structure and calculate new averaged RMSD and so on. model1.pdb | superposition | model2.pdb | now two structures are merged/superposed | calculate the averaged RMSD for the merged/superposed structure | now superpose model3.pdb to the existing superposed structure (model1.pdb+model2.pdb) | now totally 3 structures are superposed | CALCULATE AVERAGED RMSD FOR PRESENT SUPERPOSED STRUCTURE (MODEL1+MODEL2+MODEL3) and so on Could you please help me in carrying out the problem. can you help me in knowing how the script file looks. WIth regards robert Send instant messages to your online friends http://in.messenger.yahoo.com Stay connected with your friends even when away from PC. Link: http://in.mobile.yahoo.com/new/messenger/

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What's the difference of "refinement level" in MD
by Yun He 28 May '06

28 May '06

As subject, how much difference does the FAST or SLOW refinement level effect the final models in MD? Does it really worth for a loooong computation to build a more accurate model?

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code
by N.Arun Prasanna 25 May '06

25 May '06

sir, I have seen the advanced tutorial. The example there gives how to code when user wants to define restraints. But how to code for the one where I want to use the default restraint in my template? Just I want it to extract the hetatm present in the template and model it. It will be of great use if u help me in this regard. Thank you. prasanna

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Model protein with ligand bound
by N.Arun Prasanna 23 May '06

23 May '06

Sir, Is there any option to model a protein bound to ligand? Say a template used is complexed with ADP.. Regards, prasanna

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code
by N.Arun Prasanna 23 May '06

23 May '06

Sir, It will be of great help if u can send me a general py code to model using a template (1YMF) with HETATM -ADP Regards, prasanna

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Model a Tetramer from a Dimer
by Yun He 22 May '06

22 May '06

Hi, everybody, I have read some interesting threads about how to build a multi-chain model, but these questions are usually focused on building from templates with the same number of chains. Here is my question, how could I build a tetramer from a dimer, if any chain of this tetramer is similar to the chain of that dimer. Jarod

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GA341/DOPE/MolPDF which one for model selection?
by Yun He 22 May '06

22 May '06

Hi, everybody, Currently, I am working on a model based on a very low sequence-identity template (about 13%). I use an alignment to produce 30 models, and then I sort these models by their molpdf or GA341 or DOPE. However, the sorts turn out very different results, some models with higher GA341 scores takes higher DOPE scores. I am confused, which one should I choose? Jarod

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