- modeller_usage - salilab.org

Imposing dihedral restraints
by Vivek Sharma 14 Jun '06

14 Jun '06

Dear Benn, I am having some troubles in putting dihedral restraints in the system I am modelling. Firstly, I should say I want to put backbone angles (phi/psi) into a stretch of 5 amino acid residues. I mention the values (these values are from database, in fact are right and do exist in one protein) with the std. deviation value ~ 15deg. And, I am using Modeller 7v7, sorry I am slow in updating myself ;). So for e.g. I put a dihedral restraint (say phi for e.g.) for a residue like this: SET ATOM_IDS = 'C:317' 'N:318' 'CA:318' 'C:318' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 11 4 2 0 -1 0.261 So now you can see here; Form is 3 Modality is 1 Feature is 3 (dihedral angle) group is 11 (Mainchain phi dihedral restraints) Numb_atoms = 4 Numb_parameters = 2 0 Value of angle in radians Std. deviation in radians. Now when I run modeller with such restraints, in the finally obtained models, I dont see these exact values of restraints, which we mentioned explicitly, taken in by the model. Why this is so? The values of these mentioned dihedral restraints in the modelled models are far from the prescribed values. Secondly, though I dont see any violation also in concern to these values, i.e. if I have understood correctly, then violation will be reported in the log file if (optimized value - value mentioned by used)/(std. deviation) > 4.5 (approximately something like that). So this makes clear that why violation is not reported, because our values (diff/std. devn) are less than 4.5. But the question is, that when I give value of 15 degree as std. deviation (which I have to, I will come to this point later!) , then difference between optimsed value and mentioned value ~ 60 degrees, and that is very much. So again what I say is that I want to put certain values of dihedrals (backbone angles in fact) in the model, but values obtained for these angles in optimised models are far from the values mentioned in by me (because range of difference is ~60 degrees), though there are no violations reported, probably because of the above mentioned reason. PLease tell me what to do in this concern. Now as I said above that I am giving 15deg as std. deviation,but when I use smaller values like 5deg or so, the program is getting failed, it seems that it is getting difficult for it to optimise the system, with smaller values of std. deviation. Also, please tell me how to solve this problem. Last but not least, what I tried or trying is that creating the gaps in this section of 5 residues, where I am imposing backbone dihedrals, so that MODELLER doesnt find any equivalent residues in that position in templates and probably reduces the number of restraints, and in that case I may be able to impose my restraints well enough for these five residues, but still results doesnt seems to go hand in hand. Any comments in this concern also will be helpful. Details: there are two templates, MD_LEVEL is refine_3, our own alignment and paramters are used. So overall these are the problems I am at the moment facing, so any comments/details, will be very helpful. PS: The subject is different from 'Problem', :). Thanks in advance, br, Vivek Sharma University of Helsinki.

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Modeling core residues without loop regions
by Vimalkumar Velayudhan 13 Jun '06

13 Jun '06

Dear MODELLER users, I was looking for answers to the following questions? 1. What is the best approach to model proteins with large insertions (approximately 50residues) at different parts of the protein. Example AAAAAA---------------------------------BBBBBB---------------------------------------------CCCC Even if the alignment is good, I get an exceeded maxmolpdf error in the model building stage. I am not sure what value to set for the maxmolpdf . 2.Is it possible to build only the core residues without the insertions? It would be helpful if you can point me to references related to the same. -- Vimalkumar Velayudhan

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Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model
by Modeller Caretaker 09 Jun '06

09 Jun '06

Yun He wrote: > On Thursday 08 June 2006 09:40, you wrote: >> The PDB files produced by Modeller also contain the molpdf, as a REMARK >> at the top of the file, so you can just read this. If you refine the >> structure, you should write out a new PDB file, which will contain the > ~~~~~~~~~~~~~ write out?? If I refine this model with > Refmac5 in CCP4, the refined model written by Refmac5 doesn't contain any > header remark about molpdf, how should I get the molpdf? Is this molpdf the > same as the one of the model not refined, or there are any ways to > re-calculate its molpdf? Scoring functions used by different programs are almost never comparable, so you can't do this. All you can do is to, like I said, write out the refined structure and then recalculate its molpdf in Modeller. 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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loop modelling
by hori koshii 08 Jun '06

08 Jun '06

Does MODELLER has a limitation for loop modelling up to 12 or 14 residues? What if I have 20 residues? Could you please give me some suggestions how to model a loop like this please? Thanks in advance! :) __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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DOPE profile
by Tom Burghardt 07 Jun '06

07 Jun '06

Modellers I would like to make a DOPE profile for a modeled protein containing a chemically modified side chain. I used the script suggested in the Advanced Tutorial with the following lines to read the library files containing information about the modified residue. env = environ(restyp_lib_file='${LIB}/restyp_tom.lib') env.libs.topology.read(file='$(LIB)/top_heav_tom.lib') # read topology env.libs.parameters.read(file='$(LIB)/par_tom.lib') # read parameters The DOPE profile is created by the script but the modified residue is left out of the profile. Any suggestions would be appreciated. Tom -- Tom Burghardt Department of Physiology and Biomedical Engineering Mayo Clinic

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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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