- modeller_usage - salilab.org

PDBs missing chains
by Daniel Fernandez 02 Apr '10

02 Apr '10

Hi, I am trying to use modeller to fill in missing side chain or backbone atoms in the 1ahoa protein. Do you have any suggestion on how to do that using modeller, i.e., which one I should use as a template and as a target protein for that problem. I am relatively new to the software and protein modelling literature. Any help would be strongly appreciated. Best, Daniel

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Preparing input files
by Daniel Fernandez 02 Apr '10

02 Apr '10

Hi, I think I will start with a more basic question. I am new to modeller and bioinformatics in general. If I have a target protein, i.e., 1ahoa protein I want to model, how can I prepare the input files (i.e. alignment and template files) for that protein??? any suggestions? tutorials or read about this? the modeller tutorial assumes one knows how to prepare the files to be read by modeller, and I actually don't know that part. Any advise would be strongly appreciated. On Fri, Apr 2, 2010 at 12:33 PM, Daniel Fernandez <dfernan(a)gmail.com> wrote: > Hi, > > I am trying to use modeller to fill in missing side chain or backbone atoms > in the 1ahoa protein. Do you have any suggestion on how to do that using > modeller, i.e., which one I should use as a template and as a target protein > for that problem. I am relatively new to the software and protein modelling > literature. Any help would be strongly appreciated. > > Best, > > Daniel > -- Daniel F. Department of Statistics, Harvard University 1 Oxford Street, Cambridge, MA 02138

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Tethering
by abdullah ahmed 01 Apr '10

01 Apr '10

Dear Modeller users, I would like to ask if there is a function that causes "tethering" or "atom fixing" during optimization in modeller (i.e. is there a function that forces the molecule to remain close to it's original PDB during optimization?) If so, is there a way to turn it off? Thank you in advance, Abdullah Ahmed _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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Side chain dihedral angles
by abdullah ahmed 01 Apr '10

01 Apr '10

Dear Modeller users, I wanted to asked if there is a way to restrain the side-chain dihedrals to angles of my choosing. If so could you please provide a brief sample code of how to do it? Thank you in advance, Abdullah _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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side-chain restraints
by abdullah ahmed 30 Mar '10

30 Mar '10

Dear Modeller users, I have two proteins with interacting side chains. I would like to make distance restraints between their Glutamine atoms to ensure that they are a fixed distance apart. To do so I used the following code during optimization: mdl.restraints.add(forms.upper_bound(group=physical.sd_sd_distance, feature=features.distance(a['HE21:2:A'], a['OE1:24:B']), mean=1.9, stdev=0.3)) However, no change has been made to these atoms in the optimized PDB file. Furthermore, the log file shows that all 72 restraints of this type that were applied have violations. It looks as though the program has noted that restraints need to be made, but then does nothing to make these restraints. The only other restraints are: mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) Thank you in advance for your help, Abdullah Ahmed _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Weights of restraints
by abdullah ahmed 30 Mar '10

30 Mar '10

Dear Modeller users, Is there a way to give preference to (or up-weight) one set of restraints over another? I have made distance restraints (group=physical.xy_distance) as well as "restraint_type = stereo" and would like for the distance restraints to be satisfied even if they cause violations of the "stereo" restraints. Thanks in advance, Abdullah _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Re: [modeller_usage] special restrains for aromatic packing interactions
by Thomas Evangelidis 29 Mar '10

29 Mar '10

Is it possible to set the distance cutoff between a given atom of the protein and a subset of atoms in the ligand? E.g. in some crystal structures OG1 of a THR forms an H-bond with O1A of ATP, whereas in others with O2A. In that case can I force Modeller to keep (THR44:OG1 - ATP266:O1A <= 3.5+-0.1) OR (THR44:OG1 - ATP266:O2A <= 3.5+-0.1) ? 2010/3/24 Modeller Caretaker <modeller-care(a)salilab.org> > On 03/23/2010 08:46 AM, Thomas Evangelidis wrote: > >> Since the phosphate groups of ATP are forced to lie within 3.5 A. from >> the binding site residues, the Tyrosine ring will be in close proximity >> to the Adenine ring. So I was thinking about adding a Coulomb or LJ or >> SHPERE restraint including only the adenine and tyrosine rings. >> > > Right, but all the restraints you mention are atomistic pairwise > restraints. You can't restrain two rings, only two atoms. > > > If yes how can I measure the values (i.e. energy value >> for LJ) from the templates? >> > > You can measure the template distance in any reasonable PDB viewer, such as > Chimera. Then I'd suggest you just use simple Modeller harmonic pairwise > distance restraints with a mean corresponding to the measured distance, and > tweak the standard deviation until things look right. The reason I suggest > harmonic rather than Coulomb or LJ terms is that unless you're > super-confident the form of the potential is inverse square or 6-12, those > mathematical forms don't make sense. And there's no way you'd be able to > accurately parameterize either interaction short of doing a lot of high > basis set QM calculations. So you're probably better off with a simple > harmonic. > > > 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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energy units
by abdullah ahmed 25 Mar '10

25 Mar '10

Dear Modeller users, I have a question related to the calculation of energy during optimization. What are the units (Joules/calories/ Kilo joules etc?) of the energy calculated? (The "current energy" value in the log-file, for example, is a number. I'd like to know the units that correspond to it) Thanks in advance! Abdullah _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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error in using mutate_model
by Anna Marabotti 24 Mar '10

24 Mar '10

Hallo, I tried to model a mutant of a protein using the mutate_model.py script available in the Wiki section of MODELLER site at: http://www.salilab.org/modeller/wiki/Mutate%20model. Therefore, after copying the script on a executable file, I opened the black window to launch Modeller commands and typed, as suggested: python mutate_model.py my_modelname my_respos my_resname my_chain > my_log.log but obtained the error: "python is not recognized as internal and/or external command, or as an executable, or as a batch file" despite I have Python installed on my PC. I also tried to launch the command without "python" and typed: mutate_model.py my_modelname my_respos my_resname my_chain > my_log.log and this time the error was: File "C:\Programmi\Modeller9v7\mutate_model.py", line 4, in <module> from modeller import * File "C:\Programmi\Modeller9v7\modlib\modeller\__init__.py", line 69, in <module> import _modeller ImportError: No module named _modeller The program ends without writing the .log file. I used this script with the previous versions of Modeller, on the same PC, without any problem. It's the first time I use this script since I installed Mod9v7 on my PC, but I've already used Modeller 9v7 on the same PC without problems. Could anybody suggest me how to do? Many thanks in advance and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabotti(a)isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito"

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Fw: mutation error
by leuven 23 Mar '10

23 Mar '10

Dear: I try to make mutation model by this scrips: http://salilab.org/modeller/wiki/Mutate%20model When I typed command in terminal: py2 1-nh-active.pdb 97 VAL A>mute-native.log It is said: ATOM 1 CB THR A 1 57.352 108.506 46.727 1.00 21.29 A ^ SyntaxError: invalid syntax I don't know where is the mistake. Thank you very much.

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