- modeller_usage - salilab.org

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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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 ^

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Restraints in table 6.1
by abdullah ahmed 22 Mar '10

22 Mar '10

Dear Modeller users, I have a few very long (and perhaps naive) questions regarding "Table 6.1: List of physical Restraints types" If the Hydrogen bonding restraint is applied, does it automatically incorporate all possible Hydrogen bonds in the file, or do the specific hydrogen bonding atoms have to be specified? (Also could you maybe provide a short piece of code showing how this restraint can be applied?)Are the Phi, Psi, omega, and Chi restraints used to lock the angles of the backbone and the the side chain into specific values or are they used for something else all together?What do the accessibility, absposition, dihedral_diff and SAX restraints do? Thank you in advance for your replies, Abdullah Ahmed _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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Lennard Jones Restraints
by abdullah ahmed 19 Mar '10

19 Mar '10

Dear Modeller users, If Lennard Jones restraints are activated during optimization using "env.edat.dynamic_sphere = True" What does this do exactly? Thank you in advance, Abdullah _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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set topology for autobuilder.
by Knut J Bjuland 19 Mar '10

19 Mar '10

I used thesse commando to set toplogy information when doing an alignment. BUt it did work when I wanted to build it. What kind of command should I invoke to add thesse information in the build phase of modeller. env.libs.topology.read(file='$(LIB)/top_allh.lib') env.libs.parameters.read(file='$(LIB)/par.lib') _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969

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If I disable the default N and C-term patched, must I manually apply them?
by wayj86 wayj86 19 Mar '10

19 Mar '10

Hi all, I hope to model a protein which is only a part of a big one (i.e. not up to its real N or C-terminal). So I turn off the default N and C patches with "patch_default=false". In this case, must I manually apply neutral patches, like ACE and CT3 to my model? I mean, can Modeller work wothout any N and C-term patches? I asked this because my next step is docking, which did not require any preexisting terminal patches. Thank you. Best wishes, Stanley -- Be the change you want to see in the world.

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