March 2010 - modeller_usage

question about unusual bond length, bond angle, Chirality deviations
by Song, Hyundeok (songhk) 15 Apr '10

15 Apr '10

Dear Modeller users I generated the dimer by Modeller. Fasta sequence number of model(400) is 70 less than Fasta sequence number of template(470). Sequence identity between template and model is 24%. after selecting the template, I aligned them, and then I did loop modeling. (I attached the code at the bottom.) Finally I got final pdb structure, but when I checked my model, I found the below warning message. "Unusual bond length, unusual bond angle, Chirality deviations " I am a beginner, so I don't what should I do to correct above warning message. Please help me, Any suggestions or comments are welcomed. Thanks. Hyun. ---align2d.py---- from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='****', model_segment=('FIRST:A','LAST:B')) aln.append_model(mdl, align_codes='******', atom_files='*****') aln.append(file='******.ali', align_codes='*****') aln.align2d() aln.write(file='**************.ali', alignment_format='PIR') aln.write(file='**************.pap', alignment_format='PAP') ---model-loop.py----- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = '***************.ali', # alignment filename knowns = '*******', # codes of the templates sequence = '******') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 50 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do homology modeling

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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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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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