On Sat, Dec 25, 2010 at 11:30 PM, modeller_usage-request@salilab.orgwrote:

> Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: modified amino acids (Modeller Caretaker) > 2. DOPE and sequence/model length (Starr Hazard) > 3. Re: DOPE and sequence/model length (Modeller Caretaker) > 4. problem in doing difficuly modeling using modeller 9v8 > (ranu sharma) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Dec 2010 10:09:27 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] modified amino acids > To: Mike White mwhite@drexelmed.edu > Cc: ModellerUsage List List modeller_usage@salilab.org > Message-ID: 4D0A55D7.9050204@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/16/10 6:04 AM, Mike White wrote: > > I am trying to model a small (22 amino acids) peptide with 3 > > disulfide bonds using structures of 6 related peptides with Modeller > > 9.7. The template peptides have 1-3 modified amino acids > > (pyroglutamate, hydroxyproline, amidated C-termini) and the peptide > > to be modeled has an amidated cysteine as the C-terminus. > > Modeller cannot build models containing modified amino acids, nor can it > use structural information from modified amino acids in your templates > (the only exception is MSE, which Modeller treats as identical to MET). > > Your best option in this case is to edit your template PDB file to > convert the modified amino acids to their unmodified equivalents, build > models with regular cysteine, and modify the C-terminus of the > constructed models. > > > I tried setting env.io.hetatm= True to see if that made a difference, > > but then the routine failed with the following track back: > ... > > I'm not sure why env.io.hetatm = 'True' causes this error > > True and 'True' are two different things. True is a Python boolean; > 'True' is a string. Only the first will work here. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Thu, 16 Dec 2010 14:51:44 -0500 > From: Starr Hazard hazards@musc.edu > Subject: [modeller_usage] DOPE and sequence/model length > To: modeller_usage@salilab.org > Message-ID: 4D0A6DD0.2000407@musc.edu > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Folks, > > I have modeled some dimers of a large protein and a much shorter partner > (~350aa for X and about 80aa for Y) . There are crystal templates for > such dimers. The best resolution structures have different large and > small proteins. So I have templates with X'Y' and X''Y''. X' and X'' > are homologs as are Y' and Y''. The Y family is quite variable in > length. When homologs from distant organisms ( eg plant, fungi, fish > mammal) are aligned there are gaps compared to the mammalian templates. > > In mammals X' and X'' are in related but distinct clades. If I model a > yeast X protein to each mammalian template can I say that the yeast > protein is better represented by one or the other template based on a > DOPE score? ( the GA341 scores are not helpful since they are always > 1.000 for these models) > > This is several questions I guess. 1) Are DOPE energies normally > distributed? > Could I > statistically compare DOPE scores of models made with one template to > those from another template. > 2) I have > some evidence that longer XY pairs have "better" DOPE scores than > shorter pairs. Is there a statistical way to control for "length"? > 3) I was > just looking at DOPE scores for two models. One with from an alignment > with gaps and the other from an alignment without gaps. > The PDB > model files are different sizes yet the scores are identical. Does DOPE > ignore regions that are not in the template? > > Starr > > > ------------------------------ > > Message: 3 > Date: Mon, 20 Dec 2010 17:01:01 -0800 > From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] DOPE and sequence/model length > To: Starr Hazard hazards@musc.edu > Cc: modeller_usage@salilab.org > Message-ID: 4D0FFC4D.2060005@salilab.org > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/16/2010 11:51 AM, Starr Hazard wrote: > > This is several questions I guess. 1) Are DOPE energies normally > > distributed? Could I statistically compare DOPE scores of models made > > with one template to those from another template. > > DOPE is a sum of individual energies over all pairs of atoms in your > final model - it does not include any information from the template or > modeling process. So you can compare DOPE scores for two models of the > same sequence, regardless of their source. > > > 2) I have some evidence that longer XY pairs have "better" DOPE > > scores than shorter pairs. Is there a statistical way to control for > > "length"? > > You can't compare these directly. Use the normalized DOPE score instead, > which *is* corrected for length (it is a z score). > > > 3) I was just looking at DOPE scores for two models. One with from an > > alignment with gaps and the other from an alignment without gaps. > > The PDB model files are different sizes yet the scores are identical. > > Does DOPE ignore regions that are not in the template? > > Yes. See (1) above. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 4 > Date: Sun, 26 Dec 2010 13:00:39 +0530 > From: ranu sharma ranusharma09@gmail.com > Subject: [modeller_usage] problem in doing difficuly modeling using > modeller 9v8 > To: modeller_usage@salilab.org > Message-ID: > AANLkTikhoQUvqSQA1GkKauo9=XctiXy2v27mX-LWrtYZ@mail.gmail.com > Content-Type: text/plain; charset="iso-8859-1" > > Hello Sir/Madam, > > Good Afternoon. I am facing problem while doing Difficult modelling for my > protein. It is showing the following error. > I am attaching the .aln file, my .pdb and model.py file for your reference. > Hope to get a reply from you soon. > > > > > > Thanks & Regards. > > > *ERROR:* > > C:\Program Files\Modeller9v8\examples\ranu_basic\C4H>mod9v8 model.py > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "model.py", line 9, in ? > a.make() > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 98, in make > self.homcsr(exit_stage) > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 424, in homcsr > self.check_alignment(aln) > File "C:\Program > Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li > ne 406, in check_alignment > aln.check() > File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line > 200, in > check > self.check_structure_structure(io=io) > File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line > 209, in > check_structure_structure > return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) > _modeller.ModellerError: check_a_282E> Unable to read structural > information > for > alignment sequence: 1 2fdvA This command requires structures. > > > > > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune > > > > -- > Ranu Sharma > Msc Bioinformatics, Pune University > JRF, National Chemical Laboratory, Pune >