- modeller_usage - salilab.org

disulfide bonds in aligned structures?
by Mike White 24 Sep '07

24 Sep '07

Hello, I have been modeling a homopentamer which should have a disulfide bond in each subunit in the same position as the multiple templates that we are using (the alignments have the cys residues of the target lined up with the disulfide-forming cys in the templates). When I carry out the alignment of the templates using salign, the XX_fit.pdb files for the templates do not have the disulfides indicated using SSBOND, even though the original pdb files (XX.pdb) do have the SSBOND lines in them. I know that automodel will automatically include disulfide restraints if the templates have them. However,the returned models, while superimposing nicely on the template structure, do not have the disulfides, even though the cysteines in the model are right where the disulfide-forming cysteines are in the template. I assume that automodel uses the XX_fit.pdb files for the fitting routines, and the fact that the XX_fit.pdb files are missing the SSBOND lines is why the disulfides are present in the model. Is this correct? Can I just edit the XX_fit.pdb files to include the SSBOND lines to force the model to have the disulfides? Alternatively, I guess I could use model.patch as per node24 in the online manual to force the disulfides to be where I want them to be, but this just doesn't seem right if the templates all have the disulfide and the alignments have the cysteines where they should be. Thanks Mike White

2 1

(no subject)
by simran jeet 24 Sep '07

24 Sep '07

I have generated models for proteins but dont know how to optimize and refine those structures using modellar. I have tried using the optimize.py file to optimize with CG but i am not able to understand the script and where should I list the protein name to be optimized in that script file.

2 1

help
by huifang liu 24 Sep '07

24 Sep '07

Hello! When I finished inshalling modeller , I typied the command mod9v2. But the computer replied me with the sentance:The command can not found .Can you tell me the reason? Thanks

2 1

Re: [modeller_usage] September 70% OFF
by Viagra.com Inc 19 Sep '07

19 Sep '07

1 0

model_comparison
by Prasenjit Mukherjee 17 Sep '07

17 Sep '07

Hello Modeler users, I have a question for you. I have generated models for a sequence using one structural homologue. In one set i have used 1 crystal structure of the reference protein and generated 10 models. In the second set i have used two crystal structures of the same reference protein and generated 10 models.The sequence alignment is the same in both cases. My question is, can i compare the pdf violations of a model generated in set 1 with a model generated in set 2 ? Thank you Prasenjit K Mukherjee Graduate student Department of Medicinal Chemistry School of Pharmacy University of Mississippi Cell - 662 380 0146 Office - 662 915 1286 --------------------------------- Got a little couch potato? Check out fun summer activities for kids.

2 1

selection to model
by Alex Brown 13 Sep '07

13 Sep '07

Hi. Only a small problem. Is there any way to convert a selection object to a model object ? I would like to extract the chains from a multi-chain model and use the separate chains as individual models. At the moment, the only way I seem to be able to do this is to write the selection to a file and the read the file into a model object. Cheers, Alex Brown www.mrctechnology.org Medical Research Council Technology is a company limited by guarantee no. 2698321, incorporated in England and a charity registered in England and Wales no. 1015243, and a charity registered in Scotland no. SC037861. Regsistered office 1-3 Burtonhole Lane, Mill Hill, LONDON, NW7 1AD, UK. T: +44 (0)208 906 7100; F: +44(0)208 906 7200. This communication contains confidential information and may be legally privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any disclosure, distribution, copying or use of this communication or the information in it is prohibited and may be unlawful. If you have received this communication by mistake, please notify the sender or contact MRC Technology by telephone on 0208 906 7100 and then delete the e-mail and any copies of it. No representation is made that this email or any attachments are free of viruses. Scanning for the presence of viruses in this e-mail, and any attachments, is highly recommended and is the responsibility of the recipient.

2 1

using DOPE assessment
by saccenti＠cerm.unifi.it 11 Sep '07

11 Sep '07

Hi all, I'm wondering if using DOPE assessment is only possible to evaluate each chains indvidually. Once I get the DOPE score of the two chains, how to combine them to get an unique DOPE score for my complex? Is summing the two (or more) score reasonable? Other way, what If I create my complex as a single chain? Many thanks for suggestion Edo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

2 1

Cu(I) Parameters
by saccenti＠cerm.unifi.it 11 Sep '07

11 Sep '07

Hi all, I'm modleing a complex with a copper ion Cu(1). I searched for copper paramters in the modlib/restyp.lib but I did not find them. Are topology and suitable forcefield parameters available? Many thanks edoardo -- Dr Edoardo Saccenti CERM Magnetic Resonance Center University of Florence Fiorgen Foundation Via Luigi Sacconi n° 6 50019 Sesto Fiorentino (FI) Italy Tel: +39 055 4574281

2 1

dope_loopmodel question
by Mike White 10 Sep '07

10 Sep '07

I would like to refine my models of a homopentamer with loop refinement. In the past (Mod8) I would use loopmodel, but noticed that there is an "improved" loop modeling routine dope_loopmodel() which uses (among other things) the DOPE score in the refinement process. In various parts of the manual it mentions that the DOPE score was developed for single-chain models and shouldn't be used as an evaluative tool for multichain models. Does this also meas that the dope_loopmodel() routine shouldn't be used for loop refinement of multichain models? What's the downside of using it for multi-chain models? If so, this would be a shame since there are also other enhancements (Leonard_Jones potentials, etc.) unrelated to DOPE that would be nice to be able to use. Mike White

2 1

align_codes error
by Dave Roe 10 Sep '07

10 Sep '07

I'm receiving the following error on linux with Modeller 9.2: _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = mod2hg42 Here's the alignment line from my python file: aln = alignment(env, file='mod2hg42.fa', align_codes=('mod2hg42')) Here's the contents of mod2hg42.fa (located in the same directory): >mod2hg42 EEKLRRYLKRTVTELDSVTARLREVEHRAGEPIAIVGXACRFPGDVDSPESFWEFVSGGGDAIAEAPADRGWEPD PDARLGGXLAAAGDFDAGFFGISPREALNXDPQQRIXLEISWEALERAGHDPVSLRGSATGVYTGSSTNDYGFLA VSDPDEAHPYAITGTASSVASGRVAYCLGLEGPAXTVDTACSSSLTALHLAXESLRRDECGLALAGGVNVLSTPM VTLGFDSQGGLAADGRIKPFSKAADGYTRSEGAGVLVLQRLSAARREGRPVLAVLRGSAVNQDGASNGLIAPSGP AQQRVIRRALENAGVRAGDVDYVEAHGTGTRLGDPIEVHALLSTYGAERDPDDPLWIGAVKTNVGHLESAAGVAG VXKAVLALRHGEXPRTLHFDEPSPQIEWAVSVVSQARSWPAGERPRRAGVSSFGFGGTNAHVIVEEAPEADEPV I've tried dozens of combinations, but I can't get around this error. Any advice? -- Dave Roe roex0050(a)umn.edu

2 1