- modeller_usage - salilab.org

Re: [modeller_usage] no_subject...
by DANIEL TAYLOR 10 Mar '13

10 Mar '13

http://www.optimal-consult-hh.com/el/qlf/pyhyh/sfsf/oq.eaotw .

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Reading in a model with multiple chains?
by Patrice Peterson 19 Feb '13

19 Feb '13

Hello, I have created a number of dimeric decoys and wish to create a consensus structure. However, I'd like to omit a few residues fom the respective N- and C-termini of both chains, because they are disordered and would only get in the way of evaluating the clusters. Basically, I'd like something like this: OOMMMMMMOO/OOMMMMMMOO in which 'O' means the residue should be omitted, and 'M' means it should be included. I know I can use the model_segment argument to complete_pdb() or model.read() to select a range of residues when loading a model, but is there a way to read in a *non-contiguous* range of amino acids, as in my example? Or should I just create a new set of decoys without the residues in question (the ones labeled 'O' in the crude sketch above)? Thanks in advance! Patrice Peterson

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How NOT to add missing residues
by Anirban 08 Feb '13

08 Feb '13

Dear Sir, I am trying to model a protein for which there is a gap (resi 65 - resi 75; a loop)between two helices. I do not wish to add the missing 10 residues and want to leave the helices unjoined . But MODELLER always automatically joins the two helices (resi 64 with resi 76). How can I tell MODELLER not to join the helices? Please suggest. Regards, Anirban

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Minimize structure energy
by danashah＠post.tau.ac.il 28 Jan '13

28 Jan '13

Hi all, I've only joined this mailing list lately, so pardon me if this question was asked and answered before. We wish to perform energy minimization to a model we created. We were wondering whether we can use your automodel for that, via "use your own initial model": http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel If it's possible, what should be the alignment file, since the sequence we want to use is the same as the model? Thank you, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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leave out termini of a structure
by Ahmet yıldırım 25 Jan '13

25 Jan '13

Dear users, I have four similar structures. They are aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. Unfotunately, the first 15 residues of of all the structures are missing. I modelled the aaa.pdb using aaa.pdb, bbb.pdb, ccc.pdb and ddd.pdb. When I modelled aaa.pdb, a loop of aaa.pdb goes through the rest of the protein. i.e. occurs knot. My friend said "you should leave out the termini". How will I leave out termini of a structure with Modeller? What do you suggest? Thanks in advance -- Ahmet Yıldırım

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Searching the PDB for similar structures
by nornik 23 Jan '13

23 Jan '13

Hello! I am wondering if MODELLER can be used to search the PDB for entries structurally similar (without taking the sequence into account) to a known target structure. If not, do you know any other software for performing such a search? Thank you Niklas

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moldpdf, DOPE score and GA341 score
by Ahmet yıldırım 23 Jan '13

23 Jan '13

Dear users, I am a new user of Modeller. I have the following results: >> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- qseq1.B99990001.pdb 8602.63281 -113144.73438 1.00000 qseq1.B99990002.pdb 8773.10840 -113346.03125 1.00000 qseq1.B99990003.pdb 8349.71387 -112852.75000 1.00000 qseq1.B99990004.pdb 9365.16406 -111568.75781 1.00000 qseq1.B99990005.pdb 8553.98926 -112664.98438 1.00000 1.) What is "moldpdf", "DOPE score" and "GA341 score"? What is the meaning of them? 2.) how will I determine the best result according to the above table/results? What is the best result? Thanks in advance -- Ahmet Yıldırım

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filtering membrane proteins
by sdimicco 18 Jan '13

18 Jan '13

Dear Modellers, I have built a membrane protein by Modeller. I am aware that none of the Modeller assesment methods are likely to work well on membrane proteins.However, could I use one of the assesment methods to filter the best models among my results, and veluate the selected best models with other methods? Thank you in advance All the best Simone

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membrane protein
by sdimicco 16 Jan '13

16 Jan '13

Dear Modellers, I have built a membrane protein by Modeller. I would like to know if some of the assesment method implemented are ble to evaluate mebrane protein. If not, could you suggest some other method? Thank you in advance All the best Smone

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modeling with water, HETATM
by Krupal Jethava 11 Jan '13

11 Jan '13

Dear, I am trying to make model with Ligand (37 HetAtom) and 3 water molecule. I used the same script as in manual but getting the error that "Number of residue in alignment and pdb are different: 324 288 for alignment entry: tseq.pdb" In My alignment file: 1) query seq = 296 (residues) 2) pdb = 287 (residues) + 3 (water HETATM) + ligand (34 HETATM) align-ligand.ali has >P1;tseq.pdb structureX:tseq.pdb:FIRST:@:END ::@::: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA..... ................................* >P1;qseq sequence:qseq:FIRST:@:END ::@::: AAAAAAAAAAA--AAAAAAAAAAAAAAAAAAA..... ................................* I am using Modeller9v7 and python2.5.1 I will be very thankful for your help.

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