April 2008 - modeller_usage

modelling multiple sequences in one go
by navkaranj 08 Apr '08

08 Apr '08

hello I want to know that if I have, say about 10 target sequences that I want to model, each with a corresponding template structure, what is the sript that I will have to follow in order to model all of them in one run? Instead of 10 different scripts which make things cumbersome, I want to combine the result of all in one script in one run. please let me know if there is such a script and if there is none,could you assisst me to write one. thank you. navkaran

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Regarding DOPE model assessment values (Mohan)
by m.b.rajasekaran＠reading.ac.uk 08 Apr '08

08 Apr '08

Dear Members, I have a query regarding the DOPE score for the models.It is mentioned in the manual that models with lowest DOPE score value are reliable. I am having two models right now with values -7000 and -6000 respectively. I would like to know which one is the best among these two based on the values. Thanking You, Mohan.

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running separate files from different folders
by navkaranj 07 Apr '08

07 Apr '08

i m tryin to model a number of proteins using modeller 9v3 . i would like to know if i can run all my files from diferent folders using 1 command. is it possible to run a common command in modeller , mentioning the directory/folder of proteins to be modelled , so as to model all proteins in their designated folders

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ALIGN_CODE
by barwellj＠aston.ac.uk 07 Apr '08

07 Apr '08

Hello modellers, I have just started using the programme and have already ran into some difficulty. I am trying to do a homology model .The error message I get suggests that my alignment file does not match my pdb file. Although, all my files are in the same directory as modeller and both written in the same case. I'm not sure why it is not working? Before running the programme I edited the PDB file using DEEPVIEW to remove the antagonist from the structure. Also I used GENEDOC to produce the alignment and saved it in a PIR format. Not sure if this has something to do with my problem? attached is my PDB file (called a.pdb), my alignment file (a.pir) and my script file (called script.py) and the log file. Any help would really be appreciated

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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 19
by Vadim Patsalo 07 Apr '08

07 Apr '08

Hello, There seems to be a problem with your a.pir file. In particular, instead of structure:a.pdb:29::122::::: the file should read: structure:a.pdb:29:A:122:A:::: Note the difference, I am telling modeller to look for residue 29 of chain A in the pdb. otherwise, it looks like it looks for residue 29 of chain " ". Take a look at the manual to see how the PIR format works: http://www.salilab.org/modeller/manual/node421.html. Best, Vadim > Hello modellers, > > I have just started using the programme and have already ran into some > difficulty. I am trying to do a homology model .The error message I get > suggests that my alignment file does not match my pdb file. Although, all > my files are in the same directory as modeller and both written in the > same case. > > I'm not sure why it is not working? Before running the programme I edited > the PDB file using DEEPVIEW to remove the antagonist from the structure. > Also I used GENEDOC to produce the alignment and saved it in a PIR format. > Not sure if this has something to do with my problem? > > attached is my PDB file (called a.pdb), my alignment file (a.pir) and my > script file (called script.py) and the log file. > > Any help would really be appreciated

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Help
by matziast＠med.uth.gr 06 Apr '08

06 Apr '08

Thank you for your immediate reply, I am trying to install modeller9v3 on Scientific Linux(2.6-18-53.1.4.3I5xen). It doesn't have any glibc, only glib=2.0 but I think that it has to be installed glib=2.2. And a last question, the scripts must be written in Python and they also have to be finished with .py? Thank you in advance and I am sorry for my so simple and boring questions.

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Help
by matziast＠med.uth.gr 04 Apr '08

04 Apr '08

Hi, I am a new user of modeller and specifically modeller9v3. I am a student of Biochemistry and Biotechnology in Greece and I need this program for my diploma thesis. I read in the page of modeller that I must install python and I have to write my scripts in this language. On top of that, I must install glib>=2.2 and glibc>=2.3 but I have some problems in their installation. If I do not install them, the modeller9v3 will not work? (I am sorry for my errors in English). Thank you in advance. Maria.

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inducing kink in a helix
by Marta Rossini 01 Apr '08

01 Apr '08

Hi all, I am using Modeller to model a structure in which there is a portion - not present in the template - that I want to force to be an alpha-helix. If I introduce the secondray structure restraints in the entire corresponding region of sequence, I obtain a straightened helix. In the sequence, however, there is a Proline in correspondence of which I want to induce a little distortion of the helix. If I force the secondary structure only before and after the proline, by excluding it, I obtain some very strange angles of an helix with respect to the other, that is a too pronounced bending. Is there in Modeller a way to induce a "controlled" distortion (that in my case corresponds to control the angle between the CO and NH groups of the proline!)? thanks _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE

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FW: inducing kink in a helix
by Marta Rossini 01 Apr '08

01 Apr '08

> > Hi all, > I am using Modeller to model a structure in which there is a portion - not present in the template - that I want to force to be an alpha-helix. > If I introduce the secondray structure restraints in the entire corresponding region of sequence, I obtain a straightened helix. In the sequence, however, there is a Proline in correspondence of which I want to induce a little distortion of the helix. > If I force the secondary structure only before and after the proline, by excluding it, I obtain some very strange angles of an helix with respect to the other, that is a too pronounced bending. > Is there in Modeller a way to induce a "controlled" distortion (that in my case corresponds to control the angle between the CO and NH groups of the proline!)? > thanks > _________________________________________________________________ > Explore the seven wonders of the world > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx

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