February 2010 - modeller_usage

special restrains for aromatic packing interactions
by Thomas Evangelidis 03 Mar '10

03 Mar '10

Dear Modellers, I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic: http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_… I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here: http://salilab.org/modeller/manual/node196.html Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome. thanks, Tom

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special restrains for aromatic packing interactions
by Thomas Evangelidis 26 Feb '10

26 Feb '10

Dear Modellers, I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic: http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_… I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here: http://salilab.org/modeller/manual/node196.html Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome. thanks, Tom

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Phosphorylated Residues - Phospotyrosine (PTR)
by Jan H. Löhr 24 Feb '10

24 Feb '10

Hello everybody, my question has already been posted a couple of times - however these posts date back a couple of years. That is why I hope to find new answers to this topic. Modeller (9v7) does not recognize phosphotyrosine residues (Phosporylated tyrosines, PTR). There are three options to deal with such undefined residues: 1. Use Tyrosine instead (and optionally after modelling: replace with phosphotyrosine und minimize) This might be a good choice, if the residues were in areas far away from the region under investigation 2. Use Block Residue (rigid body) - not the most accurate way, but a good workaround (http://salilab.org/modeller/9v7/manual/node95.html) 3. Define the unknown residue according to the manual/FAQ (http://salilab.org/modeller/FAQ.html#8) I would prefer the third option and define them myself, but as the manual states, this is a "painful" process. I wonder if anyone has generated the needed files/entries for the modeler libraries. There is a page in the Modeller Wiki that allows upload of these customized files. It is empty however. Since I currently do not have access to QUANTA or CHARMM, I cannot generate the files myself. I also wonder why the library file for residues in modeller 9v7 still dates back to 1993? I hope someone can help. Thank you in advance, Cheers Jan H. Loehr University of Hamburg, Germany

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Optimization
by abdullah ahmed 24 Feb '10

24 Feb '10

Hello, I just wanted to know if it was possible to conduct optimization in such a way that Hydrogen atoms are present in the optimized structure/protein? Thanks in advance, Abdullah _________________________________________________________________ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969

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questions concerning hydrogen in optimization
by abdullah ahmed 24 Feb '10

24 Feb '10

Dear Laurent, I have a question regarding optimization using "cg.optimize". The optimized structures/proteins produced after using this function are always without hydrogens. So does this mean that: The optimization procedure removes hydrogens and does not use them during the optimization steps?If the above is true, is there a way to conduct optimization with hydrogens included? Thanks in advance, Abdullah _________________________________________________________________ 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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Error when using flex-em
by Saskia Bakker 23 Feb '10

23 Feb '10

Dear Modeller support, When trying to fit the crystal structure in an EM map using mod9v7 and the flex-em script (unmodified apart from filenames) I get the following error message: bash $> /usr/bin/python ../../scripts/flex-em.py > flex.log File "/fbs/emdisk3/emsoftware/LINUX/modeller9v7/modlib/modeller/optimizers/molecular_dynamics.py", line 50, in optimize ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars) OverflowError: check_inf__E> Atom 1 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. It happens when running in CG mode and MD mode. The map is 140x140x140 pixels, which is already 1/8 of the complete map (using the complete map gives the exact same error). There are 893 residues (6 rigid body domains) in the model I am trying to fit. It gives the same error with poly-Ala. Are these files too large? The coordinates of the pdb files that are output after the first iteration look sensible and fit well in the map (but not quite well enough). I would be very grateful for any suggestions to help solve this problem. Many thanks, Saskia

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problems with Windows installation
by Andrew Voronkov 23 Feb '10

23 Feb '10

Dear Modeller support, I've got error while running mod9v7 under Windows: FATAL ERROR: MODINSTALL9v7 environment variable not set: incomplete MODELLER installation. I haven't got such errors before. Probably this is because I am not administrator on this PC. How to solve this problem? Sincerely yours, Andrew

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importing alignment into modeller.
by Knut J Bjuland 18 Feb '10

18 Feb '10

Is there any way to import alignment created without using modeller. Do I have to manual make a new ali file in the pir format for modeller. Could you please calarify the how the alignment was imported into modeller in the difficult example from http://bioinf.cs.ucl.ac.uk/psipred/ Knut J _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969

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Asterisks in co-ordinate output
by Offord, Victoria 17 Feb '10

17 Feb '10

Hi, I couldn't find anything on this but was wondering if anyone else had come across asterisks in the pdb output file? Many thanks in advance, Victoria

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(no subject)
by Offord, Victoria 17 Feb '10

17 Feb '10

Hi, I couldn't find anything on this but was wondering if anyone else had come across asterisks in the pdb output file? Many thanks in advance, Victoria

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