- modeller_usage - salilab.org

modeling protein-DNA complex
by Betty Shen 02 Mar '04

02 Mar '04

Hi modellers, I would like to build a model of a protein-dna complex based on the x-ray structure of a homologous protein in a protein-dna complex I would use the exact DNA sequence in the model just to provide some constrain on the protein. I noticed that there are nucleotides in the restyp.lib. But I cannot find examples on how to enter DNA sequence in the align.ali file. Has anybody tried modelling with DNA in MODELLER? I would appreciate it very much if someone can give me some or point me to where I can find some examples. Thanks a bunch in advance. Betty Betty Shen Fred Hutchinson Cancer Research Center

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[modeller_usage] Virus warning, previous warning was a virus and did not originate from salilab.org
by Ursula Pieper 02 Mar '04

02 Mar '04

Hello, a virus email just succeeded to go to the modeller_usage mailing list. Please don't open the attachment in the email titled: [modeller_usage] Warning about your e-mail account. Sorry about this and best regards, Ursula ---------------------------------------------- Ursula Pieper, Ph.D. Laboratory of Andrej Sali Mission Bay Genentech Hall 600 16th Street, Suite N474P University of California, San Francisco San Francisco, CA 94143-2240 email: ursula(a)salilab.org phone: 415-514-4233

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reference
by Manal Swairjo 01 Mar '04

01 Mar '04

Hi modellers, I am a new user of Modeller and I would like to know how to report its results in a manuscript. Can you refer me to a recent paper in which the program was used successfully? thanks Manal Manal A. Swairjo, Ph.D. The Skaggs Institute for Chemical Biology The Scripps Research Institute Mail drop: BCC379 10550 North Torrey Pines Rd. La Jolla, CA 92037 Tel: (858) 784-9486 Fax:(858) 784-8990

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[modeller_usage] B-factor error is to be ignored in theoretical modelling ?
by Nataraj Balkrishnan 26 Feb '04

26 Feb '04

Dear modellers, I have checked whatif report for my throreticaly modeled protein and other existing theoreticaly modeled protein from PDB for B-factor error, in all cases it shows extreme value of B-factor errror . I want to know whether for theoretical modelling this B-factor error is to be ignored or any other way of solving this problem in modeller routine? please let me know. Yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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can genetics link with mathematics
by rathan kar 26 Feb '04

26 Feb '04

hi everybody i have a query which is not linked with the present discussion as whether the codons a,g,c,t which are in random order in a gene seqn be linked with any sort of random number generator in mathematics, and has anybody worked on such topics .plz reply me with links Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more.

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pdf-score
by marc.gasser＠pharma.ethz.ch 25 Feb '04

25 Feb '04

Hi, is there a way to calculate a pdf-score with modeller in order to see badly modelled residues? cheers, marc

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<modeller> objective function??
by Stefanie Offermann 24 Feb '04

24 Feb '04

Hello, I am a new user of the program modeller and actually it works quite well. So now I have a lot of different models and want to choose the best one. I know that there is the modeller objective function but I don't understand completely how this function is calculated. If I compare two models with high differences in the objective function e.g. 500 and 4000 with the programm procheck I cannot find big differences. a second question: how many loop models should normally be calculated? 25 are many and the computer is calculating and calculating.... thank you in advance for answering!! Steffi

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Question about running modeller
by En Yun 23 Feb '04

23 Feb '04

Hi, I had recently managed to install Modeller6 successfully on the SGI Irix OS. However when I tried to run it using mod model-default.top, the log file displayed the following error msg: rdactio_534E> Command not recognized: SET_ATOM_FILES_DIRECTORY = '/gt/usr4/roger' Would appreciate any advice on this. Thanks. En

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mutation
by Jaimin Shah 23 Feb '04

23 Feb '04

Hello Dr. Owen. I am sorry I did not explain well. I am not able to compute H-bonds using Swiss-PDBViewer and I am getting "Unrealistic B-factor 0.0" in the log file of the mutant protein. (I had generated the mutant protein using the MUTATE_MODEL command of MODELLER.) Any suggestions will be appreciated. > Hi Jaimin, > > What do you mean by compute H-bonds? If you mean you want to add hydrogen > atoms and calculate some kind of energy i'd suggest using a molecular > mechanics program such as CHARMM. Hope this is of help! > > Owen > > > Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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How to correct Bumps
by Nataraj Balkrishnan 21 Feb '04

21 Feb '04

Dear modellers, My modelled protein having error of bumps(non bonded atomic condact) for some about 10 atom positions according to What IF error report. What is the appropriate TOP script or routine to correct those error(bumps) causing atom postions ? Thank you in advance, Yours B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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