March 2004 - modeller_usage

Adding a ligand
by Shamshad Zarina 17 Mar '04

17 Mar '04

Dear All, I am interested in adding ligand like glucose to one particular residue in my protein (which is not present in my template). Any ideas? Thanks for any help. Best, Shamshad __________________________________ Do you Yahoo!? Get better spam protection with Yahoo! Mail. http://antispam.yahoo.com/tools

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Any thesis reg modeller project work
by Nataraj Balkrishnan 16 Mar '04

16 Mar '04

Dear modellers, Can any one send me the copy of Mr.A.Sali Ph.D. thesis, PDF file .If not could you please send me the link where I can download the same at free of cost. And more could you please send me the link where A.sali.et al.'s paper on 'comparative modelling of protein' (those are refered in Modeller6v2's manual ) is freely downloadable. And more any of yours thesis in modeller regarding protein modelling would be greatly appreciated for my thesis preparation work. Thank you in advance. yours truly, B.Nataraj ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html

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Why should add ourself ligand in protein?
by Nataraj Balkrishnan 16 Mar '04

16 Mar '04

Dear modeller, I want to know what is the purpose of adding ligand in protein by ourself in Modeller, what will be the useful outcome that we can expect by adding ligand in our model in Modeller? I mean is there any routein in Modeller6v2 to study the active site or interaction of our added ligands and protein? Please let me know. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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ModWeb question
by alarcon＠lncc.br 15 Mar '04

15 Mar '04

Dear All When sending a query sequence to modweb, this will suggest a tridimensional model homology-related to a specific template (which has a experimental structure determined). The question is ; When using Modeller stand alone we can make an alignment between our query sequence and several templates in order to better define regions of structural similarity. ModWeb works also in this way ? I mean, the model contructed for the query sequence is based lonely in one template ? So, is correct to assume that the ModWeb procedure is less accurate than the modeller when used "manually" due the one-template basis of calculation? Thanks in advance Frank Alarcon ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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pyroglutamate
by Han Choe 15 Mar '04

15 Mar '04

Dear Modellers, How do I denote pyroglutamate as one letter in the alignment file? I tried small "p" but it did not work. In three letter, I use "PCA". Cheers, Han

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Request
by ram kumar 04 Mar '04

04 Mar '04

Hello modeller users , Generally state me the reasons for getting the errors like 1. structure not read , 2. Alignment sequence not found in PDB , 3. Unknown residue type / Non-standard residue type , 4. if the log file shows number of aligned aligned positions as zero . The errors stated by me is quoted in the mailing list by others but i was'nt been able to get a clear picture of overcoming these errrors thus provide me an detailed facts in eradicating these errors . bye RAM Yahoo! India Insurance Special: Be informed on the best policies, services, tools and more.

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Reply to ram
by Nataraj Balkrishnan 03 Mar '04

03 Mar '04

Hello Ram, The problem could be becoz of not converting your *.pdb file into *.ent extension . And also your PDB coordinate file not starting with theh residue number 1 (since in some cases PDB coordinates starts with residue number other that 1) and also make it sure if you deal with single segment of PDB ,remove chain ID from your coordinate data. Hope it works , For more clarification send me your TOP and Alignment file, I try to fix your problem Good Luck, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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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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