Dear Andrej, I tried eveything you suggested. My system is R10000 with IRIX6.3. mod_r10000-IRIX6.2 won't run under IRIX6.3. When I tried mod_iris4d, it worked under both IRIX5.3 and IRIX6.3. If it is compiled under IRIX5.3, will it not be efficient under IRIX6.3? Thank you very much Yi
Hi, Yi! I guess you won't loose much in efficiency running mod_iris4d under IRIX6.3. At least it works! Happy landings! Azat. Yi Liu wrote: > > > Dear Andrej, > > I tried eveything you suggested. My system is R10000 with IRIX6.3. > mod_r10000-IRIX6.2 won't run under IRIX6.3. When I tried mod_iris4d, it > worked under both IRIX5.3 and IRIX6.3. If it is compiled under IRIX5.3, > will it not be efficient under IRIX6.3? > > Thank you very much > > Yi -- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
Dear Azat, I have made a mutant by removing 7 residues from the original protein which structure is known. The deletion is in a loop conecting two b-strands. What I what to do is to get a model for this new mutant using the original structure as template? Could I improve the model using also as template the structures of other proteins related to the original one and which are trying to emulate by making my mutants? Thanks in advance. Sincerely, Pedro Reche ================================================================================= Dr. Pedro Antonio Reche Gallardo Dept. of Biochemistry, U. of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, England, UK Phone: +44 (0)1223 333662 Fax: +44 (0)1223 333661 par@mole.bio.cam.ac.uk, par32@cus.cam.ac.uk http://www-ccmr-nmr.bioc.cam.ac.uk/~par
Hi, Pedro! Sure, you can. It is standard example in the manual. Specify whatever sequences you want as template, put them into .seq file and you will get a result. One comment: I would modify the automatic alignment when the wild type was as a template. The alignment program will probably align all the residues of the mutant with their counterparts in wild type. I would de-align several residues flanking the gap. Please refer to the manual for more details. Regards, Azat. Dr P.A. Reche wrote: > > Dear Azat, > > I have made a mutant by removing 7 residues from the original protein > which structure is known. The deletion is in a loop conecting two > b-strands. What I what to do is to get a model for this new mutant using > the original structure as template? Could I improve the model using also > as template the structures of other proteins related to the original one > and which are trying to emulate by making my mutants? > Thanks in advance. > > Sincerely, > > Pedro Reche > > ================================================================================= > Dr. Pedro Antonio Reche Gallardo > Dept. of Biochemistry, U. of Cambridge, > 80 Tennis Court Road, CB2 1GA, Cambridge, England, UK > Phone: +44 (0)1223 333662 > Fax: +44 (0)1223 333661 > par@mole.bio.cam.ac.uk, par32@cus.cam.ac.uk > http://www-ccmr-nmr.bioc.cam.ac.uk/~par -- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
Dear Azat, Just a single question, should it make any difference to use the SMALL executable modeller with respet the ENOURMOUS one? Thanks. ================================================================================= Dr. Pedro Antonio Reche Gallardo Dept. of Biochemistry, U. of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, England, UK Phone: +44 (0)1223 333662 Fax: +44 (0)1223 333661 par@mole.bio.cam.ac.uk, par32@cus.cam.ac.uk http://www-ccmr-nmr.bioc.cam.ac.uk/~par
Dr P.A. Reche wrote: > > Dear Azat, > Just a single question, should it make any difference to use the SMALL > executable modeller with respet the ENOURMOUS one? > Thanks. ENORMOUS can handle up to 2000 residues in a chain. SMALL - two times less. > ================================================================================= > Dr. Pedro Antonio Reche Gallardo > Dept. of Biochemistry, U. of Cambridge, > 80 Tennis Court Road, CB2 1GA, Cambridge, England, UK > Phone: +44 (0)1223 333662 > Fax: +44 (0)1223 333661 > par@mole.bio.cam.ac.uk, par32@cus.cam.ac.uk > http://www-ccmr-nmr.bioc.cam.ac.uk/~par -- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
participants (3)
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Azat Badretdinov -
Dr P.A. Reche -
Yi Liu