December 2003 - modeller_usage

Upper limit distance restraint
by Miha Pavsic 03 Dec '03

03 Dec '03

Hello Modeller users, I am looking for a way to specify upper limit distance restraint between CA atoms of two residues (eg., max 10 A between CA:25 and CA:187). Can someone please give me an example of doing this? Regards, Miha Pavsic *** Miha Pavsic, PhD Student Josef Stefan Institute Dept. of Biochemistry and Molecular Biology Jamova 39, SI-1000 Ljubljana, Slovenia

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problem in installing
by rathankar rao 02 Dec '03

02 Dec '03

hi i have installed modeller6v2 in c:/ in windows68se OS, i also recieved my license key from the author but on entering the license key to modenv.bat and mod.bat, it says wrong license the license provided to me is ****. i dont know how to go with it plz advice N.Rathankar Assistant Proffessor in physics Madanapalle Institute of Technological Sciences (MITS). INDIA WEBSITE: http://www.geocities.com/rathankar/ --------------------------------- Do you Yahoo!? Free Pop-Up Blocker - Get it now

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Re: [modeller_usage] malign3d will not align multiple structures
by Mark Daniels 01 Dec '03

01 Dec '03

Hello Oliver- Thank you for the reply. MALIGN3D does not require an alignment file if the structural models have a 1:1 sequence correspondence. In my case I am aligning five models of the same protein. I figured out what the problem was by looking at the .top files in the examples/tutorial-model folder of modeller6v2. As it turns out, I have to add the command SET ALIGN_CODES = 'atip' 'atip' 'atip' 'atip' 'atip' with which MALIGN3D properly loads the five model atip.Bxxx files. The Sanchez and Sali Methods in Molecular Biology article does not mention this (and neither does the manual). Regards- Mark J Daniels markjd(a)scripps.edu Department of Cell Biology The Scripps Research Institute La Jolla, CA On Mon, 1 Dec 2003, Oliver Hucke wrote: > Hi Mark, > > I miss the specification of the alignment file in your top script. I > suppose modeller needs an initial alignment - at least that's how I use > MALIGN3D. The atom files are specified in the alignment file, not in the > script. Please have a look at the example given in the section on > MALIGN3D in the manual. This works fine for me. The initial alignment > can be obtained with the commands SEQUENCE_TO_ALI and MALIGN. > > Hope this helps, > Oliver > > Mark Daniels wrote: > > Hello all- > > > > I'm trying to run malign3d to align multiple models but the routine > > only 'sees' the first structure and does nothing. I'm using the > > malign3d.top file format described in the Sanchez and Sali 2000 Methods > > in Molecular Biology article: > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 > > SET MAXRES = 700 > > SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; > > 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' > > SET WRITE_FIT = on > > MALIGN3D > > > > All the atip.Bxxxx files contain a reasonable structure. Running the > > malign3d.top routine shown above fails to produce any .fit files and > > shows the following error: > > > > openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 > > malign3_327W> Only one structure; nothing done. > > > > Would anyone be able to advise me on what I'm missing here or doing wrong? > > > > Thanks in advance- > > > > Mark Daniels > > The Scripps Research Institute > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > > > -- > _______________________________________________________________ > > Oliver Hucke, Dr. > Health Sciences Building - K418C > University of Washington 1959 NE Pacific St. > Dept. of Biochemistry phone: (206) 685 7046 > Box 357742 fax : (206) 685 7002 > Seattle, WA 98195-7742 email: ohucke(a)u.washington.edu > _______________________________________________________________ > > >

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malign3d will not align multiple structures
by Mark Daniels 01 Dec '03

01 Dec '03

Hello all- I'm trying to run malign3d to align multiple models but the routine only 'sees' the first structure and does nothing. I'm using the malign3d.top file format described in the Sanchez and Sali 2000 Methods in Molecular Biology article: SET OUTPUT_CONTROL = 1 1 1 1 2 SET MAXRES = 700 SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' SET WRITE_FIT = on MALIGN3D All the atip.Bxxxx files contain a reasonable structure. Running the malign3d.top routine shown above fails to produce any .fit files and shows the following error: openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 malign3_327W> Only one structure; nothing done. Would anyone be able to advise me on what I'm missing here or doing wrong? Thanks in advance- Mark Daniels The Scripps Research Institute

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