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Re: [Jmol-users] How to merge two pdb file?
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From: Eric M. <em...@mi...> - 2007-02-12 17:20:24
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Dear Qiang, Because Jmol is not a modeling program,=20 Jmol-users is not the best place to discuss your=20 project. It would be better to discuss your=20 project on either the Protein Data Bank=20 discussion, or the DeepView discussion. People=20 there can give you expert advice. You can find=20 these discussions at http://molvisindex.org#disc DeepView can do a structural alignment of the=20 peptides in each of your models. In brief, use=20 DeepView's Windows menu to open the Control Panel=20 Window. There, select the residues in each=20 peptide that you wish to align. Then use the Fit=20 menu, Fit Molecules from Selection. Before you do a structural alignment, probably=20 you want to pick one model from the NMR ensemble.=20 Olderado will pick the "most representative"=20 (closest to average) model for you: http://pqs.ebi.ac.uk/pqs-nmr.html I cannot advise you on docking, but you can get advice from the PDB= discussion. -Eric At 2/11/2007, Qiang Zhong wrote: >Dear Eric Martz: > I will very happy to tell you what I want to do,and eager to receive= your >letter.there are two molecular protein_A and protein_B. > Protein_A is a enzyme, it have a target=20 > peptide, Protein_B is a regulatory >protein, the NMR structure of protein_B is a=20 >complex which contain protein_B and >target peptide of protein_A, Now They are=20 >relaxation state, I want to merge the >two molecular to make a complete complex of=20 >protein_A and protein_B.Dock program >is what I want to use firstly.But there may be another better way,because= they >have a common target peptide in structure.So maybe you can tell me what is >better. > > >=D4=DA=C4=FA=B5=C4=C0=B4=D0=C5=D6=D0=D4=F8=BE=AD=CC=E1=B5=BD: > >From: Eric Martz <em...@mi...> > >Reply-To: > >To: Qiang Zhong <zqi...@we...>, > jmo...@li... > >Subject: Re: [Jmol-users] How to merge two pdb file? > >Date:Sun, 11 Feb 2007 15:20:00 -0500 > > > >Dear Qiang, > > > > Paul Pillot's advice is good. > > > > We can help you better if we know what kind of "merge" you want to do. > > > > Do you want to structurally align two models of the same molecule > > ("on top of each other"), so you can see where they are the same and > > where they differ? > > > > Or do you want to ligate two models of different parts of a molecule, > > to build a complete model from the two parts? > > > > Or something else? > > > > -Eric > > > > At 2/10/2007, you wrote: > > >Hellow: > > > > > > I have download new jmol-11.0, I want to use it to edit > > > protein structure.Now > > >I have two protein structure,They have two=20 > same fragments,I want to merge two > > >protein at the same fragments.I don't know how to do?Could someone > > >tell me how to > > >do, Thank you very much! > > > > > > > > > > > > > > > > > >------------------------------ > > >Qiang Zhong > > > > > >Key Lab of Agricultural Animal Genetics, Breeding and Reproduction > > >of Ministry of Education > > > > > >College of Animal Sciences and Technology > > > > > >Huazhong Agricultural University > > > > > >Wuhan,Hubei, 430070 > > > > > >PR China > > > > >= >------------------------------------------------------------------------- > > >Using Tomcat but need to do more? Need to support web services,= security? > > >Get stuff done quickly with pre-integrated=20 > technology to make your job easier. > > >Download IBM WebSphere Application Server v.1.0.1 based on Apache= Geronimo > >= >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 > > >_______________________________________________ > > >Jmol-users mailing list > > >Jmo...@li... > > >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Eric Martz, Professor Emeritus, Dept Microbiology > > U Mass, Amherst -- http://www.umass.edu/molvis/martz > > > > Biochem 3D Education Resources http://MolviZ.org > > See 3D Molecules, Install Nothing! - http://firstglance.jmol.org > > Protein Explorer - 3D Visualization: http://proteinexplorer.org > > Workshops: http://workshops.proteinexplorer.org > > World Index of Molecular Visualization Resources: http://molvisindex.org > > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > > Atlas of Macromolecules: http://atlas.proteinexplorer.org > > PDB Lite Macromolecule Finder: http://pdblite.org > > Molecular Visualization EMail List (molvis-list): > > http://bioinformatics.org/mailman/listinfo/molvis-list > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ |