Dear Qiang, Because Jmol is not a modeling program, Jmol-users is not the best place to discuss your project. It would be better to discuss your project on either the Protein Data Bank discussion, or the DeepView discussion. People there can give you expert advice. You can find these discussions at http://molvisindex.org#disc
DeepView can do a structural alignment of the peptides in each of your models. In brief, use DeepView's Windows menu to open the Control Panel Window. There, select the residues in each peptide that you wish to align. Then use the Fit menu, Fit Molecules from Selection. Before you do a structural alignment, probably you want to pick one model from the NMR ensemble. Olderado will pick the "most representative" (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 > peptide, Protein_B is a regulatory >protein, the NMR structure of protein_B is a >complex which contain protein_B and >target peptide of protein_A, Now They are >relaxation state, I want to merge the >two molecular to make a complete complex of >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. > > >ÔÚÄúµÄÀ´ÐÅÖÐÔø¾Ìáµ½: > >From: Eric Martz <[EMAIL PROTECTED]> > >Reply-To: > >To: Qiang Zhong <[EMAIL PROTECTED]>, > [email protected] > >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 > 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 > 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=lnk&kid=120709&bid=263057&dat=121642 > > >_______________________________________________ > > >Jmol-users mailing list > > >[email protected] > > >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 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated 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=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
