Re: [ccp4bb] per-residue RMSD calculation for homologous structure
SSM - see superpose task under Coordinate utilities. This matches secondary structure and gives RMSD for CAs - inceredibly useful program.. Eleanor On 11/19/2010 10:55 PM, Srivastava, Dhiraj (MU-Student) wrote: Hi All does anyone know any software that can calculate and print out RMSD of every residue (c alpha will be good) for homologous structures which has only 30-40 % sequence similarity? I looked on the web but all the software that I found require the sequence to be the same for both structure. Thank you Dhiraj
[ccp4bb] per-residue RMSD calculation for homologous structure
Hi All does anyone know any software that can calculate and print out RMSD of every residue (c alpha will be good) for homologous structures which has only 30-40 % sequence similarity? I looked on the web but all the software that I found require the sequence to be the same for both structure. Thank you Dhiraj
Re: [ccp4bb] per-residue RMSD calculation for homologous structure
On Friday, November 19, 2010 02:55:54 pm Srivastava, Dhiraj (MU-Student) wrote: Hi All does anyone know any software that can calculate and print out RMSD of every residue (c alpha will be good) for homologous structures which has only 30-40 % sequence similarity? I looked on the web but all the software that I found require the sequence to be the same for both structure. This is not a well-defined calculation. In regions where the structures do not superimpose well, how do you decide which C-alpha pairs with which? What about insertions/deletions? Usually it only makes sense to calculate RMSD over those residues which line up structurally, so it won't be every residue. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] per-residue RMSD calculation for homologous structure
I looked on the web but all the software that I found require the sequence to be the same for both structure. most modern programs perform some kind of local-global alignment first to define the corresponding residues and then compute the statistics. BR
Re: [ccp4bb] per-residue RMSD calculation for homologous structure
Dear Dhiraj; Please try the following web site http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html Here you will find a number of option for structure base sequence alignment no matter what is the similarity of your structures. Regarding the RMSD of every residues you can find this option by using the Dalilite server. Good luck Bashir On Fri, November 19, 2010 23:55, Srivastava, Dhiraj (MU-Student) wrote: Hi All does anyone know any software that can calculate and print out RMSD of every residue (c alpha will be good) for homologous structures which has only 30-40 % sequence similarity? I looked on the web but all the software that I found require the sequence to be the same for both structure. Thank you Dhiraj -- Muhammad Bashir Khan ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
