I am surprised if the numbers are wrong, maybe your chosen superposition isn't the same as that used for superpose - there are 2 methods available - are you using the secondary structure matching, or the assigned residue match? Eleanor dodson On 5 Aug 2012, at 15:17, Zhou, Tongqing (NIH/VRC) [E] wrote:
> Dear All, > > I am trying to obtain the pairwise Ca-distances between corresponding > residues of two antibody light chains. CCP4 Superpose can output the > distances in the log file, but the numbers seem to be wrong when examed by > eye. Is there a way to calculate the pairwise distance between two pdb? > > Thanks, > > Tongqing > > Tongqing Zhou, Ph.D. > Staff Scientist > Structural Biology Section > Vaccine Research Center, NIAID/NIH > Building 40, Room 4609B > 40 Convent Drive, MSC3027 > Bethesda, MD 20892 > (301) 594-8710 (Tel) > (301) 793-0794 (Cell) > (301) 480-2658 (Fax) > ****************************************************************************** > The information in this e-mail and any of its attachments is confidential and > may contain sensitive information. It should not be used by anyone who is not > the original intended recipient. If you have received this e-mail in error > please inform the sender and delete it from your mailbox or any other storage > devices. National Institute of Allergy and Infectious Diseases shall not > accept liability for any statements made that are sender's own and not > expressly made on behalf of the NIAID by one of its representatives. > ******************************************************************
