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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. > ******************************************************************