I've been trying for days to make a proper model of my large (1058
residue) membrane protein, PMCA. It needs to contain a calcium ion, but
I can't get modeller to put it in. I'm sorry the attached files are so
big, but it's a big molecule.
I'm sending this as 2 messages, zipped up using Winzip; If I try to put
it in a single message, it bounces, and I think all of these files are
needed to diagnose the problem. I'm trying to model PMCA based on the
only known homolog 1EUL. 1EUL contains 2 calcium ions, and I expect the
PMCA version to contain only one of them, as indicated in the alignment
file. No matter what I try, the PMCA file produced has the calcium
removed. The file I have renamed as PMCA E1.pdb is the final file
produced in the attempt enclosed here and described in the log file. I
did this one using an MS-DOS box under Windows 98, but the same kinds of
errors occur in Windows 2000. Thanks for your attention.
John T. Penniston, Ph.D.
Dept. of Biochemistry and Molecular Biology
Guggenheim 16, Mayo Clinic
200 First St. SW
Rochester, MN 55905 USA