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Heteroatom problem, message 2



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 Penniston

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John T. Penniston, Ph.D.
Dept. of Biochemistry and Molecular Biology
Guggenheim 16, Mayo Clinic
200 First St. SW
Rochester, MN 55905 USA


Attachment: error2.zip
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