On Tue, Nov 28, 2006, Steve Seibold wrote:
>
> Is there a way to change HIE to HID "in" xleap? That is without going
> "edit unit". I have looked at "help" in xleap, but cannot determine if I
> can do this or not.
>
> I realize I could just change the pdb file, but I already have whole
> molecule (very large!) with metals etc coordinated to residues etc in
> xleap and was hoping not to have to scratch all the work to go back to
> pdb file.
>
If you want to change *all* HIE to HID, you could use the addPdbResMap
command, something like
addPdbResMap {
{ "HIE" "HID" }
}
But there is no easy way to just change certain histidines (e.g. those bonded
to metals) and leave others alone.
I don't know what you mean by "scratch all the work to go back to the pdb
file". If you didn't save your leap commands in a file for re-use later, this
will be a good learning experience :-). You can generally go through the
leap.log file and extract the commands used by the previous run; try this
grep '^>>' leap.log > leap.in
Then edit the leap.in file to be sure it does what you want. Then you can
take rerun all the things you did before on your modified pdb file.
...regards....dac
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Received on Wed Nov 29 2006 - 06:07:49 PST
