AMBER Archive (2006)

Subject: Re: AMBER: Trouble with Leap

From: Scott Brozell (
Date: Mon Oct 09 2006 - 20:42:38 CDT


On Mon, 9 Oct 2006, Biswa Ranjan Meher wrote:

> Dear Amber users
> I am having trouble with Leap. The problem is that I want to edit one
> protein in xleap. I loaded one pdb file in xleap and by edit selected
> atoms from the menu bar selected all the atoms of the protein. But strange
> thing is that in the spread sheet editor (editor table) I got the
> lists of atoms of FEW residues but NOT ALL. So my querry here is that, is there any
> tricks, which I am missing here to visualize all the atoms of all the
> residues of the protein concern in the spread sheet editor?
> I am running xleap on a Linux (redhat 8.0) system.
> Has anyone else run into this problem and knows how to correct it?

No. For example, I loaded 228 residue 1E1J, edited that unit,
and can scroll down to what seems to be the last residue.
I note that it takes a couple of seconds for the table contents to
catch up to rapid scrolling and that the end of the scroll extends
past the end of the contents of the table.
But I do not see any obvious failure.
You'll need to provide a detailed example to reproduce any problems
that you have.

>From a different perspective, why would one want to edit a big protein
this way ? Anything that can be done in the editor can be done with
the LEaP command line (as far as I know).



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