Re: AW: AW: AW: tclBC incorrect output

From: Cruz-Chu Eduardo Roberto (
Date: Fri May 04 2012 - 02:43:20 CDT

Dear P-L Chau;

Getting the coordinates from the PDB is straightforward. You must check your script. The script you used works for the files in the tutorial, but now if you use your own PDB, first check that such PDB is similar to the one in the tutorial.

Now, I can bet $1000 that the coordinates in the PDB match the ones you get from the tcl console. Just do something like :


set all [ atomselect top all ]
set allIndex [ $all get index ]
$all delete

foreach index $allIndex {

set oneSel [ atomselect top "index $index" ]
set oneXYZ [ $oneSel get { x y z } ];

puts "$index $oneXYZ"

$oneSel delete;
unset oneXYZ


unset allIndex




On May 4, 2012, at 9:19 AM, P.-L. Chau wrote:

> Thank you for your message.
>> Check if the coordinates printed match to another atom in the pdb. So we
>> know if it is a issue of the atom numbers or the getcoord command.
>> Possibly the getcoord command starts the atom numbers with zero, while
>> pdb starts with 1. If so, the atom numbers needs to be decreased by 1.
>> Also, check if the atomnumbers put from the first part of the script
>> match the right CA atoms in the pdb.
> The coordinates printed match NONE of the atoms in the PDB file. Could I
> ask you if there is some way to check the getcoord command?
> Thank you very much indeed!
> P-L Chau

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