VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Thu Nov 29 2007 - 02:24:56 CST

Hey Jin Tao,

as far as I understood, the state in vmd contains only visualization, i.e. all
the different representations viewing angle, colors etc.
For your problem, you should save the modified coordinates in a file (e.g xyz
or pdb format, for instance my_coord.xyz), save the state in a file (for
instance my_state.vmd), and modify the file name of the coordinates in the
latter (a line containing "mol new" or "mol add" into:
mol new my_coord.xyz type xyz waitfor all ).

eddi

On Thursday 29 November 2007 06:14, TaoJin wrote:
> Hello, VMD
>
> I applied a transformation matrices to change a protein’s coordinates and
> then saved the state. But when I reopened the state I found the protein’s
> coordinates come back to the original coordinates, that is, the coordinate
> didn’t change. I tried several times and all were that. It seems like that
> state can’t save the coordinate you have changed even by applying
> transformation matrices. However, when you save the pdb, the coordinate
> changes by applying the transformation matrices can be saved. So I am
> curious if there is any method to solve this problem that can't saving the
> changed coordinate in a state?
>
>
> Thank you for your help!
> Jin Tao
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> 用 Live Search 搜尽天下资讯！
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-- 
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Eduard Schreiner                     e-mail: eduard.schreiner_at_theochem.rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                              http://www.theochem.rub.de
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