[Molvis-list] Question on centering of different PDBs

Elmar Krieger elmar at cmbi.ru.nl
Thu Apr 27 09:19:24 EDT 2006

Hi Gunnar,

> I have a quick question about centering different PDB files. Currently I'm working with 4 different PDB files that need to be centered on the 0,0,0 coordinate. Unfortunately, I have not had much success so far since each PDB file opens up in different locations given their own coordinate systems.
> Is there a software (preferably free/opensource) that will allow me to center all the PDBs on the world origin and save them back out?

You can do that with the free YASARA View ( http://www.yasara.org/viewdl ).

1) The manual way:
Click File > Load > PDB file (make sure that the 'Center' button is 
*CHECKED* to center the structure at 0/0/0)
Click File > Save as > PDB file, select the structure and *UNCHECK* the 
'Transform' button to keep the current atom coordinates

2) The automatic way:
Run the following macro, e.g. from the command line with
yasara center.mcr

for id in '1crn','5tim'
   LoadPDB (id),center=yes
   SavePDB all,(id)_centered,transform=no

This will create the file '1crn_centered.pdb' etc.
If you need more details, just contact me off-list.

All the best,

Elmar Krieger, PhD
YASARA Biosciences & CMBI Outstation Austria
Neue-Welt-Hoehe 13/b
A-8042 Graz

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