Hi Wen You can write out coordinates of a PDB model relative to another model such volume you hand docked to, using Model Panel (under Favorites menu or Tools/Inspectors menu). Show the Model Panel dialog, click on the PDB model in the list, press the "Write PDB" button in the right column of the Model Panel. Then a Save file dialog comes up and at the bottom is a checkbutton that says "Save relative to model chosen in model panel when 'OK' is hit". You then click on the volume listed in the Model Panel that the PDB coordinates should be relative to. Then press OK in the Save dialog. A bit crazy. We'll probably improve this confusing interface in a future release. Tom
From: Wen Jiang <wjiang@bcm.tmc.edu> Subject: Re: chimera questions Date: Thu, 10 Jun 2004 17:06:28 -0500 To: Thomas Goddard <goddard@cgl.ucsf.edu>
Tom, Is it possible to do manual fit of PDB to a density map in Chimera then save the transformed PDB coordinates to a new PDB file? If it is not possible, how to read out the transformations applied to the PDB model? Thanks,
Wen