[Chimera-users] Difference between atoms' coordinates on screen and in a PDB file

[Elaine Meng]

Maybe I'm not understanding the question.  You could make a Chimera command file (just a text file, filename ending in .com or .cmd) that has the move commands in it.  You could first open the original structures and then open the Chimera command file, which would execute the commands.  If you are making an animation with a script, those commands could be at the beginning of the script before the recording.  My only other idea is to just save a Chimera session, which can later be restored.
Elaine

On Sep 14, 2012, at 11:26 AM, Mateusz Dobrychłop wrote:

> Hi Elaine,
> 
> Thank you for your reply!
> 
> I'm trying to recreate the components' moves from another software (in order to record it and export it to a movie file). The software generates a text "history" file with a list of all the moves the components make and a PDB file which is a result of those transformations. After applying all the transformations listed in the history file using Chimera, the stuff that's displayed on screen does not match the "result" model from this other software. Hovewer, if I save the result of my Chimera transformations into a PDB file, it perfectly matches the result file from the other software.
> 
> What I'm trying to say is that the PDB file that I create is actually okay, but I'm trying to generate an animation so I much more care about the things that are displayed in Chimera window.
> 
> Is there maybe a way to move (not save) the structures relatively to one of them?
> 
> Mateusz
> 
> 2012/9/14 Elaine Meng <meng at cgl.ucsf.edu>
> Hi Mateusz,
> To retain the spatial relationships between the structures when you have moved them independently, you need to save the PDBs "relative to" the same model.  For example, save models 0,1,2 all relative to 0.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:
> 
> > Hello,
> > I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)?
> > Mateusz
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users