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

Mateusz Dobrychłop dobry at g.pl
Fri Sep 14 11:26:53 PDT 2012

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


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
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