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

Tom Goddard goddard at sonic.net
Fri Sep 14 13:17:17 PDT 2012

Hi Mateusz,

   I don't understand exactly what is going wrong for you.  But maybe an 
example will help.  If you have two models #0 and #1 you can move #1 
relative to #0 in 100 steps each 0.5 Angstrom along the x axis with a 

     move x 0.5 100 model #1 coord #0

The "coord #0" option is important here.  It says move along the x-axis 
of the model #0 coordinate system.  If you leave off that option it 
moves along the horizontal axis displayed on the screen.  That is 
different from the x-axis of model #0 if you have rotated the models.  
The "turn" command also accepts the coordinate system option.  Here is 
documentation for the move command


and examples of other commands useful in movie making



-------- Original Message --------
Subject: Re: [Chimera-users] Difference between atoms' coordinates on 
screen and in a PDB file
From: Mateusz Dobrychłop
To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
Date: 9/14/12 11:26 AM
> 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
>     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
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