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 command

    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

    http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html

and examples of other commands useful in movie making

    http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html

Tom

-------- 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@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
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