[Chimera-users] Difference between atoms' coordinates on screen and in a PDB file
goddard at sonic.net
Fri Sep 14 13:17:17 PDT 2012
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?
> 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 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users