<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi Mateusz,<br>
<br>
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<br>
<br>
move x 0.5 100 model #1 coord #0<br>
<br>
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<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html</a><br>
<br>
and examples of other commands useful in movie making<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html">http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html</a><br>
<br>
Tom<br>
<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Difference between atoms' coordinates
on screen and in a PDB file<br>
From: Mateusz Dobrychłop <br>
To: UCSF Chimera Mailing List <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a><br>
Date: 9/14/12 11:26 AM<br>
</div>
<blockquote
cite="mid:CAMJBqiwHzGgsc1rASkoLs1kdomtZx_eq8qLk88uHi9J_BL+MXA@mail.gmail.com"
type="cite">Hi Elaine,
<div><br>
</div>
<div>Thank you for your reply!</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Is there maybe a way to move (not save) the structures
relatively to one of them?</div>
<div><br>
</div>
<div>Mateusz<br>
<br>
<div class="gmail_quote">2012/9/14 Elaine Meng<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
Mateusz,<br>
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.<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb">
<div class="h5"><br>
On Sep 13, 2012, at 6:26 PM, Mateusz Dobrychłop wrote:<br>
<br>
> Hello,<br>
> 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: <a moz-do-not-send="true"
href="http://i.imgur.com/gtGBN.png" target="_blank">http://i.imgur.com/gtGBN.png</a>
). 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)?<br>
> Mateusz<br>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Chimera-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
</pre>
</blockquote>
<br>
</body>
</html>