[Chimera-users] Help with coordinates please

drew richardson drew_andalso_lou at hotmail.com
Wed Feb 1 15:39:33 PST 2017

Hi Elaine,

Thank you so much for getting back to me so quickly. Your reply was most useful. I eventually made a slightly different image just from the commands you suggested.

Kind Regards


Drew Richardson

ID: 27927431

(1st year biochemistry)

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 01 February 2017 18:57
To: drew richardson
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Help with coordinates please

Hi Drew,
Welcome to Chimera!

Although you can save and reset positions with "savepos" and "reset" commands, the positions are only saved within your session, so you would have to save a session file (which also saves the current position automatically) and others would have to open that session file to get the same exact positions.

However, I understand the advantages of simply sharing a series of commands instead of a whole  session file.  Unfortunately if you have moved things around with the mouse it is not simple to figure out the commands to give you the same position.

What I have done in the past is to (try to) regenerate model position(s) using only commands ("move" to translate, "turn" to rotate, "scale" to zoom, "window" or "focus" to center the view on items of interest, "matchmaker" to superimpose, etc.).  The alternative is to just share the commands to do everything EXCEPT the positioning, and leave that up to the other people to do interactively, like you did.

There is also a "matrixget" command to write transformation matrices to a file, and "matrixset" to apply that file to set model positions, but that again has the disadvantage of requiring you to share a separate file.

Command manual pages here:
Commands Index - University of California, San Francisco<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
Commands Index. Commands are entered into Chimera's Command Line. Past commands can be accessed from the Command History, and commands can be placed in an executable ...

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 Feb 1, 2017, at 8:48 AM, drew richardson <drew_andalso_lou at hotmail.com> wrote:
> Hi,
> I am very new chimera and I am having to use it for a project at university. I have to create a picture from chimera and then list commands so anybody can recreate it just by typing in the commands in the command box.
> The problem I am having is: once I have rotated and zoomed manually using the mouse I don't know how to recreate that position and view by using typed commands. I can't even seem to find anywhere the coordinates of the new rotation.
> Could you please help me? How do I recreate the zoom and rotation using commands only, so that anyone wanting to recreate the view I have can do it just by typing in a list of commands after loading my original PDB file?
> Kind regards
> rew Richardson

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