[Chimera-users] view along a crystal axis

[Michael Elbaum]

Hi again,


One bug-let. Once I invoke the meshmol, I can no longer go back to the Unit Cell tool to create a new lattice, even if I deselect or even delete the new model generated from the Outline. The lattice parameters have disappeared. Hard to say if this is worth fixing, but just to be aware...


best,
Michael

________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Michael Elbaum
Sent: Saturday, January 9, 2021 7:46:32 PM
To: Tom Goddard; Chimera
Subject: Re: [Chimera-users] view along a crystal axis


Hi Elaine and Tom,


Thanks for your suggestions. They were very helpful. A combination of the meshmol and align and the "old way" works well. There is still an arbitrary rotation in the visible plane. (Is there an align command that works along the x axis rather than the line of sight?) To take care of that I choose two "atoms" along an orthogonal axis, align those, and then if necessary 'turn y 90'. It's not automatic but seems to be precise.


best wishes,

Michael

________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Saturday, January 9, 2021 2:06:03 AM
To: Chimera
Cc: Michael Elbaum
Subject: Re: [Chimera-users] view along a crystal axis

Hi Michael,

  A small additional trick can let you align the view along an axis.  You can turn the unit cell outline into a stick display made of fake atoms and bonds using the "meshmol"  command.  Then you can select two of the outline corner atoms and use the align command.

  Tom

open 1a0s
# Use menu Tools / Higher-Order Structure / Unit Cell to show copies and cell outline
# Ctrl-click on cell outline to select it
meshmol #0 1
# Select two corner "atoms" of the meshmol outline, ctrl click, then shift ctrl click.
align sel
set projection orthographic

[cid:38EFE46A-46C7-4C59-8C75-8BD4719342A8]
On Jan 8, 2021, at 9:32 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

Hi Michael,
I can't think of a direct way to align the view on a crystallographic axis... there is an "align" command to exactly align specified atoms along the line of sight in the center of the window:

<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/align.html>

However, there may not be atoms that lie exactly along or parallel to the crystallographic axis, or it may not be easy to identify them.

One roundabout way might be to use the Crystal Contacts tool (in menu under Tools... Higher-Order Structure) and click "Show Contacts" which shows the outline as markers and links.  Markers are essentially fake atoms, so you could select the two corners of the outline box you want to align (Ctrl-click, Shift-Ctrl-click) and then use command "align sel" ... then hide or delete the markers and links after you get the desired alignment.

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/crystalcontacts/crystalcontacts.html>

You might not want that in the center of the window, however, so additional translation ("move" commands) may be required afterwards.
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

I couldn't do the "atom" selection with the box shown by Unit Cell because I think it is just a mesh and the whole box gets selected instead of corners.

Other related commands...

Command "reset" will give coordinate Z axis along the line of sight.

Command "set projection orthographic" may be helpful to turn off perspective.

Since the alignment is somewhat of a rigamarole, you may prefer to keep doing it your current way!

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




On Jan 8, 2021, at 6:09 AM, Michael Elbaum <michael.elbaum at weizmann.ac.il<mailto:michael.elbaum at weizmann.ac.il>> wrote:

Hi.   I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this.
thanks for your help,
Michael
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