Hi Elaine,

  I was a bit confused by the ChimeraX open MTZ documentation because it sounds like it can only fetch structure factors (.mtz) from the PDB.  But users to X-ray structures have their own MTZ files and it seems that those can be opened too by specifying a file name in the open command and the "structureModel" option of an already open atomic model.

usage open format mtz
open names [structureModel a structure specifier] [overSampling a number] [autoFreeFlags true or false]
    — read and display data
  names: file names to open; a name of 'browse' will bring up a file browser

Maybe the documentation should mention that a local .mtz file can be opened too.

Tom


On Jul 6, 2023, at 10:12 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Oh, my coworker pointed out that you may be using Chimera because you mentioned version 1.17.2.  ChimeraX and Chimera are two different programs, and only ChimeraX can be used to open MTZ files.  The current version of ChimeraX is 1.6.

So you have to download and use ChimeraX, install the Clipper plugin (which is only for ChimeraX), and then follow the instructions in the link for opening MTZ files.

Elaine

On Jul 6, 2023, at 9:59 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Natalie,
Everything I know on this topic is written in the documentation linked below, and yes, as it says therein, you do need to have Clipper installed.  Then title of the section is "Open/Save Options from Clipper":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper>

I can't think of anything else to say without getting more details from you.  What is the problem?  Which part are you confused about?  What did you try?  What happened? Did you follow the instructions in the link?

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

On Jul 6, 2023, at 9:14 AM, Natalie Walsh <natalie.walsh@slu.edu> wrote:

Hello, I previously asked a question (sent to the wrong email, oops!) about not being able to use MTZ maps in Chimera X (I was using 1.17.1, I just installed 1.17.2 today and still have the same issues). These were the instructions previously provided:

"The instructions of how to open MTZ files with ChimeraX are here:

<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html*clipper__;Iw!!K543PA!Ox1LZzNzQApDmf7FvKaDJGumXWt0NeuwNfk6UeYLbEMsLtJnGth1NmoB2F8f8-JfrmqDlapDcFwTVbDcaCwb$ >

"Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option..." with example command, etc."

I read through the like and am still confused. I have also installed the Clipper Plugin (although I am unsure if it was installed correctly) since I saw somewhere that might be needed.

Thanks,
Natalie Walsh


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