[Chimera-users] Open MTZ file

[Hernando J Sosa]

Thanks Elaine,
As you indicated chimera does read the dsn6 format. It does not recognize the extension .dsn6 (the one given in the PDB  files) but in the Open->Type selection dialogue there is the option 'BRIX or DSN6 density map' that works.

Thanks again,

Hernando


___________________________________
Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone (718) 430-3456
FAX (718) 430-8819
emai:  hernando.sosa at einsteinmed.org<mailto:hernando.sosa at einsteinmed.org>
___________________________________


________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, August 20, 2020 12:33 PM
To: Hernando J Sosa <hernando.sosa at einsteinmed.org>
Cc: Chimera User Help <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Open MTZ file

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Hi Hernando,
Chimera does not convert MTZ to density maps, sorry, as discussed in various older posts.
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I don't really understand the part about dsn6: that is already a density map format, so if you have that, you could try opening it as dsn6 (e.g. by using filename ending with .omap or .brix).
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ChimeraX can read mtz files if you both:
(1) already have an atomic structure that goes with the mtz
(2) download and install the Clipper bundle from the ChimeraX Tool Shed
(start ChimeraX, then use menu Tools... More Tools to get to the Tool Shed)

More details on opening MTZ in ChimeraX:
<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fopen.html%23clipper&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4a1ec04e612a4bd16b4708d84526bd5f%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637335379979958416&sdata=5jturcnSN4OWsZ5GlSimFRZnpn50YU%2FntKSUvQazlV0%3D&reserved=0>

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

> On Aug 20, 2020, at 8:35 AM, Hernando J Sosa <hernando.sosa at einsteinmed.org> wrote:
>
> Is there a way to read/convert MTZ or dsn6 (?)  crystallography electron density as provided by the Protein Data Bank files in chimera?
>
> I know that Phenix has a routine to convert mrc density fles (readable by Chimera) into   MTZ  files (readable in Coot but not Chimera) but  not the other way around.
>
> Thanks
>
> Hernando

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