Hi Sharyn,

If you want to try something still in the development stages, the ISOLDE plugin to ChimeraX (our next generation Chimera program) reads MTZ files. You would install the ChimeraX daily build, run it and use Tools / More Tools… to get the ISOLDE plugin developed by Tristan Croll at University of Cambridge. It only works on Linux and Mac. Keep in mind that ChimeraX does not have a lot of the Chimera features — check out the ChimeraX web site to see if it might be useful to you. Here is some info on ISOLDE

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde

Tom

On Feb 22, 2018, at 9:39 AM, Elaine Meng wrote:

Hi Sharyn, Sorry, Chimera does not read or convert mtz files. (By the way, the address for Chimera questions is chimera-users@cgl.ucsf.edu , CC’d here.)

Previous posts to this list suggest some other program such as CCP4 fft can be used to create a map file from an mtz file, for example: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-February/000700.html

You can search the Chimera-users mail archive for topics like "mtz" from here: http://www.rbvi.ucsf.edu/chimera/docs/feedback.html

I hope this helps, Elaine

---

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

...

From: Sharyn Endow, Ph.D. sharyn.endow@duke.edu Sent: Thursday, February 22, 2018 5:01 AM Subject: Open MTZ file

Is it possible to open an .mtz file in Chimera?

Sharyn A. Endow, PhD
Professor of Cell Biology, DUMC
Professor of NBD, Duke-NUS
PO Box 3709
450 Sands Bldg/Research Drive
Durham, NC 27710  USA
T 919 684-4311  F 919 681-9929

---

Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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@einsteinmed.orgmailto:hernando.sosa@einsteinmed.org ___________________________________

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

CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.

Hi Hernando, Chimera does not convert MTZ to density maps, sorry, as discussed in various older posts. https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users%2F2014-May%2F009936.html&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4a1ec04e612a4bd16b4708d84526bd5f%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637335379979958416&sdata=xfi9g9u6OSoNm1uzcritIhyY8P1ORenSl1cTZJnEbY4%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato.cgl.ucsf.edu%2Fpipermail%2Fchimera-users%2F2006-February%2F000700.html&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4a1ec04e612a4bd16b4708d84526bd5f%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637335379979958416&sdata=WcAa5VLSrUPOntv6vAvVSKqiBQKuIQsQc7QBDO39zuI%3D&reserved=0

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). https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Ffiletypes.html%23volume&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C4a1ec04e612a4bd16b4708d84526bd5f%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637335379979958416&sdata=iWXVBvjwJvTZQbNr9hwyExbL11FjAG%2BrenKZNQLy6ec%3D&reserved=0

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@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