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.org<mailto: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