Greetings, I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"
Hi Geoffrey, It's probably not the header per se, but the format. Chimera interprets files with the .map suffix as CCP4 density map format, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> but that is not necessarily the format written by phenix.refine. I'm looking online and it says phenix.refine writes ASCII X-PLOR format. In that case, you might try renaming the file with the .xplor suffix and then try opening it in Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 2, 2009, at 1:46 PM, Geoffrey Feld wrote:
Greetings, I'm trying to make a figure showing off my best density from a 2Fo- Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read? Thanks, -- Geoffrey K. Feld
Hi Geoffrey, The maps output from phenix.refine are in ASCII X-PLOR format. http://www.phenix-online.org/documentation/refinement.htm#anch2 The file suffix ".map" is assumed by Chimera to be a different format CCP4 map format. To read your maps set the File Type in the Chimera Open dialog to "all (ask type)" and after you choose the file and press the open button tell it the map is "CNS or XPLOR density map". Alternatively rename the with file suffix ".xplor" or ".cns" so Chimera will automatically recognize the type. A third approach is to use the Chimera command-line (Favorite menu) and a command like "open xplor:mymap.map" with the "xplor:" prefix in front of the file name. Tom -------- Original Message -------- Subject: [Chimera-users] phenix map not reading in chimera From: Geoffrey Feld To: chimera-users Date: 12/2/09 1:46 PM
Greetings,
I'm trying to make a figure showing off my best density from a 2Fo-Fc map I generated using phenix.refine. The output file has a .map suffix. However, Chimera gives an error about the header, which I've included: MRC header value nsymbt (538976288) is invalid. How do I give Chimera a map with a header it can read?
Thanks,
-- Geoffrey K. Feld
Department of Chemistry 492 Stanley Hall University of California, Berkeley
"Vigilia pretium libertatis"
participants (3)
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Elaine Meng -
Geoffrey Feld -
Thomas Goddard