I found that the origin of /mrc/ maps is read correctly and can be used to place one map in respect of another. For example: 1.mrc (origin: 10,0,0) is going to be shifted 10 pixels with respect of map 0.mrc (origin: 0,0,0). I can not reproduce the same behavior with CCP4 format (.map) . The origin is not read correctly. Thank you.
Hi Eduardo, This may be an issue for Tom Goddard to address in more detail (and he should be back soon), but I thought I would mention that you can change the origin after reading in the map data. To do that, from the Features menu in Volume Viewer, choose "Origin and Scale" - this will open a section of the dialog where you can enter the origin that you want. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Eduardo, The MRC and CCP4 map file formats are almost identical. There is a difference in how the origin is specified though. In MRC 2000 format some of the reserved extra space in the standard CCP4 header is used for xorigin, yorigin, and zorigin floating point values. The standard CCP4 format does not have these fields and the origin is instead determined using integer ncstart, nrstart, nsstart header values. These *integer* origin values are only adequate for subvolumes of crystallographic density maps. When you say that the CCP4 map does not align correctly does Chimera report your 1.mrc map origin as (0,0,0) instead of the desired (10,0,0)? If that is the case then I believe the problem is with the code that wrote the map. It did not set the ncstart, nrstart, nsstart parameters to specify a (10,0,0) origin (and it will be impossible in CCP4 format unless the grid plane spacing evenly divides 10 because the origin header values must be integers). Tom
participants (3)
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Eduardo Sanz-Garcia -
Elaine Meng -
Tom Goddard