Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh Graduate student Dept.of Biochemistry Purdue University
Hi Rakesh, Our volume expert is away right now, but I would suggest using the "Help... Report a Bug" dialog and attaching an example of a file needed to reproduce this problem. It may be that these files do not adhere to the MRC format, or at least as Chimera expects it. Please include your email address in the bugreport if you wish feedback when someone is able to look at this in more detail. I see a note in the documentation <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#mrcout> that MRC files output by Chimera are in MRC 2000 format, and "Older MRC-reading programs or programs expecting CCP4 format will read such files successfully but may not align the data correctly with other data sets." However, I don't know specifically what subtypes of MRC format are handled on input, or if some simple editing could solve the problem. Sorry I don't know more, 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 Aug 24, 2010, at 1:45 PM, rjoshi@purdue.edu wrote:
Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh
Dear Rakesh, Chimera is not able to read mtz files directly. You need to convert the mtz file into a ccp4 or XPLOR map format using a program like fft (distributed with the CCP4 suite). Then Chimera should be able to read it in. You may also want to ask for the feature to be added :O) Terry On 8/24/2010 2:27 PM, Elaine Meng wrote:
Hi Rakesh, Our volume expert is away right now, but I would suggest using the "Help... Report a Bug" dialog and attaching an example of a file needed to reproduce this problem. It may be that these files do not adhere to the MRC format, or at least as Chimera expects it. Please include your email address in the bugreport if you wish feedback when someone is able to look at this in more detail.
I see a note in the documentation <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#mrcout> that MRC files output by Chimera are in MRC 2000 format, and "Older MRC-reading programs or programs expecting CCP4 format will read such files successfully but may not align the data correctly with other data sets."
However, I don't know specifically what subtypes of MRC format are handled on input, or if some simple editing could solve the problem.
Sorry I don't know more, 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 Aug 24, 2010, at 1:45 PM, rjoshi@purdue.edu wrote:
Hi, i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise. Cheers Rakesh
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-- PaulaTherese Lang Postdoctoral Scholar Alber Lab, UC Berkeley http://ucxray.berkeley.edu/ringer.htm
Hi Rakesh, An MTZ file contains structure factors, not a density map. Basically a Fourier transform is needed to get the density map from the structure factors. There is a Chimera feature request (#201) http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests to have Chimera calculate the map from the structure factors. It is not an entirely trivial calculation since symmetry and missing structure factors must be accounted for. Chimera density map features are aimed at electron microscopy rather than x-ray crystallography and Chimera is missing useful features for x-ray maps. For example Chimera will not automatically periodically extend a unit cell map to cover a display molecule as COOT does. For now you'll need to calculate the density map using other software. Tom
Hi,
i am having problems loading electron density files from CCP4 and Phenix. The error message reads "Bad MRC grid size (129737328,-319356160,1145110528)". Please advise.
Cheers Rakesh
Graduate student Dept.of Biochemistry Purdue University
participants (4)
-
Elaine Meng -
rjoshi＠purdue.edu -
Terry Lang -
Tom Goddard