Hi Greg, I tested writing the molmap output to MRC format with the current Chimera production release 1.2540 (newer than the 1.2509 version you are using) and it gave the correct non-zero origin. Could you try with 1.2540? Chimera writes MRC 2000 format which uses floating point xorigin, yorigin, zorigin fields instead of ncstart, nrstart, nsstart integer origin header values. I'm not clear how your C++ fix that modifies the header is working, but I don't think it worthwhile for me to debug an old version of Chimera. If you can produce the problem in the current Chimera production release then I'll look into it. Tom Grigore Pintilie wrote:
Hi Tom,
Thanks for the quick response! Actually, and sorry for not specifying previously, I am writing the file to MRC format... From my understanding of this fromat, it also requires specification of the origin as an integral grid index (in the field nstart).
I've now gotten around this problem by writing a little C++ program that reads the mrc file, changes the nstart field, and then writes the mrc file again. I put the correct origin, which i get from chimera right after generating the map, as a floating point number, in the variable o, and then in the C++ program change nstart as follows:
nstart[0] = (int) round ( o[0] / step[0] ); nstart[1] = (int) round ( o[1] / step[1] ); nstart[2] = (int) round ( o[2] / step[2] );
(step is the variable that contains the dimensions of the grid cells)
this works perfectly, when i load the mrc file again, it has the correct position and origin. It's rather strange that chimera doesn't seem to save the origin properly. It would be nice to not have to call my C++ program, and also it might help others using chimera... although I can understand the dilemma with the origin specified as an integer...
Greg
On Tue, Aug 19, 2008 at 1:23 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:
Hi Greg,
The trouble is you are writing out the map in BRIX format which I believe only allows integer grid index values for the origin of the map. The molmap command creates a map whose origin is not at an integral grid index.
I could be wrong about the BRIX format, it may allow floating point origin values, but the documentation for BRIX does not say and gives example code for writing the file which uses integer format. I guess the next step is to try writing a floating point origin in to the text BRIX header and open it in O and see what happens (error, misaligned, or correctly aligned).
To avoid this problem you can write your map out in MRC format.
Tom
Grigore Pintilie wrote:
Hello,
I'm wondering why when I generate a density map from a pdb structure (using the molmap command) and then save it, once I reopen it it seems to have shifted with respect to the structure. I'm noticing that before saving it, the generated map has a certain origin (shown in the Coordinates pane in the Volume Viewer), and then when I reopen it the origin appears as 0 0 0. If I copy the origin shown initially and then paste it into the origin of the opened file, this shifts the map to the correct position, but why isn't the right origin saved with the file?
I'm using alpha version 1 build 2509 2008/05/01, platform win32
Many thanks,
Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users