[Chimera-users] Saving BRIX volume file, missing data

[Thomas Goddard]

Hi Miguel,

   I just tested saving volume data in BRIX file format on Chimera 1.4 
and also with the current daily build and both worked correctly, nothing 
left out.  Could you send me an MRC map that when I open it and save it 
as BRIX does not work correctly?  Also please give me the exact Chimera 
version and operating system (Help / About Chimera...).

   BRIX format saves only 8-bit values.  So if you have a large range of 
values -- say most map values are 0-10 and then one is 10000, then all 
the 0-10 values will be reduced to the same value (0) when it is forced 
into the 8-bit BRIX value range by a linear scaling.

Thanks,
	Tom


> Hi Tom,
>
> Thank you! This way I can extend the number of total torsions at least ten times, though I'm not sure I'm gaining much with that. I will see better once I start filling VdW volumens.
>
> Just a remark: I have noticed something wrong with brix format maps: they are not saved properly, a part of them is left out. I haven't found out whether this is a problem with a certain count threshold, or a number of grid points, the fact is that a good part of the map is lost. This happens whether I save it from the script as you say or from the GUI using the File menu of the Volume Viewer. So I am using MRC format for the time being, which works fine in all cases.
>
> Best regards,
>
>
> Miguel
>
> Le 17 mai 2010 à 19:40, Thomas Goddard a écrit :
>
>> Hi Miguel,
>>
>>   The Python call to save your volume data model v in a file is
>>
>> 	v.write_file('/tmp/myfile.brix', format = 'dsn6')
>>
>> If you do not want to create the volume model you can instead directly write out the grid object.
>>
>>     from VolumeData import save_grid_data
>>     save_grid_data(grid, path, format)
>>
>> I figured this out by looking at the write_file() Python code in
>>
>> 	chimera/share/VolumeViewer/volume.py
>>
>> The allowed formats are listed in the file_writers variable in
>>
>> 	chimera/share/VolumeData/fileformats.py
>>
>>   Tom
>>