Hello Chimera users This might be a somewhat “of-topic” question though I thought that this would be a good place to start. When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map. My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files? I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at. Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated. Best regards // Gustaf
Hi Gustaf, I guess it would be possible to make some AWK script to get the maximum density value in an XPLOR map file. You would need to ignore the first 7 lines then take the maximum of the values on the remaining lines. An example XPLOR file is shown below. It seems saner to use an XPLOR file reader to read each file and then get max value, Chimera Python code could do that. Some Python code to open a map file and get the matrix values is shown here https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py <https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py> Tom This line is ignored 1 sean mooney generated grid density 40 -19 20 40 -19 20 40 -19 20 40.000 40.000 40.000 90.000 90.000 90.000 XYZ -19 0.00000 0.00000 0.00000 0.00000 0.00000 2.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ...
On Sep 25, 2020, at 12:21 AM, Gustaf Olsson <gustaf.olsson@lnu.se> wrote:
Hello Chimera users
This might be a somewhat “of-topic” question though I thought that this would be a good place to start.
When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map.
My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files?
I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at.
Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated.
Best regards // Gustaf
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participants (2)
-
Gustaf Olsson -
Tom Goddard