[Chimera-users] Python script for reading volume values at atom positions

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 19 10:12:45 PST 2017


Hi Kyle,
Yes, it is also implemented as the command “measure mapValues”, see:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues>

It includes a “report” option to send the values to the Reply Log.  

Then you could save Reply Log contents to a file, but that requires a bit of python shown at the bottom of this page:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

Another possibility is in “measure mapValues” use name “bfactor” and then save as PDB file with “write” command.  That would force rounding to fit into the bfactor column, however.

So maybe that script would be more efficient, if it works or could be modified to work, but somebody else would have to help with that!
Best,
Elaine

> On Jan 19, 2017, at 9:54 AM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
> 
> Hi Elaine,
> 
> Thanks for this, absolutely excellent tool but I really need to script
> this, command line or python. I have 28 maps and 6 models per map you
> see...
> 
> I don't think there's a command line implementation of this?
> 
> Thanks,
> Kyle
> 
>> On 19 Jan 2017, at 09:46, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Kyle,
>> I can’t answer about the old script, but if it is feasible for you to do interactively, there is a "Values at Atom Positions" tool included in Chimera.  It’s in the menu under Tools… Volume Data, and it assigns the interpolated values as an atom attribute.  You can write out the values using the File menu of the Render by Attribute tool, which automatically pops up when you click the Histogram button to assign the values.
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html>
>> 
>> I hope this helps,
>> Elaine
>> 
>> 
>>> On Jan 18, 2017, at 7:36 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
>>> 
>>> Dear chimera dev and users,
>>> 
>>> Can anyone confirm with the latest chimera version (i’m running v1.11.2 build 41376) if this python script for measuring map values at atoms works for them?
>>> 
>>> The script was reported previously on the users list here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001587.html
>>> 
>>> For me I get a python import error:
>>> from VolumeViewer import Data_Region, full_region, Rendering_Options
>>> 
>>> Thanks for your insight!
>>> 
>>> Best wishes,
>>> Kyle




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