[Chimera-users] Volume viewer levels question

[Elaine Meng]

Hi Markus,
If your map file actually has that information in it, I don’t see why not… but evidence suggests your map doesn’t have that full range of information in it.  I.e. it does not have values above the value to which it resets when you adjust the slider. That’s why I said maybe it was written out incorrectly, or in a different format than the script expects.
Elaine

> On May 15, 2018, at 12:29 PM, Markus Heller <mheller at cdrd.ca> wrote:
> 
> Hi Elaine,
>  
> Here's a bit of background: this map is the result of a mapping using H2O as probe done by PLI [1].  I would like to adjust the contour levels to look like the red contour levels in Panel B in the attached figure (figure 4 from [1]).  How can I achieve this, or is this not possible in Chimera?
>  
> Thanks
> Markus
>  
> [1] Verdonk et al., J. Med. Chem 2016, 59, 6891--6902; DOI: 10.1021/acs.jmedchem.6b00716
>  
> <image001.png>
>  
> > -----Original Message-----
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Tuesday, May 15, 2018 11:06 AM
> > To: Markus Heller <mheller at cdrd.ca>
> > Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Volume viewer levels question
> >
> > Hi Markus,
> > The behavior you describe is like entering some value that is higher than what is
> > in your map, so there is no contour surface any more.   Then when you move the
> > slider, it resets to the maximum value found.  Not sure why you expect higher
> > levels, but maybe whatever program that wrote the file didn’t write bigger values,
> > or didn’t write the format correctly.
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> > > On May 15, 2018, at 10:15 AM, Markus Heller <mheller at cdrd.ca> wrote:
> > >
> > > Hi all,
> > >
> > > I have an issue displaying a map file that I opened using the insightgrid.py
> > script.
> > >
> > > When displaying the grid at the highest level I can get, the levels are still too
> > low, but when I set the levels higher by typing something into the level field (e.g.
> > 1.2e+03 instead of the 1e+03), the levels disappear altogether as shown in the
> > second screenshot.  As soon as I adjust the slider, the levels reset to 1e+03.
> > What am I doing wrong?
> > >
> > > Thanks
> > > Markus
>  
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