[Chimera-users] Volume viewer levels question

[Markus Heller]

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



[cid:image001.png at 01D3EC48.52B943B0]



> -----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<mailto: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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