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 [cid:image001.png@01D3EC35.74E6A210] [cid:image004.png@01D3EC35.9B86A230]
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@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
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@01D3EC48.52B943B0]
-----Original Message-----
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Tuesday, May 15, 2018 11:06 AM
To: Markus Heller <mheller@cdrd.ca>
Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@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@cdrd.ca<mailto:mheller@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
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@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@cgl.ucsf.edu> Sent: Tuesday, May 15, 2018 11:06 AM To: Markus Heller <mheller@cdrd.ca> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@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@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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participants (2)
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Elaine Meng -
Markus Heller