[Chimera-users] problem with electron density map

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 7 10:48:21 PDT 2018

Hi Steffi,
Did you try the other two things I mentioned?  (subregion full, or from the discussion in the previous post, “vop cover”)

Secondly, how do you know it is not showing all of your map?  If it’s a problem with scale (map shrunken relative to molecule) you can use Volume Viewer menu: Features… Coordinates to adjust voxel size.

Without having your exact data we can’t be sure what the issue is.

> On Aug 7, 2018, at 2:18 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote:
> Dear Elaine and Tom,
> thanks for your comments!
> Unfortunately, after changing to "all" and playing around with threshold nothing changes.
> Any further ideas?
> Thanks
> Steffi
> Tom Goddard <goddard at sonic.net> schrieb/wrote::
>> Hi Steffi,
>>  When Chimera opens a map larger than a certain size it only shows one plane.  Pressing the “All” button below the histogram that appears when a single plane is shown will show all the planes.  The size threshold for showing one plane is set using menu Volume Viewer / Features / Data Display Options.
>> 	Tom
>>> On Aug 6, 2018, at 9:48 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Hi Steffi,
>>> If it is only showing a subregion you can use Volume Viewer menu "Features… Subregion selection” to show subregion options in the dialog, and then click the “Full” button in those options.
>>> However, I’m somewhat mystified, because I can’t think of a reason why it would show only a subregion automatically (without your telling it to).  There is an option that, when the data is over a specified size, only shows one plane to start with, but your image looks like more than one plane is shown.  To set options related to initial display of large data, use Volume Viewer menu “Features… Data display options”
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#disp-options>
>>> Another related issue is making an X-ray map cover the atomic coordinates as discussed in this recent post, but (at least to me) your image doesn’t look like that kind of situation.
>>> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014637.html>
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>> On Aug 6, 2018, at 2:50 AM, kesgin-schaefer at chemie.uni-hamburg.de wrote:
>>>> Dear all,
>>>> I have a problem with my electron density map: if I load the map in chimera, it will only show a subregion of the map and after "fit to model"  the model will not be completely covered (see attachment).
>>>> Any suggestions about how to solve the problem would be much appreciated.
>>>> Thanks
>>>> Steffi

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