[Chimera-users] problem with electron density map

kesgin-schaefer at chemie.uni-hamburg.de kesgin-schaefer at chemie.uni-hamburg.de
Tue Aug 7 02:18:11 PDT 2018

Dear Elaine and Tom,

thanks for your comments!

Unfortunately, after changing to "all" and playing around with  
threshold nothing changes.
Any further ideas?


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
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription:  
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list