<div dir="ltr">Hi Elaine,<div><br><div>Sorry for my delay as I was trying the ways you described above. Thanks a lot for that.</div><div>I have another question as below:</div><div>How can I have color gradient along the map dimensions? For example along X.</div><div><br></div><div>Thanks and best,</div><div>Yanhe</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> 于2021年5月17日周一 下午3:14写道:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Yanhe,<br>
I guess you mean you have no atomic structure fitted inside, only the map? Zones are defined using atomic coordinates.<br>
<br>
However, without any atoms, you can interactively (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see:<br>
<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html</a>><br>
<br>
It is in the menu, Tools... Volume Data... Volume Eraser. <br>
<br>
Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger. <br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html</a>><br>
<br>
This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu: Regions... Hide) <br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 17, 2021, at 1:00 PM, Yanhe Zhao <<a href="mailto:yanhezhao1990@gmail.com" target="_blank">yanhezhao1990@gmail.com</a>> wrote:<br>
> <br>
> To whom may concern,<br>
> <br>
> This is Yanhe Zhao, from UT Southwestern Medical Center.<br>
> <br>
> I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information.<br>
> Thanks a lot in advance for any input. <br>
> <br>
> Best regards,<br>
> Yanhe<br>
<br>
</blockquote></div>