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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Thanks for the so quick reply Dr. Elaine.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">One more question, can chimera calculate the volume of voxels for density map?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian">Tianming<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:DengXian"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="color:black">发件人</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Elaine
Meng <meng@cgl.ucsf.edu><br>
</span><b><span style="color:black">日期</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">
</span><span style="color:black">星期三</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">, 2022</span><span style="color:black">年</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">9</span><span style="color:black">月</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">21</span><span style="color:black">日</span><span style="font-family:"Calibri",sans-serif;color:black">
</span><span style="color:black">下午</span><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">3:09<br>
</span><b><span style="color:black">收件人</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Tianming Qu <tqu@fsu.edu><br>
</span><b><span style="color:black">抄送</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
</span><b><span style="color:black">主题</span></b><b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"> Re: [chimerax-users] cropping map to red part<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:11.0pt">Hi Tianming,<br>
Sorry no, ChimeraX can save maps (volume data) in several formats, but not .dx<br>
<br>
You can use command "save formats" to list the possible formats in the Log, or see the list at our website here:<br>
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html*mapformats__;Iw!!PhOWcWs!1Y4X9rQfuEq8ZsOGcet7K95FdmjdltcLZcBMIhDzXCBX6m4QcWQzl_U1ZuinD0kYIi8i19J92G-9rQ$ ><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>
<br>
> On Sep 21, 2022, at 11:52 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Dr. Elaine,<br>
> <br>
> I tried the way you suggested, it is helpful. One more question is that, the one I am trying to work on now, the colored map, is a density map read from .dx file. Is there any way I can save the edited map (aftering cropping and erasing) as a new .dx file?<br>
> <br>
> Best,<br>
> Tianming<br>
> <br>
> </span><span style="font-size:11.0pt">发件人<span lang="EN-US">: Elaine Meng <meng@cgl.ucsf.edu><br>
> </span>日期<span lang="EN-US">: </span>星期三<span lang="EN-US">, 2022</span>年<span lang="EN-US">9</span>月<span lang="EN-US">21</span>日 上午<span lang="EN-US">11:12<br>
> </span>收件人<span lang="EN-US">: Tianming Qu <tqu@fsu.edu><br>
> </span>抄送<span lang="EN-US">: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
> </span>主题<span lang="EN-US">: cropping map to red part<br>
> <br>
> Hi Tianming,<br>
> You didn't say what your coloring means: whether it is color by distance or some property. However, you can get parts of a map by various different methods:<br>
> <br>
> (1) volume zone (hide some parts by some distance from some atoms)<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html*zone__;Iw!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4ttYW3lG7A$ ><br>
> <br>
> (2) interactively using the Map Eraser tool to set some parts to zero<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/maperaser.html__;!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4tvUR5JHYw$ ><br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html*erase__;Iw!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4tuz8_GQpg$ ><br>
> <br>
> (2) interactively cropping the map box, e.g. in Volume Viewer choosing display style "box" and using the mouse to "crop volume"<br>
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html__;!!PhOWcWs!0DKqwfdTFNswYzmNztpdwEHNL-g-Xq9RRb3z0J8PDSjtr2PqTq7LtJUyLwvp8-ms7JBh4ttEG0MYpA$ ><br>
> <br>
> I prefer to avoid zooming -- there are so many users and so many questions it would be too many meetings!<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>
> <br>
> > On Sep 21, 2022, at 6:32 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> > <br>
> > Dear ChimeraX group,<br>
> > <br>
> > My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins.<br>
> > I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result:<br>
> > <image001.png><br>
> > <br>
> > I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want.<br>
> > <br>
> > Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help.<br>
> > <br>
> > Best,<br>
> > Tianming<o:p></o:p></span></span></p>
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