<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hi Elaine</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thanks - this works.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
On a similar note, I was thinking if we can use this surface (generated from the surface command using a pdb) to cave out the volume that this surface encloses within a cryo-EM map. The other complementary part as well would be helpful - the volume outside
this surface (but enclosed within the cryo-EM map).</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I thought of the 'vop subtract' command but it requires 2 volumes and I am not sure how I can use the surface to subtract. Also, the surface generated does not seem to have a model number, so I am not sure where to start. </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I am not sure I want to use 'molmap' command using the pdb - it does not seem to overlap very well with the surface and depends on the resolution and the contour threshold specified.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Just to recap,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<ol>
<li>how do we use the surface (generated from the pdb) to cut out volumes from a cryo-EM map?</li><li>if we have to end up using a molmap command to subtract the volume from the cryo-EM map, what resolution (and contour threshold) of the volume would you suggest to have a 'surface' equivalent (which I think is the solvent-accessible surface).<br>
</li></ol>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thanks</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Yaikhomba</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 27 November 2020 00:05<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Coloring pdb surface by different colors</font>
<div> </div>
</div>
<div style="word-wrap:break-word; line-break:after-white-space">Hi Yaikhomba,
<div class="">Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the "color" command. </div>
<div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple</a>></div>
<div class=""><br class="">
</div>
<div class="">As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option. For example, these commands would show molecular surface for 2gbp and color the
parts of the surface orange for residues 50-100 and 126-135 in chain A:</div>
<div class=""><br class="">
</div>
<div class="">open 2gbp</div>
<div class="">surface</div>
<div class="">color /A:50-100,126-135 orange target s</div>
<div class=""><br class="">
</div>
<div class="">image of result attached.</div>
<div class=""><br class="">
</div>
<div class="">This page explains command-line specification (how to specify parts of the structure instead of the whole structure):</div>
<div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html</a>></div>
<div class=""><br class="">
</div>
<div class="">I hope this helps,</div>
<div class="">Elaine<br class="">
<div class="">-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<br class="">
<img id="x_DF8913E7-019D-4EB8-8A18-EBAD0B31DB90" width="320" height="225" class="" data-outlook-trace="F:1|T:1" src="cid:5777477E-3CC4-4238-8FFF-43A01A79A82E@gateway.sonic.net"></div>
<br class="">
<blockquote type="cite" class="">On Nov 26, 2020, at 12:48 PM, Y. Mutum <<a href="mailto:ym337@cam.ac.uk" class="">ym337@cam.ac.uk</a>> wrote:<br class="">
<br class="">
Hi<br class="">
<br class="">
I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow.<br class="">
Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow?<br class="">
<br class="">
I tried the surface command option but it seems to color the entire surface in a uniform color.<br class="">
<br class="">
Any suggestions would be very helpful.<br class="">
<br class="">
Thanks<br class="">
Yaikhomba<br class="">
_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">
Manage subscription:<br class="">
https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class="">
</blockquote>
<br class="">
</div>
</div>
</body>
</html>