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<p style="margin-top:0;margin-bottom:0">Hi Tom,</p>
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<p style="margin-top:0;margin-bottom:0">OK, thanks that makes much more sense now. I'm looking to somewhat automate the process of converting between PDBs and conventional modelling formats. With a tool like meshlab, the vertex colours can be copied on to the
faces reasonably easily, but I was wondering if there is a way this could be done directly on the XML files in the COLLADAs, so that a second program didn't have to be used.</p>
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<p style="margin-top:0;margin-bottom:0">If you've any other thoughts about the best way to approach this I'd be grateful.</p>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MRSB</span><br>
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<div><span style="font-size:10pt">University of Warwick<br style="">
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Mob: +44 (0) 7536 042620 | </span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
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<div><span style="font-size:10pt">Jointly working in:<br style="">
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<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS </span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
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<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a> | ORCID: <span id="ms-rterangepaste-start"></span><span>orcid.org/0000-0002-9569-6738</span><span id="ms-rterangepaste-end"></span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> 25 June 2018 18:42:06<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Exporting STL/COLLADA/OBJ with textures</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Joe,
<div class=""><br class="">
</div>
<div class=""> As web searches will indicate, OBJ file format does not support vertex colors. Triangle faces can be colored with a MTL file, but to color each triangle a different color will make immense files. The materials in the MTL file are usually used
to make an entire object a single color. Chimera does not create or read MTL files. Chimera does not use triangle coloring, it uses vertex coloring where the color smoothly varies across the triangle. More commonly 3D formats and generic 3D scene software
(e.g. Blender) use textures instead of vertex colors. Texture coordinates (u,v) are given for each vertex and the color is looked up in a texture image using u,v as the x,y coordinates in the image. Since Chimera does not use textures it does not have the
u,v coordinates for the vertices. It is not easy to make the texture coordinates because you usually want them to have continuity across the surface. Without continuity, for instance if you just assign random u,v to lookup a color in an image you run into
the problem that the u,v values are interpolated across a triangle which leads to a rainbow of colors as the texture image is interpolated from u1,v1 at one vertex to a far away u2,v2 at another vertex of the same triangle.</div>
<div class=""><br class="">
</div>
<div class=""> In short you aren’t going to get vertex colors from the OBJ format that does not support vertex colors. While other formats like Collada support vertex colors, a lot of software just ignores those and only handles texture coloring.</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
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<blockquote type="cite" class="">
<div class="">On Jun 25, 2018, at 4:48 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Hi Elaine,</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Ok thank you. DAE do indeed seem to render the colours properly as I can see them in Mac Preview, though seemingly not in other tools as you say.</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">I don't suppose there is any way for chimera to write the colours out as an MTL file since this seems to be the approach other tools take.</div>
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<div class="" style="margin-top:0px; margin-bottom:0px">I'm not very familiar with these file formats, but it seems to have something to do with colours being applied on vertices but not faces.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Any more info you have would be appreciated.</div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Thanks, </div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Joe</div>
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<span class="" style="font-size:10pt">M.Sc. B.Sc. (Hons) MRSB</span><br class="">
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<span class="" style="font-size:10pt"></span>
<div class=""><span class="" style="font-size:10pt">PhD Student</span></div>
<div class=""><span class="" style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div class=""><span class="" style="font-size:10pt">University of Warwick<br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt">Coventry<br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt">CV47AL<br class="">
Mob: +44 (0) 7536 042620 | </span><span class="" style="font-size:10pt">Email:<span class="x_Apple-converted-space"> </span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a></span></div>
<div class=""><span class="" style="font-size:10pt"><br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt">Jointly working in:<br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP" class="">Waterfield Lab</a><span class="x_Apple-converted-space"> </span>(<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS </span><span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
and Infecti</span><span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div class=""><span class="" style="font-size:10pt">and the <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP" class="">Gibson Lab</a> (Warwick Chemistry)<br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt"><br class="">
</span></div>
<div class=""><span class="" style="font-size:10pt">Twitter:<span class="x_Apple-converted-space"> </span><a href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a> | </span><span class="" style="font-size:10pt">Website:<span class="x_Apple-converted-space"> </span></span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" class="" style="font-size:10pt">MOAC
Page</a> | ORCID: <span id="x_ms-rterangepaste-start" class=""></span><span class=""><a href="http://orcid.org/0000-0002-9569-6738" class="">orcid.org/0000-0002-9569-6738</a></span><span id="x_ms-rterangepaste-end" class=""></span></div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>23 June 2018 15:46:57<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Healey, Joe<br class="">
<b class="">Cc:</b><span class="x_Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [Chimera-users] Exporting STL/COLLADA/OBJ with textures</font>
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<div class="x_PlainText">Hi Joe,<br class="">
As per the “export” docs...<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html</a>><br class="">
<br class="">
COLLADA export includes colors but many readers do not interpret them correctly.<br class="">
OBJ export is only single color per surface piece.<br class="">
STL export does not include colors.<br class="">
X3D, WebGL, ... are more complete and may include what you want.<br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <span class="x_Apple-converted-space"> </span><br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
> On Jun 23, 2018, at 6:34 AM, Healey, Joe <<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>> wrote:<br class="">
><span class="x_Apple-converted-space"> </span><br class="">
> Hi,<br class="">
> Is it possible for Chimera to somehow export the textures/colour mappings of the models when saving the scene as a .dea/.obj/.stl?<br class="">
> At the moment I can export the models, including surfaces (with correct transparency) but I haven't found an option for texturing/colouring?<br class="">
> Cheers<br class="">
> Joe<br class="">
<br class="">
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