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Dear Eric and Elaine,<br>
<br>
thanks very much, the bfactor + rangecolor - option works for me and
Elaine's points might come in handy at a later point in time.<br>
<br>
Best,<br>
Christian<br>
<br>
<br>
<br>
On 09/16/2010 08:38 PM, Elaine Meng wrote:
<blockquote cite="mid:D43714AD-8C05-438A-8883-80524E736A5D@cgl.ucsf.edu"
type="cite">Hi Christian,
<div>I would only add a couple of points to Eric's suggestion to use
the "bfactor" attribute. These may or may not be relevant to your
situation:</div>
<div><br>
</div>
<div>(1) Coloring by attribute is particularly nice for
continuous-valued things, because they can be mapped to continuous
gradations of color. I can't tell whether you want continuous coloring
(e.g. red gradually shading to blue from one value to another) or
discrete (e.g. exactly red for one group, exactly blue for another
group). In the Render by Attribute tool, your value distribution will
be shown in a histogram. One way to achieve discrete coloring would be
to bracket each value with two thresholds (the vertical colored sliders
that define the color mapping on the histogram) of the same color. Or,
you could use commands something like</div>
<div><br>
</div>
<div>color hot pink @/bfactor=1</div>
<div>color orange @/bfactor=2</div>
<div><br>
</div>
<div>(2) Attributes could also be assigned with a separate input
file, instead of the PDB file. It is a simple tab-separated column
format, description and examples here:</div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile</a>></div>
<div><br>
</div>
<div>That allows assigning multiple different attributes without
having to make more PDB files. These attributes can be of different
value types (float, integer, boolean, color, character string), they
can be named anything you want instead of just bfactor, and if they are
floating-point numbers of high precision you can use more digits than
are available in the bfactor field in standard PDB format.</div>
<div>Elaine</div>
<div>
<div><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;">
<div>
<div>----------</div>
<div>Elaine C. Meng, Ph.D. </div>
<div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div>
<div>Department of Pharmaceutical Chemistry</div>
<div>University of California, San Francisco</div>
<div><br>
</div>
</div>
</span></div>
<div>
<div>On Sep 16, 2010, at 11:08 AM, Eric Pettersen wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word;">Hi Christian,
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>I'm
happy you like Chimera enough to mis-use in in this way! :-) However,
I don't think "rainbow" is the way to go here. Rainbow only affects
connected strings of residues. For example, if you rainbow a protein
system, waters and ligands will retain their original colors (and for
your system, Chimera really has no way of knowing that your "residues"
aren't peptide ligands).</div>
<div><span class="Apple-tab-span" style="white-space: pre;"> </span>SInce
you are creating your own PDB files anyway, what I suggest is that your
put your "grouping info" into the bfactor field. Then you can use the
Render by Attribute tool (or the rangecolor command) to color your
points based on their bfactor.</div>
<div><br>
</div>
<div>--Eric<br>
<br>
<div><span class="Apple-style-span"
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<br>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
---<br>
Christian Schudoma, M.Sc.<br>
Ph.D. Student<br>
<br>
Bioinformatics Group <br>
Max Planck Institute of Molecular Plant Physiology<br>
Am Muehlenberg 1<br>
14476 Potsdam-Golm<br>
Germany<br>
<br>
phone: +49 (331) 567-8624<br>
email: <a class="moz-txt-link-abbreviated" href="mailto:schudoma@mpimp-golm.mpg.de">schudoma@mpimp-golm.mpg.de</a><br>
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