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Hi Mike,<br>
<br>
I see your test file contains Cu1 and Chimera shows that in a
label as CU1 with all upper case. That surprises me. Our expert on
that Eric Pettersen can explain it next week. You may be right that
Chimera knows the atomic elements and could selectively capitalize
labels according to your preferences when the atom name matches the
element symbol. Again it is something Eric can advise on.<br>
<br>
Tom<br>
<br>
<br>
<blockquote type="cite">Tom,
<div><br>
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<div>Thanks for the reply.</div>
<div><br>
</div>
<div>The file is a PDB, a file with the first few lines is
attached.</div>
<div><br>
</div>
<div>I was hoping that since Chimera understood atom names well
enough to color them that there would be a file with atoms names
used for labeling.</div>
<div><br>
</div>
<div>If this is something I can change in my installation, great,
if not, no worries. I use a mac. I've already changes the python
file to understand the non-sttandard space group P21/N.</div>
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<div>Cheers,</div>
<div>Mike</div>
<div><br>
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<div><<<
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<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab &
Molecular Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<div><br>
</div>
<div><>< <>< <><
<>< <>< <><
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<div>Beckman Institute, Room 116</div>
<div>Phone: (626) 395-2734</div>
<div>Fax: (626) 449-4159</div>
<div>e-mail: <a href="mailto:mikeday@caltech.edu">mikeday@caltech.edu</a></div>
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<div>On Feb 11, 2011, at 2:27 PM, Tom Goddard wrote:</div>
<br class="Apple-interchange-newline">
<div bgcolor="#ffffff" text="#000000"> Hi Mike,<br>
<br>
Does the FE1 name come from a PDB or Mol2 file you
opened? If that name appears in the file, one obvious
approach is to change the file replacing FE1 with Fe1. I'm
not sure if that will break code that expects FE1. I don't
think there are any options in Chimera to manipulate the
case of names displayed in labels. I believe Chimera just
uses the capitalization of names it obtains from the file it
read in.<br>
<br>
I guess Chimera could have some option to manipulate the
case of atom names in labels. But it seems very
specialized. Someone looking at a protein with a C-alpha
atom named CA generally does not want Ca. This also
indicates that it isn't possible to know if an atom name
refers to an atomic element (e.g. Fe = iron, Ca = calcium)
or something else (like C-alpha).<br>
<br>
Tom<br>
<br>
<blockquote
cite="mid:E9381733-3388-4514-B7F6-304A7E35A93B@caltech.edu"
type="cite">How do I make the default label for metal
atoms be upper and lower case?
<div><br>
</div>
<div>For instance in an iron compound, if I issue label ~H
from the command line the result will be FE1 where I
prefer Fe1, etc., etc.</div>
<div><br>
</div>
<div>This is true for all two letter atom names.</div>
<div><br>
</div>
<div>Thanks<br>
<div> <span class="Apple-style-span" style="font-size:
20px;"> </span>
<div style="font-size: 20px;">
<div>
<div>
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<div>Cheers,</div>
<div>Mike</div>
<div><br>
</div>
<div><<<
------------------------------------------------------------------------>>></div>
<div>Dr. Michael W. Day</div>
<div>Director - X-ray Crystallography Lab
& Molecular Observatory</div>
<div>California Institute of Technology</div>
<div>Mail Code 139-74</div>
<div>Pasadena, CA 91125</div>
<div><br>
</div>
<div><>< <><
<>< <>< <><
<>< <>< <><
<>< <><</div>
<div><br>
</div>
<div>Beckman Institute, Room 116</div>
<div>Phone: (626) 395-2734</div>
<div>Fax: (626) 449-4159</div>
<div>e-mail: <a moz-do-not-send="true"
href="mailto:mikeday@caltech.edu">mikeday@caltech.edu</a></div>
<div><<<
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<span class="Apple-style-span" style="font-size:
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