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[Jmol-users] [Fwd: H's added to serine and cysteine; undo command]
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From: Jeff C. <coh...@cs...> - 2011-08-08 22:05:56
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<font face="Times New Roman, Times, serif">Oops. My question (1) makes
no sense. Of course, the position of the NH hydrogen is fixed. Please
excuse this silly error.</font><br>
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<td>H's added to serine and cysteine; undo command</td>
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<td>Mon, 08 Aug 2011 14:53:11 -0700</td>
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<th align="right" nowrap="nowrap" valign="baseline">From: </th>
<td>Jeff Cohlberg <a class="moz-txt-link-rfc2396E" href="mailto:coh...@cs..."><coh...@cs...></a></td>
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<td><a class="moz-txt-link-abbreviated" href="mailto:coh...@cs...">coh...@cs...</a></td>
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<td>California State University, Long Beach</td>
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<th align="right" nowrap="nowrap" valign="baseline">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:jmo...@li...">jmo...@li...</a></td>
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<pre>Two issues concerning Jmol 12.2RC1:
First issue: In Jmol-users Digest, Vol 62, Issue 38 (July 38), Bob
Hanson, in discussing Jmol 12.2's capacity for adding hydrogens to a
structure, said, "For HIS, Jmol adds H to both atoms (as though the HIS
were protonated), and for OH and SH, the algorithm doesn't try to find
hydrogen bond donors."
I have two questions about this:
1) Does the statement imply that with NH hydrogens the program DOES try
to find hydrogen bond donors? (I think this is the case, since when I
tried this on the active site of chymotrypsin, 6GCH, both NH groups of
the oxyanion hole (G193 and S195) were pointing to the carbonyl carbon
of the inhibitor).
2) What criterion IS used to determine the angle at which the H extends
from the O of serine or the S of cysteine?
Second issue: The UNDO and REDO buttons seem to work fine, but the
script console commands "undo" and "redo" don't.
Thanks in advance
Jeff Cohlberg
--
Jeffrey A. Cohlberg, Professor and Chair
Department of Chemistry and Biochemistry
California State University, Long Beach
Long Beach, CA 90840
562-985-4944 fax 775-248-1263
<a class="moz-txt-link-abbreviated" href="mailto:coh...@cs...">coh...@cs...</a>
</pre>
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<pre class="moz-signature" cols="72">--
Jeffrey A. Cohlberg, Professor and Chair
Department of Chemistry and Biochemistry
California State University, Long Beach
Long Beach, CA 90840
562-985-4944 fax 775-248-1263
<a class="moz-txt-link-abbreviated" href="mailto:coh...@cs...">coh...@cs...</a>
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