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<div class="" style="word-wrap:break-word">Dear Elaine,
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<div class="">For the first time in about three years, I need to do a little more modeling. We sequenced an NADase and I used Galaxy to create a model using a known CD38 structure as a template (attached). Chimera displayed everything, but the disulfide
bonds, of course. So I entered the specifications for those manually into the PDB file (attached). Two of the disulfides displayed properly, but four appear as thin dashed lines. At least one, at the C-terminus is clearly way too long. </div>
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<div class="">I tried to do an energy minimization, but while Chimera executed the steps, nothing in the structure moved. It used to be that one could watch the structure flex as it assumed the most energetically favorable conformation, but not this time,
yet some of the disulfide bond lengths are clearly wrong.</div>
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<div class="">I also tried to use the set length command, in the forms: set length 2.05 / Set Length [2.05] but Chimera does not like either of these commands. If the manual included examples of the command format for each command, that would be really useful,
because it is not clear where the syntax problem lies.</div>
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<div class="">As always, thanks for your help!</div>
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<div class="">Sincerely yours,</div>
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<div class="">Steve </div>
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Steven D. Aird<br class="">
Technical Editor<br class="">
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Okinawa Institute of Science and Technology Graduate University<br class="">
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