[Chimera-users] Chimera and DelphiController

Nihshanka Debroy ndebroy at gmail.com
Fri Jul 28 10:35:35 PDT 2006

     My name is Nihshanka Debroy, and I am a graduate student at Duke
University. I recently joined this mailing list. I was wondering if I could
ask a couple of questions about the software.
     The first one is more related to Delphi. I have been using the Delphi
Controller tool in Chimera, and I have been getting warnings that certain
radii records are missing from my .siz file, and some residues have a net
positive charge. I used the default files provided when installing Delphi. I
was wondering if anyone has faced this problem before. Is there an online
database where I could get the missing radii and charge values for atoms and
residues ?
     Secondly, I am trying to generate the Connolly surface for certain
proteins. What I have been doing so far is running Delphi Controller and
assigning a probe radius of 1.4 Angstroms in the Parameter section. I just
wanted to make sure that this is different from the molecular surface (MS)
that is generated when simply choosing Actions->Surface->Show.

Thank you for your time.
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