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<DIV><FONT face="MS UI Gothic">Thank you, Tsjerk;</FONT></DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic">I would like to try. But I have never used a kind
of modeler soft. Does SwissPDB voewer works as a modeler soft ? Is it
possible to save corrected pdb file using SwissPDB viewer ? If not, what
software is available ?</FONT></DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic">Many Thanks.</FONT></DIV>
<DIV><FONT face="MS UI Gothic"></FONT> </DIV>
<DIV><FONT face="MS UI Gothic">Hiromichi </FONT></DIV>
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style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt MS UI Gothic">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt MS UI Gothic; font-color: black"><B>From:</B>
<A title=tsjerkw@gmail.com href="mailto:tsjerkw@gmail.com">Tsjerk
Wassenaar</A> </DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Sent:</B> Thursday, November 17, 2005
6:00 AM</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Subject:</B> Re: [gmx-users] How to
correct incomplete pdb file</DIV>
<DIV><BR></DIV><BR>Hi Hiromichi,<BR><BR>You have to add missing side chains
using a modeler. When you load the protein in SwissPDB Viewer, this will
automatically be done. Be sure to also check the protein for missing residues.
This should be indicated in the PDB file. The option -ignh is of no use at all
in this case. <BR><BR>Tsjerk<BR><BR><BR>-- <BR><BR>Tsjerk A. Wassenaar,
M.Sc.<BR>Groningen Biomolecular Sciences and Biotechnology Institute
(GBB)<BR>Dept. of Biophysical Chemistry<BR>University of
Groningen<BR>Nijenborgh 4<BR>9747AG Groningen, The Netherlands <BR>+31 50 363
4336<BR>
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