<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Modeller is quite powerful when building general homology models, but might be a bit of overkill just to fix a sidechain. You can try a simple frozen approximation and just scan for individual rotamers - we have a very naive web implementation (screws up chain identifiers right now) at</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><A href="http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php">http://lorentz.immstr.pasteur.fr/pdb/frozen_submission.php</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR><DIV><DIV>On Nov 17, 2005, at 6:12 PM, Nathan C. Rockwell wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px">You might try Modeller, available from the Sali lab web site (salilab.org, I think, but easiest to just google it). Other options have recently been compared in Protein Science 14:1315-27.<BR> <BR> nr<BR> <BR> <BR> On 11/16/05 7:20 PM, "Hiromichi Tsurui" <<A href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</A>> wrote:<BR> <BR> </SPAN></FONT><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px">Thank you, Tsjerk;<BR> <BR> 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 ?<BR> <BR> Many Thanks.<BR> <BR> Hiromichi <BR> </SPAN></FONT><BLOCKQUOTE type="cite"><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"> <BR> ----- Original Message ----- <BR> <BR> <B>From:</B> Tsjerk Wassenaar <A href="mailto:tsjerkw@gmail.com"><mailto:tsjerkw@gmail.com></A> <BR> <BR> <B>To:</B> Discussion list for GROMACS users <A href="mailto:gmx-users@gromacs.org"><mailto:gmx-users@gromacs.org></A> <BR> <BR> <B>Sent:</B> Thursday, November 17, 2005 6:00 AM<BR> <BR> <B>Subject:</B> Re: [gmx-users] How to correct incomplete pdb file<BR> <BR> <BR> <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> </SPAN></FONT></BLOCKQUOTE></BLOCKQUOTE><FONT face="Verdana, Helvetica, Arial"><SPAN style="font-size:12.0px"><BR> </SPAN></FONT><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------------------</DIV><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>