<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Paula,<DIV> Chimera expects a PSF/DCD combo, not a PDB/DCD combo. The underlying package I use for DCD support, MD Tools for Python, does a good job of handling PSF files but its PDB file support leaves a lot to be desired, which is why the PDB part is omitted from Chimera. Nonetheless, I hacked up a couple of the MD Movie files to sort of handle your PDB file. I say "sort of" because I had to add CONECT records to your file or else all the trajectory bonds would be missing.</DIV><DIV> I will probably work on making it possible to use a PDB file in general instead of a PSF file for the next release (or maybe the one after).</DIV><DIV> So appended is two replacement files for your Chimera distribution (DCD.py and md_AtomGroup.py) and your PDB file with CONECT records added (x.pdb). DCD.py and md_AtomGroup.py should go in <your chimera install dir>/share/Trajectory/DCD and <install>/share/Trajectory/DCD/MDToolsMarch97 respectively, replacing files of the same name. You may want to copy the originals somewhere because you will lose the ability to use PSF/DCD combinations after putting in these hacked versions.</DIV><DIV> In case you need to add CONECT records to other PDB files, you can do this pretty easily in Chimera. After opening the PDB file in Chimera, use the command:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV> pdbrun nouser conect cat > filename.pdb</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>which will create filename.pdb in your Chimera startup directory (though "filename.pdb" could be a full path if you wanted it to go elsewhere). The above command will only work on Unix-based systems since "cat" is a Unix command.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> <BR class="Apple-interchange-newline"> </DIV><BR><DIV><DIV>On Oct 24, 2005, at 7:09 PM, Paula Petrone wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am trying to load in an MD-ensemble, using a pdb and an X-plor file .dcd.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">For some reason, it gives me "IndexError: list index out of range".</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I generated the .dcd file myself (with Fortran). VMD program seems to have no problem with it.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Is it a format problem? Is it a bug? Any suggestion?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks a lot! (I attach the files)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">paula</DIV></BLOCKQUOTE></DIV></DIV></BODY></HTML>