<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jan 1, 2008, at 1:44 PM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am dealing with the average structure (a protein complex embedded in a POCP</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">membrane and water solvated) derived with Amber's ptraj from a 1.5 ns MD.</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; ">Opening this pdb file in 1.2470 Chimera has become extremely slow. The file is</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">6.4MB. First, below the screen it is warned "Ignored bad PDB record found on</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">line #", for lines from 1 to 114154. This may take some 10 minutes.</div></blockquote><div><br class="webkit-block-placeholder"></div>These are for the water ATOM records where the atom serial number and/or residue number were "****" (what FORTRAN inserts when a number won't fit inside a field width).</div><div><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">After that, the warning message changes to "Computed secondary structure</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">assignments (see reply log)" which lasts for longer than 1 hour and 20 minutes.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">During this time, "top" command shows that python is using 12% MEM and 99% CPU.</div></blockquote><div><br class="webkit-block-placeholder"></div>Due to the fact that this is an "average" structure, Chimera's estimation of the connectivity is bad for many parts of the structure -- particularly the POP residues in the membrane. This creates a rat's nest of intra-residue connectivity which the ring-finding algorithm (designed for "reasonable" structures) takes a long time to operate on. Normally Chimera wouldn't run ring-finding as a structure opens, but due some interesting naming of hydrogens in the POP residues (e.g. RH16) it assigns some of the hydrogens to be other elements (e.g. rhodium, as per PDB atom naming rules). Since rhodium is a metal, it wants to depict it as a sphere, which means it needs to know the radius, which in turn depends on the atom type, which needs to find rings...</div><div> <br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Then, the graphics appears, with the membrane-protein-complex not centered in</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the water box.</div></blockquote><div><br class="webkit-block-placeholder"></div>This is due to the "****" waters being ignored.</div><div><br class="webkit-block-placeholder"></div><div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">I could then carry out rapid mapping of the protein residues around the</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">single-residue ligand (select protein & :ligandname z<#), which was what I</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">wanted to do.</div></blockquote><br></div><div>If you only care about the protein and ligand in your analysis, you should just edit your file to strip the waters and lipids. When I did this with the file you sent it only took moments to open.</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br class="Apple-interchange-newline"> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><div><br class="webkit-block-placeholder"></div></div></body></html>