<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francesco,<div><span class="Apple-tab-span" style="white-space:pre"> </span>You are a patient man! I have no doubt what you say is true but have no idea why processing your trajectory would be so slow if it's not a memory issue (and it doesn't seem to be based on your "top" output). Also, I have no idea why VMD would show a PDB-based trajectory one way and Chimera another. Could you send me a compressed version of your trajectory directly? Being a PDB file, it should compress a lot and therefore not be too big a problem to email. Thanks!</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><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: 16px; 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; "><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 class="Apple-converted-space"> </span></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 class="Apple-converted-space"> </span></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="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span> </div><br><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><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; ">The pdb records read as in the following examples:</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; ">For the lipid:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <span class="Apple-converted-space"> </span>20 2C21 POP <span class="Apple-converted-space"> </span>1<span class="Apple-converted-space"> </span>25.569<span class="Apple-converted-space"> </span>20.201<span class="Apple-converted-space"> </span>48.492<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span>0.00</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; ">For the protein:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>10915<span class="Apple-converted-space"> </span>HB2 ALA <span class="Apple-converted-space"> </span>117<span class="Apple-converted-space"> </span>44.211<span class="Apple-converted-space"> </span>74.567<span class="Apple-converted-space"> </span>28.832<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span>0.00</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; ">For water:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>22264<span class="Apple-converted-space"> </span>O <span class="Apple-converted-space"> </span>WAT<span class="Apple-converted-space"> </span>1771<span class="Apple-converted-space"> </span>25.558<span class="Apple-converted-space"> </span>39.417<span class="Apple-converted-space"> </span>16.580<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span>0.00</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>22265<span class="Apple-converted-space"> </span>H1<span class="Apple-converted-space"> </span>WAT<span class="Apple-converted-space"> </span>1771<span class="Apple-converted-space"> </span>25.582<span class="Apple-converted-space"> </span>39.432<span class="Apple-converted-space"> </span>16.549<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span>0.00</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM<span class="Apple-converted-space"> </span>22266<span class="Apple-converted-space"> </span>H2<span class="Apple-converted-space"> </span>WAT<span class="Apple-converted-space"> </span>1771<span class="Apple-converted-space"> </span>25.569<span class="Apple-converted-space"> </span>39.482<span class="Apple-converted-space"> </span>16.611<span class="Apple-converted-space"> </span>0.00<span class="Apple-converted-space"> </span>0.00</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; ">After that, the warning message changes to "Computed secondary structure</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><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><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; ">During all that time, I had to avoid doing anything else with the GNOME</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">interface. A second terminal for "top" had to be opened before launching</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera on another terminal window. Otherwise, spurious graphics become</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">superimposed to the Chimera window.</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 could then carry out rapid mapping of the protein residues around the</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><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; ">The same events occurred with shorter trajectories. At ca 0.7ns the time taken</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">by Chimera to work out the average-structure pdb was about 15 minutes. Clearly,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">there is an exponential trend.</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 can in part compare these events on VMD: the pdb file from 1.5ns MD is opened</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">in VMD in less than 1 minute and the resulting membrane-protein-complex is</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">centered in the water box.</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; ">Is all that caused by the not-updated atom naming by Amber? Or could the</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">execution be accelerated by calling some C routines by python?</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; ">Chimera was run on a modest desktop: Athlon 1GHz, RAM 1GB, a poor main board</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(product: K7S5A, vendor: ECS, version: 1.0), Debian Linux i386.</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</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; ">francesco pietra</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; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>____________________________________________________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Be a better friend, newshound, and<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">know-it-all with Yahoo! Mobile.<span class="Apple-converted-space"> </span>Try it now.<span class="Apple-converted-space"> </span><a href="http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ">http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ</a><span class="Apple-converted-space"> </span></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; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div> </blockquote></div><br></div></body></html>