<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way).<div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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"></div></span> </div><br><div><div>On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Ed,<br>The "write" command only allows you to save one model at a time.<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html</a>><br><br>To save multiple models to one PDB file you have to use the GUI <br>("File... Save PDB" or "Actions... Write PDB").<br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</a>><br><br>Sorry about that,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br>On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote:<br><br><blockquote type="cite">Elaine and co,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have a mess of models that I'm opening, repositioning a ligand <br></blockquote><blockquote type="cite">using match to various positions in each model. No problem there. <br></blockquote><blockquote type="cite">For each model and ligand position I select the correct chains from <br></blockquote><blockquote type="cite">that model with the repositioned ligand models but can't manage to <br></blockquote><blockquote type="cite">save coordinates. Obviously there's the save pdb dialog but for all <br></blockquote><blockquote type="cite">these models and ligands this will be more convenient scripted into <br></blockquote><blockquote type="cite">chimera commands. I've got it all working except this:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">select #6:.a-p #8 #9<br></blockquote><blockquote type="cite">write selected relative 0 #6,8,9 /path/to/file.pdb<br></blockquote><blockquote type="cite">~select<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The part it doesn't like is the model_numbers and I've tried <br></blockquote><blockquote type="cite">various permutations without success. The only way I can get it to <br></blockquote><blockquote type="cite">work is if I only specify one model number.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Can you please help me figure out how to phrase this command <br></blockquote><blockquote type="cite">correctly? An example or two on that commands page might make the <br></blockquote><blockquote type="cite">syntax easier to decipher.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thank you for your excellent program and support.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Ed<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br></blockquote><blockquote type="cite">Edward Brignole<br></blockquote><blockquote type="cite">NIH Kirschstein Postdoctoral Fellow<br></blockquote><blockquote type="cite">Francisco Asturias Lab, CB227<br></blockquote><blockquote type="cite">Center for Integrative Molecular Biosciences<br></blockquote><blockquote type="cite">The Scripps Research Institute<br></blockquote><blockquote type="cite"><a href="http://www.scripps.edu/~brignole">www.scripps.edu/~brignole</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><a href="mailto:brignole@scripps.edu">brignole@scripps.edu</a><br></blockquote><blockquote type="cite">443-653-2070 (cell)<br></blockquote><blockquote type="cite">858-784-8598 (lab)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Chimera-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite"><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>