<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Sep 4, 2009, at 5:09 PM, Rocco Varela wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello,<br><br>I have a small suggestion for an additional feature for Chimera that I think would be useful. I often look at structures of multiple small molecules, some artificial and some real, and I noticed something interesting with the way Chimera writes mol2 files.<br> <br>Here is Scenario 1: <br><br>1) I open a mol2 file that contains multiple molecules flagged as "separate" <span class="yshortcuts" id="lw_1252109286_0">MOLECULEs</span>. <br><br>2) I save the loaded file as mol2 and select "a <span style="border-bottom: 1px dashed rgb(0, 102, 204); cursor: pointer;" class="yshortcuts" id="lw_1252109286_1">single file</span> [combined @<span class="yshortcuts" id="lw_1252109286_2">MOLECULE</span> section]" for the "Save multiple models in" option.<div class="im"><br> <br>3) After saving and reloading this new mol2 file that now has a single MOLECULE section, all the "names" of the previous molecules have been lost. (ex. s-030, s-048, s-055, etc...) Instead in the <span class="yshortcuts" id="lw_1252109286_3">SUBSTRUCTURE</span> section "UNK0" is used.<br> <br></div>It would useful if Chimera could name the components of the new single molecule with the proper names. I could easily write a script to fix this after the fact but I thought it might be a useful option for other people too?<br></blockquote><div><br></div>Okay, I changed the Mol2 writer to use the model name instead of the residue type under the following conditions (only):</div><div><br></div><div>1) Combining models into a single @MOLECULE</div><div>2) All models are a single residue</div><div>3) Model names are unique and residue types are not</div><div><br></div><div>This change will be in tonight's build.</div><div><br><blockquote type="cite">Scenario 2:<br><br>1) Same as 1 above.<br>2) Now I want to save all the MOLECULEs in the file as separate mol2 files but with the proper "names" that are listed in the original file loaded. Currently the only option is to provide a common name and to append the "model number". It would be nice if we were allowed to NOT provide a common name and allow it to name all the files according to the molecule "names" not model numbers.</blockquote><br></div><div>This seems like a reasonable enough request. I will open a ticket in our Trac database for it, with you on the recipient list so you'll know when it gets done. It's a tad more work than the preceding change because aside from adding code to support it, the interface has to be changed to allow for the option and the documentation has to be updated to describe it -- whereas the other change can sneak in under the radar. :-)</div><div><br></div><div>--Eric</div><br><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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; "> 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><br class="Apple-interchange-newline"></div></span></div><br><div></div></div></body></html>