<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Sophie,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The normal PDB reader does not preserve the full text of the PDB file as is. In particular, nothing in the "coordinates" section of the file (ATOM records and beyond) is preserved as text -- it is translated into data structures. Lines above the coordinates section are preserved in the 'metadata' attribute of the structure. For a PDB file, the metadata would be a dictionary keyed on record type (<i class="">e.g.</i><span style="font-style: normal;" class=""> 'JRNL') with a </span>corresponding value of a list of lines of that record type. So if the information you are looking for is in the header lines then you are good to go. If the the information really is "at the end of the file" like you said, then you would need to implement your own reader that preserves that information. Let me know if you really need that and I will provide further guidance.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 7, 2022, at 3:20 PM, Sophie Liu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">My organization has some extra information at the end of a PDB file that I would like to be printed onto the Log Console of ChimeraX. </div><div class=""><br class=""></div><div class="">I am currently writing a bundle to do so by adding a command (however if this is best implemented by overriding the open command for PDB files then I would switch to that).</div><div class=""><br class=""></div><div class="">I am wondering how I can have the bundle work like so:</div><div class="">1. the user types a command call it, "showdata"</div><div class="">2. the bundle would read all Models (that are pdb files) that are being displayed </div><div class="">3. for each model it would read the PDB text file, and say go to indices 200-251 of the string and display that in the Log console</div><div class=""><br class=""></div><div class="">I hope this makes sense. I am mainly struggling on how to access the original PDB text of the model.</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Sophie</div></div>
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