<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 Miriam,<div class=""><br class=""></div><div class=""> Sorry! To show the map just near the atoms use Volume Viewer menu Features / Zone, select your atoms (e.g. command "select #0") and press the Zone button. This just hides the density beyond some distance (e.g. 3 Angstroms) from the selected atoms.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 20, 2020, at 1:26 PM, Miriam Gochin <<a href="mailto:mgochin@lbl.gov" class="">mgochin@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks for date shaming me!! It works - you guys are great. Is there any way to select certain parts of the map, if for example you just want to see the electron density of one molecule instead of all the symmetry copies?<div class=""><br class=""></div><div class="">Miriam</div><div class=""><br class=""></div><div class="">PS. 7 years isn't even close.</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 20, 2020 at 11:56 AM Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Miriam,<div class=""><br class=""></div><div class=""> We appreciate your long use of Chimera! That bug was fixed 7 years ago. Time to install a new Chimera.</div><div class=""><br class=""></div><div class=""><span style="white-space:pre-wrap" class=""> </span>Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 20, 2020, at 11:46 AM, Miriam Gochin <<a href="mailto:mgochin@lbl.gov" target="_blank" class="">mgochin@lbl.gov</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><span style="font-family:monospace;font-size:12.675px" class="">The 2F0-Fc map was created with Phenix. I tried the "vop cover #1 atom #0" command but got the following error:</span><br style="font-family:monospace;font-size:12.675px" class=""><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">NameError: global name 'step' is not defined</span><br style="font-family:monospace;font-size:12.675px" class=""><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class=""> File "/Applications/Chimera.app/Contents/Resources/share/VolumeFilter/cover.py", line 9, in map_covering_box</span><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class=""> g = volume.grid_data(subregion = 'all', step = step, mask_zone = False)</span><br style="font-family:monospace;font-size:12.675px" class=""><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">Hoping to figure out how to make it work.</span><br style="font-family:monospace;font-size:12.675px" class=""><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">Many thanks,</span><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">---------------------------------</span><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">Miriam Gochin</span><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class="">Touro University California / LBL</span><br style="font-family:monospace;font-size:12.675px" class=""><span style="font-family:monospace;font-size:12.675px" class=""><a href="mailto:miriam.gochin@tu.edu" target="_blank" class="">miriam.gochin@tu.edu</a></span><div class=""><a href="mailto:mgochin@lbl.gov" target="_blank" class="">mgochin@lbl.gov</a></div><div class=""><span style="font-family:monospace;font-size:12.675px" class="">707-638-5463</span> <br class=""></div></div>
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