<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">FYI, I added a control for transparent background to the Save dialog for the relevant formats (PNG, TIFF). Will be in tomorrow's daily build.<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 class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Oct 9, 2020, at 2:35 AM, Karjalainen, Mikael <<a href="mailto:mikael.p.karjalainen@jyu.fi" class="">mikael.p.karjalainen@jyu.fi</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi!<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">My last email went only for one user, so I will send this one to repeat that saving transparent png pictures worked. Thank you!<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Regards,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Mikael<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" style="color: purple; text-decoration: underline;" class="">goddard@sonic.net</a>><span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>torstai 8. lokakuuta 2020 20:01<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>Karjalainen, Mikael <<a href="mailto:mikael.p.karjalainen@jyu.fi" style="color: purple; text-decoration: underline;" class="">mikael.p.karjalainen@jyu.fi</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] Error "Cannot determine format for"<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><p style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Mikael,<o:p class=""></o:p></p><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: "Times New Roman", serif;"> If I use menu File / Save... to save a PNG image it logs a command in the Log panel that looks like<br class=""><br class=""> save C:/Users/goddard/Desktop/test.png width 746 height 466 supersample 3<br class=""><br class="">The transparentBackground option is not in the save dialog but at least this gives you an idea of the format of the command. Most ChimeraX user interface actions log equivalent commands so looking at the Log is a good way to see the command syntax.<br class=""><br class=""> Tom<br class=""><br class=""><br class=""><o:p class=""></o:p></p><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On 10/8/2020 9:50 AM, Eric Pettersen wrote:<o:p class=""></o:p></div></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Okay, in tomorrow's daily build you will be able to just use "format png".<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">--Eric<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On Oct 8, 2020, at 9:05 AM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Mikael,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Right now, if you don't provide the .png suffix, you have to use a<span class="Apple-converted-space"> </span><b class="">format</b> value of "png image" rather than just "png". Will probably change that to just "png", but right now your command should be:<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>save C:\Users\a\Desktop\k format "png image" supersample 4 transparentBackground true<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">--Eric<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>Eric Pettersen<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span class="apple-tab-span"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On Oct 8, 2020, at 8:01 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">meng@cgl.ucsf.edu</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Mikael,<br class="">The first one is definitely wrong because you should not include the square brackets in the command. They are shown in usage descriptions to indicate optional arguments, as explained here:<br class=""><br class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html" style="color: purple; text-decoration: underline;" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html</a>><br class=""><br class="">Make sure the pathname is correct. Maybe you cannot specify the drive in the pathname (the "C:") ... however, I'm on Mac and can't test this directly, but the other developers would know. You could try specifying pathname without drive to see where it goes. On Mac, this works to put a file on the Desktop under my home directory:<br class=""><br class="">save ~/Desktop/blah.png super 4 transparent true<br class=""><br class="">As in my example, you can just specify format with filename suffix (e.g. "k.png") instead of using the format option, but using the format option like you did should also be OK.<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><br class=""><o:p class=""></o:p></div><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On Oct 8, 2020, at 12:41 AM, Karjalainen, Mikael <<a href="mailto:mikael.p.karjalainen@jyu.fi" style="color: purple; text-decoration: underline;" class="">mikael.p.karjalainen@jyu.fi</a>> wrote:<br class=""><br class="">Hi!<span class="Apple-converted-space"> </span><br class="">I am trying to get transparent background in png pictures, but it is not working and I get error “Cannot determine format for". Only way to get this is by using command line? I am writing something like:<br class=""><br class="">save C:\Users\a\Desktop\k [ format png ] [ supersample 4 ] [ transparentBackground true ]<br class=""><br class="">or<br class=""><br class="">save C:\Users\a\Desktop\k format png supersample 4 transparentBackground true<br class="">Also, I have tried different variations.<span class="Apple-converted-space"> </span><br class="">Regards,<br class="">Mikael<o:p class=""></o:p></div></blockquote><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: "Times New Roman", serif;"><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: purple; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p class=""></o:p></p></div></div></blockquote></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: purple; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p class=""></o:p></div></div></blockquote></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><br class=""><br class=""><o:p class=""></o:p></div><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">_______________________________________________<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">ChimeraX-users mailing list<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline;" class="">ChimeraX-users@cgl.ucsf.edu</a><o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Manage subscription:<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="color: purple; text-decoration: underline;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p class=""></o:p></pre></blockquote><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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