<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 Alexis,<div class=""><br class=""></div><div class=""> The pseudobond reader could be improved to set the dashes. But all the pseudobonds in a pseudobond model must have the same number of dashes. So your example of setting 2 different dashes values in the file won't work.</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=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 10, 2020, at 9:51 AM, Alexis Rohou <<a href="mailto:a.rohou@gmail.com" class="">a.rohou@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Well, it's good to know I'm the only one who sometimes fails to RTFM :)<div class=""><br class=""></div><div class="">While we're on the topic of pb files, I was hoping to play with the number of dashes (since the last line of the doc for pbfiles mentions a default dashes of 8), but I guess this is not something that can be set in the pb file? I was trying something like this:</div><div class=""><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"><font face="monospace" class="">; pseudo bonds for figure<br class="">; radius = 0.05<br class="">; dashes = 3<br class="">#1/L@H42 #1/B:940@OE1 rgba(12,56,100,0.2)<br class="">#1/L@O11 #1/A:840@HH dodgerblue<br class="">#1/B:940@HE21 #1/B:887@OG dodgerblue<br class="">; dashes = 8<br class="">#10841 #1/A:840@CD2 yellow<br class="">#10884 #1/A:840@CE1 yellow<br class="">#10840 #1/B:940@HE22 yellow<br class="">#10001 #1/B:947@CZ yellow<br class="">#10002 #1/A:841@CZ yellow</font></blockquote></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 9, 2020 at 2:25 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</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">Oops, didn't read my own documentation carefully enough!<br class="">
<br class="">
When using the rgba(N,N,N,N) form only the first three numbers can be whole numbers in the range 0-255, or percentages indicated with % symbols, which I failed to do. The transparency number has to be in the range 0-1.<br class="">
<br class="">
So you would need something like the following, which also works. Tested in daily build and in release 0.92.<br class="">
<br class="">
rgba(20%,90%,90%,0.7)<br class="">
<br class="">
Sorry for the mistake -- I normally use the simpler form: 20,90,90,70<br class="">
Elaine<br class="">
<br class="">
> On Mar 9, 2020, at 2:18 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
> <br class="">
> Hi Alexis, <br class="">
> I can reproduce the problem with reading the pb file transparency using a color specification of the form:<br class="">
> <br class="">
> /a:1@c3' /a:1@n3 rgba(20,90,90,70)<br class="">
> <br class="">
> However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent:<br class="">
> <br class="">
> /a:1@c3' /a:1@n3 20,90,90,70<br class="">
> - OR -<br class="">
> /a:1@c3' /a:1@n3 #00ced155<br class="">
> <br class="">
> <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html" rel="noreferrer" target="_blank" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html</a>><br class="">
> <br class="">
> Those atoms are in PDB 1bna, for example. Tested in current daily build<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="">
>> On Mar 6, 2020, at 10:33 AM, Alexis Rohou <<a href="mailto:a.rohou@gmail.com" target="_blank" class="">a.rohou@gmail.com</a>> wrote:<br class="">
>> <br class="">
>> Thanks Elaine!<br class="">
>> <br class="">
>> Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks!<br class="">
>> <br class="">
>> Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck.<br class="">
>> <br class="">
>> Thanks again for the help. <br class="">
>> <br class="">
>> Cheers,<br class="">
>> Alexis<br class="">
>> <br class="">
>> On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">
>> Here is the more detailed description of pseudobond file format:<br class="">
>> <br class="">
>> <<a href="http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles" rel="noreferrer" target="_blank" class="">http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles</a>><br class="">
> <br class="">
> <br class="">
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</blockquote></div>
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