<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="">The “key” in your command tries to bring up the Color Key tool — which is impossible in nogui/headless mode. There is no way to place a color key solely using commands, so if you <i class="">really</i> need a color key you would have to resort to using Python code to create it. Otherwise, just drop “key” from your command and it will work.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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>
<div><br class=""><blockquote type="cite" class=""><div class="">On May 14, 2018, at 12:33 PM, NAGARAJAN <<a href="mailto:nagabioinfostar@gmail.com" class="">nagabioinfostar@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hi,<br class=""><br class=""></div> Thank you for the suggestion. I have installed the headless version and now it is working. I tried to color the surface based on b-factor using the following commnad<br class=""><br class=""> "rangecolor bfactor key 2 blue 30 red 50 yellow"<br class=""><br class=""></div> it is showing the following error "No module named Togl"<br class=""><br class=""></div><div class=""> I referred in internet and it seems this module is removed automatically during updation.<br class=""></div><div class=""><br class=""></div> Any idea how to solve this problem?<br class=""><br class=""></div>Thank you<br class=""><div class=""><div class=""><br class=""> <br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, May 11, 2018 at 6:31 PM, Eric Pettersen <span dir="ltr" class=""><<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">This line from the “primer” that Elaine mentioned in her later message covers the problem you’re having:<div class=""><br class=""></div><div class=""><span style="font-family: -webkit-standard; font-size: inherit;" class="">Note that if your script creates images then you </span><i style="font-family:-webkit-standard" class="">must</i><span style="font-family: -webkit-standard; font-size: inherit;" class=""> start the Chimera interface unless you've downloaded the "headless" version of Chimera (see the </span><a href="http://www.cgl.ucsf.edu/chimera/download.html" style="font-family:-webkit-standard" target="_blank" class="">download page</a><span style="font-family: -webkit-standard; font-size: inherit;" class="">).</span></div><div class=""><font size="3" face="-webkit-standard" class=""><br class=""></font></div><div class="">—Eric<span class="HOEnZb"><font color="#888888" class=""><font size="3" face="-webkit-standard" class=""><br class=""></font><br class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class=""><span class="m_5357708949559105611Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div class=""><span class="m_5357708949559105611Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class="m_5357708949559105611Apple-interchange-newline"><br class="m_5357708949559105611Apple-interchange-newline">
</div>
</font></span><div class=""><br class=""><blockquote type="cite" class=""><span class=""><div class="">On May 11, 2018, at 4:25 PM, NAGARAJAN <<a href="mailto:nagabioinfostar@gmail.com" target="_blank" class="">nagabioinfostar@gmail.com</a>> wrote:</div><br class="m_5357708949559105611Apple-interchange-newline"></span><div class=""><div class=""><div class="h5"><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi,<br class=""><br class=""></div> Thanks for the quick reply. I have previous experience in using Chimera GUI but not in nogui.<br class=""><br class=""></div> The main thing that I dont know is to use those commands in nogui mode. <br class=""><br class=""></div> For example: for saving image, I have used "runCommand("copy str.png") . but it is now working<br class=""><br class=""></div> Is there any link to get the informations to use commands in nogui mode<br class=""><br class=""></div>Thank you<br class=""><div class=""><div class=""> <br class=""><div class=""><div class=""><br class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, May 11, 2018 at 6:19 PM, Elaine Meng <span dir="ltr" class=""><<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br class="">
I guess you will be using commands. Here are commands for your steps<br class="">
1. open<br class="">
2. surface<br class="">
3. color<br class="">
4, copy<br class="">
Of course, you will have to include more things in those commands, various options, residue numbers, filenames etc. that you should test in the GUI first to make sure they do what you want. See also the list of commands for anything else you might want to do like rotate (turn) translate (move) zoom (scale) … and click on the link to see each command’s help with information about the command syntax and possible options.<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/chim<wbr class="">era/docs/UsersGuide/framecomma<wbr class="">nd.html</a>><br class="">
<br class="">
See also:<br class="">
getting started with commands<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/chim<wbr class="">era/docs/UsersGuide/tutorials/<wbr class="">getting_started.html</a>><br class="">
<br class="">
tips for making nice images<br class="">
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/chim<wbr class="">era/docs/UsersGuide/print.html<wbr class="">#tips</a>><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="">
<div class="m_5357708949559105611HOEnZb"><div class="m_5357708949559105611h5"><br class="">
> On May 11, 2018, at 4:09 PM, NAGARAJAN <<a href="mailto:nagabioinfostar@gmail.com" target="_blank" class="">nagabioinfostar@gmail.com</a>> wrote:<br class="">
> <br class="">
> Hi all,<br class="">
> I have to use chimera --nogui and do the following<br class="">
> <br class="">
> 1. load a structure<br class="">
> 2. make Surface representation<br class="">
> 3. Color surface of selected residues with a selected color<br class="">
> 4. save image<br class="">
> <br class="">
> Any idea how to do the 4 steps in chimera --nogui?<br class="">
> Thank you<br class="">
<br class="">
</div></div></blockquote></div><br class=""><br class=""></div></div></div></div></div></div><span class="">
______________________________<wbr class="">_________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank" class="">http://plato.cgl.ucsf.edu/<wbr class="">mailman/listinfo/chimera-users</a><br class=""></span></div></blockquote></div><br class=""></div></div></blockquote></div><br class=""><br clear="all" class=""><br class=""></div></div>
</div></blockquote></div><br class=""></div></body></html>