<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="">Hi Priyanka,<div class=""><br class=""></div><div class="">Sorry for this late reply. I am copying the chimerax-users list (if you had sent your last email to the list, somebody else would maybe have answered you earlier; also a good idea to communicate through the list because all emails are archived and that sometimes enables people to find answers to their questions directly by searching the archives).</div><div class=""><br class=""></div><div class="">Regarding you question about colors: in ChimeraX, the command "color list" will print in the log a list of colors with their names. Color names made of more than one word are listed twice: spelled with and without a space. I just checked that if you spell color names as they are listed by this command, it works. So, in your case, try spelling it "royalblue" with no space.</div><div class=""><br class=""></div><div class="">Regarding your second question, I think this should work, but I am not quite sure what you are trying to do:</div><div class=""><br class=""></div><div class=""><div class="">volume zone #1 nearAtoms sel range 2 newMap true minimalBounds false</div><div class=""><br class=""></div><div class="">in which #1 is your main map (so not necessarily #1 in your session, use the correct model number for your map as seen in the model panel) and sel is a selection of the atoms of interest (in your case "/A" for chain A), "range 2" is how many angstroms away from the model atoms you want to perform the map cut-out (I put 2 arbitrarily; try different values and use what you think is best for what you are trying to do), "newMap true" tells it to generate a new object for this map cut-out (it should show up in the model panel after you run the command) and "minimalBounds false" tells it to keep the same box size as your original map (if set to true instead, it will choose the minimal box size that encloses your map cut-out; not sure which one you need, but keeping the same box size should be safe).</div></div><div class=""><br class=""></div><div class="">Once you have this, you can write this map cut-out to a file with the following command:</div><div class=""><br class=""></div><div class="">save /path/to/your/new/map.mrc models #2</div><div class=""><br class=""></div><div class="">(replace #2 by the correct object identifier for your new map, as reported in the model panel).</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class=""><div class="">
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<div><br class=""><blockquote type="cite" class=""><div class="">On 16 Oct 2020, at 03:31, Priyanka Abeyrathne <<a href="mailto:pabeyrat@gmail.com" class="">pabeyrat@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Guillaume,<div class=""><br class=""></div><div class="">Thank you so much for your assistance. I am going to use it soon and if I happened to have questions I will let you know.</div><div class=""><br class=""></div><div class="">I have two other questions to clarify with you. </div><div class=""><br class=""></div><div class="">1. I used the following commands to color the pdb</div><div class="">seq chain /A </div><div class="">Then I highlighted the chain A</div><div class="">color sel blue</div><div class=""><br class=""></div><div class="">I can see the chain A color is blue. Now ChimeraX has really nice color scheme. I tried to color chain A to royal blue (#4169E1 26,41,88). When I use the above commands</div><div class="">seq chain /A</div><div class="">highlighted the chain A</div><div class="">color sel royal blue</div><div class="">Didn't change the color blue to royal blue. Cod you please assist me how to fix theis?</div><div class=""><br class=""></div><div class="">2. pdb of the protein has three chains (A, B and C). I have a cryo-EM structure of the same protein. How can I extract only chain A density from cryo-EM structure. I think I have to use a segment map command. Could you please assist me how to do this in ChimeraX.</div><div class=""><br class=""></div><div class="">Thank you so much.</div><div class="">Kind regards,</div><div class="">Priyanka</div><div class=""><br class=""></div><div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 12, 2020 at 3:41 AM Guillaume Gaullier <<a href="mailto:guillaume@gaullier.org" class="">guillaume@gaullier.org</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 Priyanka,<div class=""><br class=""></div><div class="">If what you need is a command that can restore the camera’s position to a previously saved state after you moved it, then this should be helpful:</div><div class=""><br class=""></div><div class="">1. set the scene the way you want it</div><div class="">2. run command "view name myview" ("myview" can be any name); what this does is assign a name to the current view (camera settings)</div><div class="">3. rotate or translate, move around, etc.</div><div class="">4. run command "view myview", which should reset the camera settings to what they were when you did step 2 above</div><div class=""><br class=""></div><div class="">I believe named views are saved with the session, so you should be able to use them even after you save and close, then reopen your .cxs file.</div><div class=""><br class=""></div><div class="">You will find more details in the documentation, with command "help view". Also here: <a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name" target="_blank" class="">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name</a></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class=""><div class="">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On 11 Oct 2020, at 22:10, Priyanka Abeyrathne <<a href="mailto:pabeyrat@gmail.com" target="_blank" class="">pabeyrat@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hi All,<div class=""><br class=""></div><div class="">Is there a save scene command in ChimeraX?</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Priyanka</div></div>
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