<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:PMingLiU;
panose-1:2 2 5 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:PMingLiU;
panose-1:2 1 6 1 0 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.apple-tab-span
{mso-style-name:apple-tab-span;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=ZH-TW link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Hi Tom,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Thank you so much for the amazing help! So is Elaine’s help.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>I’ve followed your commands, and the only place that I had to modify replacing “</span><span lang=EN-US style='font-family:"Calibri",sans-serif'>volume zone #3 near /A:66 distance 2” with “surface zone #3 near /a:66 distance 2” that you have suggested. I only had to easily change the display from surface to mesh in the volume viewer.</span><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>The reason is that ChimeraX instructed me, as shown below, that a keyword was expected with the volume zone and distance 2 as shown below.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal style='background:#DDDDDD'><b><span lang=EN-US style='font-family:"Calibri",sans-serif'><a href="help:user/commands/volume.html#zone"><span style='color:windowtext'>volume zone</span></a> #3 nearAtoms /a:66 <span style='background:crimson'>distance 2</span><o:p></o:p></span></b></p><p class=MsoNormal><b><span lang=EN-US style='font-family:"Calibri",sans-serif'>Expected a keyword</span></b><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Best wishes,<br></span><span lang=EN-US style='font-family:"Calibri",sans-serif'><br>Winston<br><br><o:p></o:p></span></p></div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Tom Goddard [mailto:goddard@sonic.net] <br><b>Sent:</b> Tuesday, June 15, 2021 1:37 AM<br><b>To:</b> Wen-Jin Winston Wu <winston@gate.sinica.edu.tw><br><b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br><b>Subject:</b> Re: [chimerax-users] dual conformation<o:p></o:p></span></p></div></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Hi Winston,<o:p></o:p></span></p><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US> Yes, you are right that resfit only shows one conformation. It would be nice it it could show more than one.<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US> If you use two copies of the atomic model as Elaine suggests you can easily have it show the density around both, but not with resfit. Instead just give the command to show the zone<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US> </span></span><span lang=EN-US>surface zone #3 near /a:66 distance 2<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>This will show the map zone around #1 and #2 residue 66. Here are the commands I used to make the image below.<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>open 7a5v<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>open 7a5v<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>hide #1,2 atoms,cartoon<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>show /a:66<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>view<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>altlocs change B #2/A:66<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>open 11657 from emdb<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>volume zone #3 near /A:66 distance 2<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>volume #3 style mesh level 0.025 subdividesurface true<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US> </span></span><span lang=EN-US>Tom<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><img border=0 width=390 height=388 id="_x0038_4A791CF-C0E7-4D21-8958-8F693009255A" src="cid:image002.jpg@01D761C5.CF07DE90"><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US><br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal><span lang=EN-US>On Jun 13, 2021, at 9:04 AM, Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></span></p></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Hi Elaine,<br><br>Thanks a lot for the helpful suggestion! I have tried your suggested command<br>I understand it now that for resfit, the ChimeraX daily build is designed to<br>display one conformer at a time, but not both of the resfit results for the<br>two conformers at the same time.<br><br>Best wishes,<br><br>Winston<br><br><br>-----Original Message-----<br>From: Elaine Meng [</span><span lang=EN-US><a href="mailto:meng@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>mailto:meng@cgl.ucsf.edu</span></a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>]<span class=apple-converted-space> </span><br>Sent: Sunday, June 13, 2021 11:37 PM<br>To: Wen-Jin Winston Wu <</span><span lang=EN-US><a href="mailto:winston@gate.sinica.edu.tw"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>winston@gate.sinica.edu.tw</span></a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>><br>Cc: ChimeraX Users Help <</span><span lang=EN-US><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>chimerax-users@cgl.ucsf.edu</span></a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>><br>Subject: Re: [chimerax-users] dual conformation<br><br>Hi Winston,<br>In my previous example with two copies (#1 using one altloc for 66 and #2<br>using the other altloc for 66), you could just specify which copy to resfit,<br>e.g.<br><br>resfit #1/a:66 map #3<br>- OR -<br>resfit #2/a:66 map #3<br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Chimera(X) team<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br><br style='caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><br></span><span lang=EN-US><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>On Jun 13, 2021, at 12:34 AM, Wen-Jin Winston Wu via ChimeraX-users<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br style='caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><br></span><span lang=EN-US><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>Hi Elaine,<br><br>Many thanks for your prompt reply and help!<br>I have used the daily build "ChimeraX 1.3.dev202106110002", and am<span class=apple-converted-space> </span><br>able to show the two alternative conformation following your suggested<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>commands.<br style='caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><br></span><span lang=EN-US><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>The remaining wish for me is showing the fitted density map onto each<span class=apple-converted-space> </span><br>of the alternative conformation and have them display simultaneously.<br><br>It seems that the command " resfit /a:66 map #3" only fits one<span class=apple-converted-space> </span><br>specific conformation. Is there any way that I could specify conformer A<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>or B?<br style='caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><br></span><span lang=EN-US><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Of course, if this is unavailable, I will go back to Chimera 1.15. (I<span class=apple-converted-space> </span><br>am new to Chimera).<br><br>Best wishes,<br><br>Winston<br><br>-----Original Message-----<br>From: Elaine Meng [<a href="mailto:meng@cgl.ucsf.edu">mailto:meng@cgl.ucsf.edu</a>]<br>Sent: Sunday, June 13, 2021 5:25 AM<br>To: Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw">winston@gate.sinica.edu.tw</a>><br>Cc: <a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br>Subject: Re: [chimerax-users] dual conformation<br><br>Hi Winston,<br>ChimeraX is different from Chimera in that it only "uses" (and shows)<span class=apple-converted-space> </span><br>one alternate location at a time. This prevents weird behavior in<span class=apple-converted-space> </span><br>various calculations that can arise from having more than one copy of<span class=apple-converted-space> </span><br>the same atom (e.g. H-bonding, molecular surface, etc.)<br><br>However, in recent daily builds there is an "altlocs" command to list<span class=apple-converted-space> </span><br>these alternate locations and control which one is shown. This<span class=apple-converted-space> </span><br>command is not in the 1.2 release, you would need to use a ChimeraX<span class=apple-converted-space> </span><br>1.3 daily build from April<br>28 or later.y<br><br>To see two alternate locations of a residue at the same time,<span class=apple-converted-space> </span><br>currently you would need to open the structure twice and use the<span class=apple-converted-space> </span><br>"altlocs" command to change one copy to use the other alternate location.<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Example commands:<br style='caret-color: rgb(0, 0, 0);font-variant-caps: normal;text-align:start;-webkit-text-stroke-width: 0px;word-spacing:0px'><br></span><span lang=EN-US><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>open 7a5v<br>open 7a5v<br>hide<br>show :66<br>view :66<br>altlocs list :66<br><br> ... Log shows:<span class=apple-converted-space> </span><br>7a5v #1/A TYR 66 has alternate locations A and B (using A) 7a5v #2/A<span class=apple-converted-space> </span><br>TYR 66 has alternate locations A and B (using A)<br><br>...Alternatively, this command would list all of the alternate<span class=apple-converted-space> </span><br>locations found for all residues:<br><br>altlocs list<br><br>...Then to change to altloc B of residue 66 in the second copy of your<br>structure:<br><br>altlocs change B #2/A:66<br><br>If you don't care about seeing different altlocs at the same time, you<span class=apple-converted-space> </span><br>don't need to open multiple copies. We realize that opening multiple<span class=apple-converted-space> </span><br>copies can be inconvenient, so we have discussed having a graphical<span class=apple-converted-space> </span><br>interface and showing the altlocs for a residue all at once (similar<span class=apple-converted-space> </span><br>to the Rotamers tool showing multiple sidechain rotamers at the same<span class=apple-converted-space> </span><br>time, and maybe even tabulating H-bonds, clashes, and density fit) but<span class=apple-converted-space> </span><br>that has not been implemented yet.<br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Chimera(X) team<br>Department of Pharmaceutical Chemistry University of California, San<span class=apple-converted-space> </span><br>Francisco<br><br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>On Jun 12, 2021, at 9:42 AM, Wen-Jin Winston Wu via ChimeraX-users<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>Hi,<br>I am trying to use Chimera X to display an amino acid with dual side<span class=apple-converted-space> </span><br>chain<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>conformations (PDB code: 7a5v) together with its cryoEM density map<br>(EMDataResource: EMD-11657).<span class=apple-converted-space> </span><br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>For example, Tyr 66 have two side chain conformations, however using<span class=apple-converted-space> </span><br>the<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>command below, it only showed one conformation.<br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>resfit /a:66 map #1 (a very nice command, by the way)<br><br>I then used Chimera 1.15 to view the PDB coordinate, and it showed<span class=apple-converted-space> </span><br>two<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>side chain conformations for Tyr66 (as I saw in PyMol); on the other<span class=apple-converted-space> </span><br>hand, Chimera X only shows a single conformation.<br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Is there any way to display the two alternative conformations using<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Chimera X?<br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>Thanks a lot for your time, and possible help!<br>Best wishes,<br>Winston<o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br><image1.png>_______________________________________________<br>ChimeraX-users mailing list<br><a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a><br>Manage subscription:<br><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><o:p></o:p></span></p></blockquote><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br></span><span lang=EN-US><img border=0 width=842 height=729 id="_x0039_2633472-4F3C-4D5E-9B3B-D5D89554B054" src="cid:image003.png@01D761C5.CF07DE90"><img border=0 width=842 height=729 id="_x0034_07AAECB-5CD1-4454-9651-8B3DC83ECD08" src="cid:image004.png@01D761C5.CF07DE90"></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>ChimeraX-users mailing list<br></span><span lang=EN-US><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>ChimeraX-users@cgl.ucsf.edu</span></a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>Manage subscription:<br></span><span lang=EN-US><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p></o:p></span></p></div></blockquote></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></div></body></html>