<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=utf-8"><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:新細明體;
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:"\@新細明體";
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:"新細明體",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:"新細明體",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;color:#1F497D'>Hi Tom,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Thank you so much again!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>It works perfectly! <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><br>Winston<br><br></span><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 9:22 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> Oops! Yes I used the "surface zone" command I think but wrote "volume zone" by mistake. But you might want to use "volume zone" and change the "distance 2" option to "range 2" (unfortunately they use different names for that option). The surface zone and volume zone do about the same thing but volume zone is more efficient in that it only computes the mesh for the subregion you are showing while surface zone computes the mesh for the whole map and just hides most of it which can be slow to update when you are trying to change the threshold level.<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> Also you can set mesh style with the volume command -- that is done by the "style mesh" option in the command I sent (volume #3 style mesh ...).<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><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 14, 2021, at 6:07 PM, Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw">winston@gate.sinica.edu.tw</a>> wrote:<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 style='font-family:"Calibri",sans-serif'>Hi Tom,</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><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.</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><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 “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:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><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.</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><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></span></b><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><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:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Best wishes,<br><br>Winston<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Tom Goddard [<a href="mailto:goddard@sonic.net"><span style='color:purple'>mailto:goddard@sonic.net</span></a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, June 15, 2021 1:37 AM<br><b>To:</b><span class=apple-converted-space> </span>Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw"><span style='color:purple'>winston@gate.sinica.edu.tw</span></a>><br><b>Cc:</b><span class=apple-converted-space> </span>ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [chimerax-users] dual conformation</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>Hi Winston,<o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> 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><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> 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><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US style='font-family:"Times New Roman",serif'> </span></span><span class=apple-converted-space><span lang=EN-US style='font-family:"Times New Roman",serif'> </span></span><span lang=EN-US style='font-family:"Times New Roman",serif'>surface zone #3 near /a:66 distance 2<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>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><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>open 7a5v<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>open 7a5v<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>hide #1,2 atoms,cartoon<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>show /a:66<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>view<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>altlocs change B #2/A:66<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>open 11657 from emdb<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>volume zone #3 near /A:66 distance 2<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>volume #3 style mesh level 0.025 subdividesurface true<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US style='font-family:"Times New Roman",serif'> </span></span><span class=apple-converted-space><span lang=EN-US style='font-family:"Times New Roman",serif'> </span></span><span lang=EN-US style='font-family:"Times New Roman",serif'>Tom<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'><img border=0 width=390 height=388 id="_x0038_4A791CF-C0E7-4D21-8958-8F693009255A" src="cid:image001.jpg@01D761C9.4DC55DE0"><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'><br><br><br><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'>On Jun 13, 2021, at 9:04 AM, Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>> wrote:<o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div><div><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 style='font-family:"Times New Roman",serif'><a href="mailto:meng@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>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 style='font-family:"Times New Roman",serif'><a href="mailto:winston@gate.sinica.edu.tw"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>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 style='font-family:"Times New Roman",serif'><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>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><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>> wrote:<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>commands.<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>or B?<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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"><span style='color:purple'>mailto:meng@cgl.ucsf.edu</span></a>]<br>Sent: Sunday, June 13, 2021 5:25 AM<br>To: Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw"><span style='color:purple'>winston@gate.sinica.edu.tw</span></a>><br>Cc:<span class=apple-converted-space> </span><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></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.</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Example commands:<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>> wrote:<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>Chimera X?<br><br><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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</span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><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"><span style='color:purple'>ChimeraX-users@cgl.ucsf.edu</span></a><br>Manage subscription:<br><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style='color:purple'>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></span><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></blockquote><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br></span><span lang=EN-US style='font-family:"Times New Roman",serif'><img border=0 width=842 height=729 id="_x0039_2633472-4F3C-4D5E-9B3B-D5D89554B054" src="cid:image002.png@01D761C9.4DC55DE0"><img border=0 width=842 height=729 id="_x0034_07AAECB-5CD1-4454-9651-8B3DC83ECD08" src="cid:image003.png@01D761C9.4DC55DE0"></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 style='font-family:"Times New Roman",serif'><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>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 style='font-family:"Times New Roman",serif'><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p></o:p></span></p></div></div></blockquote></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> <o:p></o:p></span></p></div></div><p class=MsoNormal><span lang=EN-US><img border=0 width=630 height=721 id="_x0030_496189C-7805-4DC1-B74E-1B453F529CE5" src="cid:image004.png@01D761C9.4DC55DE0"><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>