<div dir="ltr"><div>I think Jareds line should do the trick.</div><div><br></div><div>Christian<br></div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jul 17, 2018 at 6:28 PM Jared Sampson <<a href="mailto:jared.sampson@columbia.edu">jared.sampson@columbia.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div id="m_1725080374147738858bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Hi Eike - </div><div id="m_1725080374147738858bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="m_1725080374147738858bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">There is no space between the altloc and residue name fields in the PDB format (per <a href="http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM" target="_blank">HETATM specification</a>). Here, the residue name is FAH, and the altloc is A/B. Try:</div><div id="m_1725080374147738858bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="m_1725080374147738858bloop_customfont" style="margin:0px"> chain C and resseq 1 and altloc B and resname FAH and name C3</div> <div><br></div>Hope that helps.<div><br> <div id="m_1725080374147738858bloop_sign_1531844610753859072" class="m_1725080374147738858bloop_sign"></div> Cheers,<div>Jared</div><div><br><p class="m_1725080374147738858airmail_on">On July 17, 2018 at 12:11:37 PM, Schulz, Eike-Christian (<a href="mailto:eike.schulz@mpsd.mpg.de" target="_blank">eike.schulz@mpsd.mpg.de</a>) wrote:</p> <blockquote type="cite" class="m_1725080374147738858clean_bq"><span><div lang="DE" link="blue" vlink="purple"><div></div><div>
<div class="m_1725080374147738858WordSection1">
<p class="MsoNormal"><span lang="EN-US">Any idea how I can select only 1 out of the 2 alternate conformations ?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">My PDB file:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">HETATM 5039 OT AFAH C 1 10.082 15.814 2.201 0.50 24.78 O
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">HETATM 5040 C AFAH C 1 10.568 15.712 3.241 0.50 28.20 C
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">HETATM 5041 O AFAH C 1 11.451 16.466 3.591 0.50 22.71 O
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">HETATM 5042 C3 AFAH C 1 10.136 14.590 4.170 0.50 19.02 C
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">HETATM 5043 F AFAH C 1 9.265 13.714 3.608 0.50 34.13 F
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">HETATM 5044 OT BFAH C 1 10.119 15.728 2.366 0.50 24.78 O
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:Consolas">HETATM 5045 C BFAH C 1 10.613 15.673 3.487 0.50 28.20 C
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">HETATM 5046 O BFAH C 1 11.519 16.468 3.737 0.50 22.71 O
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">HETATM 5047 C3 BFAH C 1 10.307 14.473 4.424 0.50 19.02 C
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I provide <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">refinement.geometry_restraints.edits {<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> bond {<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> action = *add<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> atom_selection_1 = chain A and resseq 110 and name OD2<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> atom_selection_2 = chain C and resseq 1 and resname BFAH and name C3<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> distance_ideal = 1.43<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> sigma = 0.04<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> slack = None<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> }<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas"> }<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">But the result is:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:Consolas">Sorry: No atom selected: "chain C and resseq 1 and resname BFAH and name C3"<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Cheers, <u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Eike<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-left:36.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Christian Roth <<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>><br>
<b>Date: </b>Tuesday, 17. July 2018 at 16:03<br>
<b>To: </b>Eike-Christian Schulz <<a href="mailto:eike.schulz@mpsd.mpg.de" target="_blank">eike.schulz@mpsd.mpg.de</a>><br>
<b>Cc: </b>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
<b>Subject: </b>Re: [phenixbb] FW: Occupancy / alternate conformation Refinement<u></u><u></u></span></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Ahh I see. Yes I think you are better off letting the Asn be an amino acid and have the ligand on its own. with an appropriate link record.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Good luck!<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">Christian<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:36.0pt">On Tue, Jul 17, 2018 at 3:52 PM Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de" target="_blank">eike.schulz@mpsd.mpg.de</a>> wrote:<u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US">Hi Christian, </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US">the Asn side chain is to which the ligand attaches has only 1 conformation – hence the occupancy for all these atoms is 1.
</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US">… but using a LINK might be a good option. </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US">Thanks, </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US">Eike</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:36.0pt">
<span lang="EN-US"> </span><u></u><u></u></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="margin-left:72.0pt">
<b><span lang="EN-US" style="font-size:12.0pt;color:black">From: </span></b><span lang="EN-US" style="font-size:12.0pt;color:black">Christian Roth <<a href="mailto:christianroth034@gmail.com" target="_blank">christianroth034@gmail.com</a>><br>
<b>Date: </b>Tuesday, 17. July 2018 at 15:25<br>
<b>To: </b>Eike-Christian Schulz <eike.schu</span><span style="font-size:12.0pt;color:black"><a href="mailto:lz@mpsd.mpg.de" target="_blank">lz@mpsd.mpg.de</a>><br>
<b>Cc: </b>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
<b>Subject: </b>Re: [phenixbb] FW: Occupancy / alternate conformation Refinement</span><u></u><u></u></p>
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<div>
<p class="MsoNormal" style="margin-left:72.0pt">
<u></u><u></u></p>
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<div>
<div>
<p class="MsoNormal" style="margin-left:72.0pt">
Hi Eike, <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:72.0pt">
why have some of your ligand atoms have occupancy of 1 and some 0.5.? I have had thought all atoms of the ligand are 0.5 for the two states and you create a link for one of them to which is the intermediate. You might have to add a constrained group as well,
though nowadays phenix might handle that automatically.<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:72.0pt">
<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:72.0pt">
Cheers<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:72.0pt">
Christian<u></u><u></u></p>
</div>
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<p class="MsoNormal" style="margin-left:72.0pt">
<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:72.0pt">
On Tue, Jul 17, 2018 at 3:15 PM Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de" target="_blank">eike.schulz@mpsd.mpg.de</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal" style="margin-left:72.0pt">
Dear all, <br>
<br>
In one of my structures I appear to have a mixed state between a covalently bound intermediate and the free substrate occupying _almost_ the same position. I can model the states nicely in coot, but during refinement the molecules “fly” apart - although
the occupancy was limited to 0.5 for their overlapping atoms. <br>
<br>
I have tried to model the free ligand as an alternate conformation of the covalent intermediate:
<br>
<br>
HETATM 852 N ASB A 110 10.523 15.702 10.022 1.00 14.48 N
<br>
HETATM 853 CA ASB A 110 9.974 15.713 8.664 1.00 15.11 C
<br>
HETATM 854 C ASB A 110 8.635 16.385 8.683 1.00 14.31 C
<br>
HETATM 855 O ASB A 110 8.563 17.443 9.233 1.00 13.03 O
<br>
HETATM 856 CB ASB A 110 10.053 14.307 8.091 1.00 11.72 C
<br>
HETATM 857 CG ASB A 110 9.774 14.157 6.621 1.00 15.26 C
<br>
HETATM 858 OD1 ASB A 110 10.688 14.485 5.644 1.00 19.29 O
<br>
HETATM 859 OD2 ASB A 110 8.693 13.880 6.340 1.00 13.36 O
<br>
HETATM 860 C1 AASB A 110 10.637 15.649 3.353 0.50 27.61 C
<br>
HETATM 861 C2 AASB A 110 10.231 14.480 4.266 0.50 32.98 C
<br>
HETATM 862 O1 AASB A 110 11.505 16.454 3.690 0.50 31.63 O
<br>
HETATM 863 O2 AASB A 110 10.085 15.787 2.280 0.50 21.80 O
<br>
HETATM 4742 O2 BASB A 110 10.072 15.815 2.191 0.50 24.78 O
<br>
HETATM 4743 C1 BASB A 110 10.573 15.717 3.221 0.50 28.20 C
<br>
HETATM 4744 O1 BASB A 110 11.449 16.458 3.619 0.50 22.71 O
<br>
HETATM 4745 C2 BASB A 110 10.107 14.567 4.152 0.50 19.02 C
<br>
HETATM 4746 F BASB A 110 9.287 13.735 3.610 0.50 34.13 F<br>
<br>
Although I have provided a new CIF file for the ligand named according to the alternate conformation this causes phenix to crash.
<br>
<br>
How can I correctly refine these overlapping atoms ?<br>
<br>
Thanks for your advice, <br>
<br>
Eike<br>
<br>
<br>
<br>
<br>
<br>
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