I am doing joint refinement of a perdeuterated protein, and I am having a problem with alternate conformations - the deuterium occupancies don&#39;t match the overall occupancies for their conformation:<br><br>ATOM&nbsp;&nbsp;&nbsp; 335&nbsp; N&nbsp; APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.154&nbsp;&nbsp; 0.897&nbsp; 15.243&nbsp; 0.38&nbsp; 8.64&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 336&nbsp; CA APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 12.556&nbsp;&nbsp; 0.209&nbsp; 16.391&nbsp; 0.38&nbsp; 7.61&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 337&nbsp; CB APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.743&nbsp;&nbsp; 0.043&nbsp; 17.350&nbsp; 0.38 12.47&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 338&nbsp; CG APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.713&nbsp;&nbsp; 1.102&nbsp; 16.926&nbsp; 0.38&nbsp; 9.70&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 339&nbsp; CD APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.594&nbsp;&nbsp; 1.126&nbsp; 15.443&nbsp; 0.38 13.59&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 340&nbsp; C&nbsp; APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 11.414&nbsp;&nbsp; 0.974&nbsp; 17.057&nbsp; 0.38 13.42&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 341&nbsp; O&nbsp; APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10.559&nbsp;&nbsp; 0.334&nbsp; 17.671&nbsp; 0.38 15.65&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 342&nbsp; DA APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 12.236&nbsp; -0.672&nbsp; 16.112&nbsp; 0.48&nbsp; 5.78&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 343&nbsp; DB2APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.454&nbsp;&nbsp; 0.173&nbsp; 18.268&nbsp; 0.43 15.49&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 344&nbsp; DB3APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.128&nbsp; -0.841&nbsp; 17.229&nbsp; 0.52 10.36&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 345&nbsp; DG2APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.460&nbsp;&nbsp; 1.959&nbsp; 17.300&nbsp; 0.60 13.82&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 346&nbsp; DG3APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.610&nbsp;&nbsp; 0.852&nbsp; 17.197&nbsp; 0.30 14.04&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 347&nbsp; DD2APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.850&nbsp;&nbsp; 1.996&nbsp; 15.097&nbsp; 0.48 12.84&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 348&nbsp; DD3APRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.119&nbsp;&nbsp; 0.413&nbsp; 15.046&nbsp; 0.40&nbsp; 8.63&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 349&nbsp; N&nbsp; BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.163&nbsp;&nbsp; 0.886&nbsp; 15.240&nbsp; 0.62&nbsp; 8.58&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 350&nbsp; CA BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 12.606&nbsp;&nbsp; 0.252&nbsp; 16.438&nbsp; 0.62&nbsp; 7.70&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 351&nbsp; CB BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.777&nbsp;&nbsp; 0.307&nbsp; 17.423&nbsp; 0.62 11.89&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 352&nbsp; CG BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.973&nbsp;&nbsp; 0.224&nbsp; 16.548&nbsp; 0.62 11.13&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 353&nbsp; CD BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.616&nbsp;&nbsp; 1.094&nbsp; 15.375&nbsp; 0.62 13.76&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 354&nbsp; C&nbsp; BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 11.399&nbsp;&nbsp; 0.972&nbsp; 17.012&nbsp; 0.62 13.34&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 355&nbsp; O&nbsp; BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10.491&nbsp;&nbsp; 0.304&nbsp; 17.514&nbsp; 0.62 15.31&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 356&nbsp; DA BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 12.371&nbsp; -0.680&nbsp; 16.253&nbsp; 0.23&nbsp; 7.26&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 357&nbsp; DB2BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.760&nbsp;&nbsp; 1.148&nbsp; 17.905&nbsp; 0.72 12.42&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 358&nbsp; DB3BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13.734&nbsp; -0.446&nbsp; 18.034&nbsp; 0.19 14.30&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 359&nbsp; DG2BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.759&nbsp;&nbsp; 0.552&nbsp; 17.012&nbsp; 0.87 14.63&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp; 360&nbsp; DG3BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.094&nbsp; -0.695&nbsp; 16.264&nbsp; 0.40&nbsp; 9.68&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 361&nbsp; DD2BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.807&nbsp;&nbsp; 2.022&nbsp; 15.580&nbsp; 0.43 11.93&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>ATOM&nbsp;&nbsp;&nbsp; 362&nbsp; DD3BPRO A&nbsp; 19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.083&nbsp;&nbsp; 0.798&nbsp; 14.578&nbsp; 0.31&nbsp; 8.63&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; D&nbsp; <br>
<br>I am using these refinement options:<br>&nbsp; refine {<br>&nbsp;&nbsp;&nbsp; strategy = *individual_sites *rigid_body *individual_adp group_adp tls \<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *occupancies group_anomalous<br>&nbsp;&nbsp;&nbsp; sites {<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; individual = None<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; rigid_body = None<br>&nbsp;&nbsp;&nbsp; }<br>&nbsp;&nbsp;&nbsp; occupancies {<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; individual = None<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; remove_selection = None<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; constrained_group {<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; selection = None<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; }<br>&nbsp;&nbsp;&nbsp; }<br>}<br><br>and <br>&nbsp; hydrogens {<br>
&nbsp;&nbsp;&nbsp; refine = *individual riding<br>&nbsp;&nbsp;&nbsp; refine_adp = one_b_per_residue one_b_per_molecule *individual<br>&nbsp;&nbsp;&nbsp; refine_occupancies = one_q_per_residue *one_q_per_molecule individual<br>&nbsp;&nbsp;&nbsp; contribute_to_f_calc = True<br>&nbsp; }<br>
What refinement options should I be using to keep the D occupancies the same as the rest of their conformation? Hope you can help!<br><br>Regards,<br>Anna<br><br><br><div class="gmail_quote">2009/2/4 Pavel Afonine <span dir="ltr">&lt;<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>&gt;</span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">


  

<div bgcolor="#ffffff" text="#000000">
Hi Carsten,<br>
<br>
they should definitely add up to 1. If the PDB file contains altloc
identifiers, then those atoms should be picked up automatically and you
don&#39;t need to specify any selections. For example, make sure you have
something like this in your PDB file (the starting occupancies can be
any):<br>
<br>
<font face="Courier New, Courier, monospace">ATOM&nbsp;&nbsp;&nbsp;&nbsp; 49&nbsp; N&nbsp;&nbsp; MET A&nbsp;
10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.832 -11.001&nbsp;&nbsp; 0.570&nbsp; 1.00 11.55&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 50&nbsp; CA AMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.523 -10.377&nbsp;&nbsp; 0.709&nbsp; 0.70
12.44&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 51&nbsp; CA BMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.574 -10.279&nbsp;&nbsp; 0.718&nbsp; 0.30
12.42&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 54&nbsp; CB AMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.580&nbsp; -9.129&nbsp;&nbsp; 1.601&nbsp; 0.70
14.67&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 55&nbsp; CB BMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.822&nbsp; -8.921&nbsp;&nbsp; 1.394&nbsp; 0.30
13.99&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 60&nbsp; CG AMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.245&nbsp; -8.462&nbsp;&nbsp; 1.951&nbsp; 0.70
18.00&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 61&nbsp; CG BMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.545&nbsp; -8.166&nbsp;&nbsp; 1.727&nbsp; 0.30
17.90&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 66&nbsp; SD AMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.659&nbsp; -7.204&nbsp;&nbsp; 0.780&nbsp; 0.70
19.47&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; S&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 67&nbsp; SD BMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.792&nbsp; -6.615&nbsp;&nbsp; 2.600&nbsp; 0.30
26.45&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; S&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 68&nbsp; CE AMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.520&nbsp; -5.730&nbsp;&nbsp; 1.337&nbsp; 0.70
20.21&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 69&nbsp; CE BMET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.371&nbsp; -5.566&nbsp;&nbsp; 1.271&nbsp; 0.30
26.12&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 76&nbsp; C&nbsp;&nbsp; MET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.021 -10.028&nbsp; -0.671&nbsp; 1.00
10.57&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; <br>
ATOM&nbsp;&nbsp;&nbsp;&nbsp; 77&nbsp; O&nbsp;&nbsp; MET A&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2.780&nbsp; -9.724&nbsp; -1.578&nbsp; 1.00
11.30&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; O&nbsp; </font><br>
<br>
and then everything should be OK.<br>
Unfortunately, I can&#39;t tell much about the selections you use without
looking at the PDB file, so in your case I would just try the above
suggestion.<br><font color="#888888">
<br>
Pavel.</font><div><div></div><div class="Wj3C7c"><br>
<br>
<br>
On 2/4/2009 12:15 PM, Schubert, Carsten [PRDUS] wrote:
<blockquote type="cite">
  <pre>Hi,

I am trying to sort out some issues with the constrained occupancy refinement in phenix 1.4.3. The structure I am working on is fairly high resolution ~1.4A and it looks as if a couple of the alternative conformations would benefit from occupancy refinement, no hydrogens are present yet.

I defined the constrained groups like this:

    occupancies {
      individual = None
      remove_selection = None
      constrained_group {
        selection = chain A and resid 66 and altid A
        selection = chain A and resid 66 and altid B
      }
      ....

I expected that the sum of occupancies would be restrained to 1, which they should according to the manual, but the refinement gives me occupancies of 0.7 for altid A and 0.34 for altid B, starting values were both 0.5.  Similar discrepancies were also present in other groups, like 0.5 A, 0.37 B etc. The latter is the largest deviation from 1 I have seen in thus far. The alternate conformations were generated in coot, by splitting at the CA position.

Is this a rounding error I just have to contend with or is there some other parameter I need to tweak?

Cheers,

	Carsten

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