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<div>Dear Sam,</div>
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<div>at 1.5A you might expect to see holes in the aromatic rings and at least a den in the proline residue.</div>
<div>The region of your screen shot is quite noisy - either you integrated your data too far into the noise, or there is more than one conformation of the side chain. You can split the range of offending residues, including 1-2 either side, and see if coot
models the second one reasonably.</div>
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<div>Best,</div>
<div>Tim<br>
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<div id="divRpF63072" style="direction: ltr;"><font size="2" face="Tahoma" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Sam Tang [samtys0910@gmail.com]<br>
<b>Sent:</b> Friday, April 26, 2019 2:38 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> [phenixbb] modelling into positive densities<br>
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<div dir="ltr">Hello,<br clear="all">
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<div><font color="#000000"><span style="font-size:12.7273px">I am refining a structure solved to 1.5A by MR. Rw/Rf were 0.17/0.22 which seem acceptable to me. At the very beginning part of the protein the electron density is a bit wobbly. I am able to build
the residues into the positive densities. But after phenix.refine the chain always shifts away a bit and leaves the green blobs there. </span></font></div>
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<div>(Photo: <a href="https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R" target="_blank" rel="noopener noreferrer">https://drive.google.com/open?id=1UngAJuEUt1S0LwPybMJLw2E1xA4cNM3R</a>)<br>
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<div>I am thinking if this can be solved by adjusting the target weights. Or can I apply certain restraints only to those few residues?</div>
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<div>I refined XYZ (reciprocal space), XYZ (real space), individual B-factors, TLS and occupancies.</div>
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<div>Thanks in advance.</div>
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<div>Regards</div>
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<div>Sam</div>
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