<div dir="ltr">Hi Luca,<div><br></div><div>Thanks for pointing this out. It looks like I introduced a bug when I refactored some of the torsion NCS code. I'll work up a fix today which will be available in the next nightly release.</div>
<div><br></div><div>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Oct 3, 2013 at 3:58 AM, Luca Pellegrini <span dir="ltr"><<a href="mailto:lp212@cam.ac.uk" target="_blank">lp212@cam.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Pavel,<br>
<br>
Yes, I am using torsion angle NCS in phenix.refine. I don't mean the NCS matrices, but the torsion NCS details. Here's an example of the REMARK 3 NCS that Phenix 1.8.2-1309 used to write in the PDB header and that have disappeared from the PDB header with Phenix 1.8.3-1479 and 1.8.4-1496:<br>
<br>
REMARK � 3 �TORSION NCS DETAILS.<br>
REMARK � 3 � NUMBER OF NCS GROUPS : 1<br>
REMARK � 3 � NCS GROUP : 1<br>
REMARK � 3 � � SELECTION � � � � �: chain 'A'<br>
REMARK � 3 � � SELECTION � � � � �: chain 'B'<br>
REMARK � 3 � � RESTRAINED TORSIONS: 4042<br>
REMARK � 3 � � BELOW LIMIT RMSD � : 0.620<br>
REMARK � 3 � � ALL RESTRAINT RMSD : 4.081<br>
REMARK � 3 � �Histogram of differences under limit:<br>
REMARK � 3 � � � 0.000 - � �1.500: 3932<br>
REMARK � 3 � � � 1.500 - � �3.000: 87<br>
REMARK � 3 � � � 3.000 - � �4.500: 5<br>
REMARK � 3 � � � 4.500 - � �6.000: 4<br>
REMARK � 3 � � � 6.000 - � �7.500: 1<br>
REMARK � 3 � � � 7.500 - � �9.000: 0<br>
REMARK � 3 � � � 9.000 - � 10.500: 0<br>
REMARK � 3 � � �10.500 - � 12.000: 0<br>
REMARK � 3 � � �12.000 - � 13.500: 1<br>
REMARK � 3 � � �13.500 - � 15.000: 0<br>
REMARK � 3 � �Histogram of differences over limit:<br>
REMARK � 3 � � �15.000 - � 22.400: 0<br>
REMARK � 3 � � �22.400 - � 29.800: 0<br>
REMARK � 3 � � �29.800 - � 37.200: 0<br>
REMARK � 3 � � �37.200 - � 44.600: 0<br>
REMARK � 3 � � �44.600 - � 52.000: 1<br>
REMARK � 3 � � �52.000 - � 59.400: 3<br>
REMARK � 3 � � �59.400 - � 66.800: 0<br>
REMARK � 3 � � �66.800 - � 74.200: 0<br>
REMARK � 3 � � �74.200 - � 81.600: 4<br>
REMARK � 3 � � �81.600 - � 89.000: 4<br>
<span class="HOEnZb"><font color="#888888"><br>
Luca<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On 3 Oct 2013, at 00:39, Pavel Afonine wrote:<br>
<br>
> Hi Luca,<br>
><br>
> when NCS is enabled phenix.refine uses torsion angle NCS by default.. This may explain why you don't get NCS matrices in your PDB file. Is that the case?<br>
><br>
> Pavel<br>
><br>
> On 10/2/13 1:26 AM, Luca Pellegrini wrote:<br>
>> Hello,<br>
>><br>
>> I have noticed that Phenix 1.8.4-1496 (as well as 1.8.3-1479) appears to have stopped writing the REMARK 3 NCS in the PDB header. Is this so? It is useful to have that info when it comes to depositing the coordinates.<br>
>><br>
>> Many thanks,<br>
>> Luca<br>
>><br>
>> Luca Pellegrini<br>
>> Department of Biochemistry<br>
>> University of Cambridge<br>
>> 80 Tennis Court Road<br>
>> Cambridge CB2 1GA - UK<br>
>><br>
>> Email: <a href="mailto:lp212@cam.ac.uk">lp212@cam.ac.uk</a><br>
>> Tel: 0044-1223-760469<br>
>> Fax: 0044-1223-766002<br>
>> Sanger building, room 3.59<br>
>><br>
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<br>
Luca Pellegrini<br>
Department of Biochemistry<br>
University of Cambridge<br>
80 Tennis Court Road<br>
Cambridge CB2 1GA - UK<br>
<br>
Email: <a href="mailto:lp212@cam.ac.uk">lp212@cam.ac.uk</a><br>
Tel: 0044-1223-760469<br>
Fax: 0044-1223-766002<br>
Sanger building, room 3.59<br>
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