Did you look in the .geo file?<div>It should show you all NCS pair distances. Very large differences between NCS copies will be flagged as "excessive".</div><div>Ralf</div><div><br><div class="gmail_quote">On Sat, Jan 14, 2012 at 10:51 AM, Luca Pellegrini <span dir="ltr"><<a href="mailto:lp212@cam.ac.uk">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">I think I discovered what was happening to my DNA molecule during refinement, that caused distortion of the phosphate groups. It was something along the lines of what Dale suggested, I mention it here so that it might be useful to others.<br>
<br>
I have two DNA molecules in the ASU and I didn't realised that I had accidentally swapped OP1 and OP2 in 3 out of 28 phosphates (so that, if the two DNA molecules were superimposed, OP1 ended on top of OP2). Because I had NCS restraints on during refinement, I guess phenix was trying to move OP1 in one DNA molecule towards the NCS-equivalent position of OP1 in the second molecule, hence the altered geometry.<br>
<br>
I have fixed the atom nomenclature problem and now the geometry of my DNA is ok. I appreciate that most people tend to avoid such mistakes ;-) but perhaps it would be good if phenix could flag situations such as these.<br>
<br>
Luca<br>
<br>
On 6 Jan 2012, at 16:15, Pavel Afonine wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Luca,<br>
<br>
phenix.refine always generates a *.geo file that lists all the geometry restraints (bonds, angles, planarities, chiralities, dihedral, non-bonded, ncs(if any)) used in refinement for all atoms. For each restraint it list current model value, target (library) value, etc.<br>
<br>
Can you have a look at *.geo file for O-P bonds in question? May be this gives a hint about what's going on?<br>
<br>
Pavel<br>
<br>
On 1/6/12 4:31 AM, Luca Pellegrini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi,<br>
<br>
I have noticed that Phenix mangles O-P bond lengths and angles in the phosphate groups of my DNA chain (example in pict attached). This only happens to 3 out of 28 phosphates. The refined protein-DNA structure does not present any other unusual stereochemistry issues and refinement runs normally. Could anybody advice on what is going on and how to fix this, please?<br>
<br>
I am using Phenix-1.7.3-928. Refinement is with default target weights, hydrogens on and does not include simulated annealing. I could make the stereochemistry targets more stringent, but the default values seem strict enough (bond and angle rmsd is 0.005 and 1.225).<br>
<br>
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" target="_blank">lp212@cam.ac.uk</a><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" target="_blank">lp212@cam.ac.uk</a><br>
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