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<TITLE>RE: [phenixbb] Question about restraints in individualB-factor refinement</TITLE>
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<P><FONT SIZE=2>Thanks Pavel,Nigel:</FONT>
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<P><FONT SIZE=2>so it looks as if neither approach works and I would need to split the ligands into seperate PDB files for a truly independent B-factor refinement. </FONT></P>
<P><FONT SIZE=2>Thanks for the hint about the non-bonded interactions. That was useful.</FONT>
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<P><FONT SIZE=2>Cheers</FONT>
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<P> <FONT SIZE=2>Carsten</FONT>
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<P><FONT SIZE=2>-----Original Message-----</FONT>
<BR><FONT SIZE=2>From: phenixbb-bounces@phenix-online.org [<A HREF="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</A>]On Behalf Of Pavel Afonine</FONT>
<BR><FONT SIZE=2>Sent: Friday, May 25, 2007 12:51 PM</FONT>
<BR><FONT SIZE=2>To: PHENIX user mailing list</FONT>
<BR><FONT SIZE=2>Subject: Re: [phenixbb] Question about restraints in individualB-factor refinement</FONT>
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<P><FONT SIZE=2>Hi Carsten,</FONT>
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<P><FONT SIZE=2>for the refinement of b-factors there is no difference between two options. We use the sphere b-factors restraints which are calculated based on interatomic distances and the information about alternative conformations is not used at that point.</FONT></P>
<P><FONT SIZE=2>However if you refine the coordinates, the difference is significant: if you refine it as two separate residues then they will "see" each other for non-bonded interactions term calculation and hence will be pushed apart.</FONT></P>
<P><FONT SIZE=2>Please let me know if you still have questions!</FONT>
<BR><FONT SIZE=2>Pavel.</FONT>
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<P><FONT SIZE=2>Schubert, Carsten [PRDUS] wrote: </FONT>
<BR><FONT SIZE=2>Hi, </FONT>
<BR><FONT SIZE=2>I have a question about the handling of restraints in the individual B-factor refinement routine. </FONT>
<BR><FONT SIZE=2>What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...)</FONT></P>
<P><FONT SIZE=2>My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e.</FONT></P>
<P><FONT SIZE=2>ATOM 2724 C01AINH I 1 27.808 26.376 23.301 0.50 27.77 I C </FONT>
<BR><FONT SIZE=2>ATOM 2733 C01BINH I 1 30.898 22.496 17.340 0.50 22.15 I C </FONT>
<BR><FONT SIZE=2>... </FONT>
<BR><FONT SIZE=2>vs. scenario B) where the same ligand is modeled as 2 different residues </FONT>
<BR><FONT SIZE=2>ATOM 2724 C01 INH I 1 27.808 26.376 23.301 0.50 27.77 I C </FONT>
<BR><FONT SIZE=2>ATOM 2733 C01 INH I 2 30.898 22.496 17.340 0.50 22.15 I C </FONT>
<BR><FONT SIZE=2>.... </FONT>
<BR><FONT SIZE=2>Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of?</FONT></P>
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<P><FONT SIZE=2>Many thanks for any input. </FONT>
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<P><FONT SIZE=2>Cheers </FONT>
<BR><FONT SIZE=2> Carsten </FONT>
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