[phenixbb] Phaser Small Molecule MR

Tim Grüne tim.gruene at psi.ch
Thu May 2 02:52:34 PDT 2019

Dear Diana,
Most likely because of Sheldrick's rule. 1.7 A is a little beyond direct methods, despite the improvements with SHELXT.

On May 2, 2019 12:07:00 AM GMT+02:00, Diana Tomchick <Diana.Tomchick at utsouthwestern.edu> wrote:
>Why aren’t you using SHELX?
>Diana R. Tomchick
>Departments of Biophysics and Biochemistry
>UT Southwestern Medical Center
>5323 Harry Hines Blvd.
>Rm. ND10.214A
>Dallas, TX 75390-8816
>Diana.Tomchick at UTSouthwestern.edu<mailto:Diana.Tomchick at UTSouthwestern.edu>
>(214) 645-6383 (phone)
>(214) 645-6353 (fax)
>On May 1, 2019, at 3:22 PM, Whitley, Matthew J
><mjw100 at pitt.edu<mailto:mjw100 at pitt.edu>> wrote:
>Hello all,
>We have collected electron diffraction data to approximately 1.8 Å on a
>'small molecule' of roughly 1660 Da.  The space group (P 43 21 2) and
>unit cell parameters determined during data reduction match the known,
>published values, and our data are roughly 80% complete in all
>resolution shells from 17 - 1.8 Å.  We would like to solve this
>structure by molecular replacement in Phaser, but are having a bit of
>difficulty doing so.
>Our problems all seem to be related to specifying the composition of
>the target molecule for Phaser.  Via the phenix GUI, we can only
>specify the target composition as either protein or nucleic acid, when
>in fact the target is neither.  The chemical composition of the target
>is C72 H85 N19 O18 S5.  Is there a way to feed this chemical
>composition to Phaser and to get it to understand that the target is
>neither protein nor nucleic acid?  Furthermore, according to our
>reading of the Phaser documentation, specifying "protein" leads to an
>assumed solvent content of 50%, which is likely to be a substantial
>overestimation for this small molecule crystal.  We have also run into
>the problem of Phaser complaining that the target molecule will not fit
>into the given unit cell, which we think is due to the assumption of
>50% solvent content.
>We would be thankful for whatever advice you may have on using Phaser
>with non-protein, non-nucleic acid molecules.
>Matthew J. Whitley, Ph.D.
>Research Instructor
>W. Furey Lab
>Department of Pharmacology & Chemical Biology
>University of Pittsburgh School of Medicine
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>Medical Center
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Sent from my Android device with K-9 Mail. Please excuse my brevity.
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