[phenixbb] New Solvent Modeling/Analysis Tool

Paul Smith psmith66 at fordham.edu
Tue Oct 16 16:50:23 PDT 2018

Dear fellow PHENIX users,

My lab group has developed a new PHENIX-based tool for automated
identification and building of solvent molecules in x-ray crystal
structures.  The software, dubbed PeakProbe, and a basic README are
available on GitHub:


Fair warning: the project is still undergoing development and the linked
version generates excessive output and not all features are fully tested.
The feature extraction stage of the program is slow, figure about 1s per
peak analyzed.

Currently, PeakProbe can do the following:

-- Analyze and remodel existing solvent

-- Build water/sulfate and a few ions de novo

-- Indicate where other species, such as glycerol or PEG, should be

-- Identify possible model errors such as missing alternate conformations

PeakProbe requires only an input structure PDB (with or without solvent)
and a structure factor file in any format supported by PHENIX.  The program
uses a model derived from analysis of over 2.2 million density points in
the PDB in structures with limiting resolutions as low as 5.0A.  Features
from these points are scaled/transformed to allow comparison of input peaks
to well-defined feature distributions at any resolution followed by
calculation of the relative likelihood of a given type of solvent existing
at a given point.

Feel free to try PeakProbe and I welcome all feedback, bug reports, and
questions.  Thanks again to Nigel, Nat, Tom and all of the PHENIX/CCTBX
team for their help and for developing the battery of CCTBX tools upon
which PeakProbe is based.


The untold want, by life and land ne’er granted,
Now, Voyager, sail thou forth, to seek and find.
--W. Whitman

Dr. Paul Smith
Assistant Professor
Department of Chemistry
Fordham University
441 E. Fordham Road
Bronx, NY 10458
phone: 718-817-4461
fax: 718-817-4432
email: psmith66 at fordham.edu
office: JMH 638
PGP Public Key at https://pgp.mit.edu/
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