Ethan's X-PLOR scripts
for solvent models and structure refinement

solvent_model.inp

This script adds a discrete solvent model to your refinement, built by looking for H2O residues in a file current.solvent. Since the model is built on the fly from inside the refinement script, you can modify your solvent model at any time without having to alter your base protein structure file (generate.psf). If you have no discrete solvent model, just put the single word "END" in current.solvent.

bulksol.inp

This script adds a bulk solvent correction to your refinement using a method suggested by Dale Tronrud. It is the same approach to handling bulk solvent as is used in TNT and in SHELXL. Fcalc is corrected by a factor
F_c´ = F_c * (1. - K_sol exp(-B_sol * s)) where s = sin() / .
This correction allows you to use all low-resolution data for refinement (i.e. set your low-resolution cutoff to 100Å).

bsolref.inp

ksolref.inp

This pair of scripts helps to find the optimal values of K_sol and B_sol for your bulk solvent model. Each script takes a fixed value for one of the parameters and tests a range of corresponding values for the other. Generally two passes through the pair of scripts should yield an optimal set of K_sol and B_sol. For example:

1. Set K_sol to 0.70 and run bsolref.inp to estimate the optimal value of B_sol.
2. Set B_sol to your new estimate and run ksolref.inp to estimate a better value of K_sol.
3. Iterate once more through the pair of routines to refine these initial estimates.

Each run of one of these scripts produces a data file which may be plotted using gnuplot. Here is a sample plot generated by a simple gnuplot script.

kbsol_choice.inp

This script loops over a range of values for the parameter B_sol to help you choose appropriate values for the parameters in your bulk solvent model. Output is to several data files that can then be viewed using gnuplot. The idea is to choose values for K_sol and B_sol which yield the flattest Luzzati plot.

anisob.inp

This script calculates an overall anisotropic B correction, and adds it to the existing contents of F_partial. Both F_obs and F_c are left unchanged on exit (unlike the example scripts provided with the XPLOR tutorial).

cycle.inp

This is my main script for crystallographic refinement. It

• Reads in your current model from generate.psf and current.protein
• Constructs a discrete solvent model from any water molecules it finds in current.solvent
• Optionally adds a bulk solvent correction on top of that by invoking the bulksol.inp script
• Optionally calculates an overall anisotropic B correction by invoking the anisob.inp script
• Optionally optimizes hydrogen postions before doing anything else (XPLOR is notoriously bad at initial placement of hydrogens).
• Cycles $NCYCLES times doing first positional refinement, then optionally doing B refinement, and writing out cycle.protein and cycle.solvent at the end of each cycle. These files contain REMARKS in the header describing the current R factor, Rfree, geometry ideality, etc.
• Performs a final calculation of rms B values

xprepare.inp

All my refinement scripts invoke a file by this name to establish the XPLOR force field, refinement parameters, specify the unit cell, scattering factors, etc. This one is not very different from the sample in the XPLOR tutorial, but it does make a few choices that are influenced by what my other scripts want.