1. Getting Through Shelxpro in One Piece (also see Chapter 9)

There are two files that Shelxl runs on: the .ins file and the .hkl file.  These are both set up using Shelxpro.

NOTE:  In order to run, both files need to have the same name (ie. myfile.ins and myfile.hkl).

Here's what you need to do to set them up:

    The .ins file

In CNS terms, the .ins file is a combination of the .inp, .pdb, .par, and .top files.  It contains information on bond lengths and angles, atomic positions and thermal parameters, and instructions on what to do during least-squares refinement.  You can easily edit the .ins file with your favorite text editor.
CNS outputs a bunch of REMARK fields at the head of every .pdb file it outputs.  Among all the REMARKs is the CRYST1 line.  Make sure this is present before you begin Shelxpro.

1.  At the prompt, type     shelxpro     This will initiate the program and you'll see:

2.  Enter option: I
        this will begin the transformation of your .pdb to a .ins file.

3.  Give Shelxpro the name of your new .ins file, your old .pdb file, and then the title of your experiment (which can be anything) when it asks for it.

4.  If you kept the CRYST1 line in your .pdb file,

then the CELL and space group should default to the correct values.  The default Z (number of molecules per cell) is 4.  If you collected your data at a synchrotron source, the wavelength will not be the default 1.54178 Å.  It'll likely be something like 0.78500 Å.  Finally, if you're using your CNS output .pdb file, it will automatically calculate the atom coordinates using the transformation matrix of the current cell.

6.  Tell it which residues make up the N- and C- termini.  If there are more than one of each, enter them all at the appropriate prompt.

7.  Renumber residues if appropriate (unlikely).

8.  HKLF code is VERY important!!!  Shelxl ALWAYS works best on F2, not on F as in CNS.  As such, HKLF 4 is best.  However, this ONLY works if you've set up your .hkl file to include F2 values and not F's.  Below are the best ways to accomplish this.

9.  Shelx doesn't always know what all of your residues are supposed to be, so you have ions or chemically altered residues, you may get a message like:

10.  Finally, you're done with the general setup of your .ins file.

    The .hkl file
There are pros and cons to using the CNS-style .cv or .fob file in creating your .hkl file for Shelxl.  If keeping the same Rfree flags that you've been using in CNS is important to you, then go here.  If keeping the same Rfree flags that you've been using in CNS is not important to you, then generate your .hkl file used in Shelxl as follows either from your original Scalepack or Scala output:
From Denzo/Scalepack output:

1.  In Shelxpro enter option: [D]

2.  Type in the appropriate .sca file name and .hkl file name when prompted

3.  The end, almost.  See here for setting up Rfree flags.

From Mosflm/Scala output:

1.  Use the CCP4 package program mtz2various to convert your .mtz file to a Shelx .hkl file using the OUTPUT SHELX command

2.  The end, almost.  See here for setting up Rfree flags.

To set up your .hkl file to include Rfree flags:

To set up the same Rfree flags that you've been using in CNS, have handy the .cv or .fob file you've been working with (it must include Rfree flags written as TEST = 1).

1.  In Shelxpro, enter option [Y].

2.  Enter the old CNS-style .cv file name and the new Shelx .hkl file name when prompted.

3.  The end.

If you started with your original output from either Scalepack or Scala, then you need to set up new Rfree flags as follows:

1.  In Shelxpro, enter option: [V]

2.  Give it the old and new names of your .hkl file (these can be the same)

3.  Tell it what percent of the data you want flagged for Rfree.

4.  It's best to choose the reflections randomly.

5.  The end.

OK, now you're ready to refine your data (almost)!
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