Shelx FAQ

1. How do I calculate free R values with shelx?
2. How come my reflection file doesn't work in windows (0 reflections found)?
3. What do I do about the error message "CANNOT RESOLVE ISOR ..HOH_200 > LAST" ?
   
4. How do I get shelxwat to run?
5. I get a cryptic error - wrong number of atoms. Help
6. Why are so many distances not restrained?
7. Shelx runs forever and gets nowhere.

How do I calculate free R values with shelx?

On the CGLS card in the input *.ins file, add a -1 after the number of cycles to run

How come my reflection file doesn't work in windows(0 reflections found)?

It was prepared on a UNIX system and needs a ^M (control-M) at the end of each line. (The UNIX and NT CR/LF symbols are different.)
One solution: Use the command to_dos on the sgis to convert the file. The new file will have the correct CR/LF characters.
Note: This isn't a problem going the other way, claude can read the NT files perfectly well.
If you use vi to edit an NT file, you'll see the ^M at the end of each line.

What do I do about the error message "CANNOT RESOLVE ISOR ..HOH_200 > LAST" ?

This command restrains anisotropic temperature factors for isolated atoms (like water) to be approximately spherical. You can REM the command if you're using isotropic Bs.
The error occurs when the water atom labels are different from those specified in the command. If your water atoms are called O, change to O_200; if they are OW, change the line to read OW_200, etc.

How do I get shelxwat to run?

It's really fussy. Some hints. (1) Don't try to run it after you've added hydrogens. It will fail. (2) Shelxwat seems to make some really bizarre assumptions about uppercase/lowercase file names. In unix, try using lower case file names, say no2.ins. If you get an error message that says NO2.hkl isn't found, copy (don't move) no2.hkl to NO2.hkl. (3) In the FAQ it says that you can't have PART instructions in the waters list and all waters must be contiguous. Put any ligands, ions (citrate, phosphate, heme, etc.) before the waters in the list. (4) Let me know of other problems/solutions you find. (5) I haven't got this to run under NT at all. Let me know if you have success.

I get a cryptic error - wrong number of atoms. Help!

Somewhere in your dictionary you've listed the wrong number of atoms for a distance (or more likely) an angle restraint. SHELX restrains the (1,3) distances, not the angles directly and, therefore, only wants two atom names in the DANG_FIX statement.

Why are so many distances unrestrained?

SHELX has built in dictionaries for standard amino acid residues. If your structure has anything else, you'll have to create the dictionaries yourself. If you have good resolution (> 2 A), you will need to put some care into your choice of restraints. They should be based on small molecule structures, not pdb files. You can find dictionaries that people have used in /cld1/xtalarchive/dictionaries/shelx.

Shelx runs forever and gets nowhere.

Are your F's all zero? Seriously! Some versions of the ccp4 mtz2various program have a bug and write F=0 for all reflections when a SHELX reflection file is chosen as the output file. Take another path to the shelx file (for instance, through a cns file.)