Online Help for SF-Tool - File Formats and Inputs

Our Experimental Data Validation tools require two user-provided files.

1. your fully refined Coordinate File in either mmCIF or PDB format.
2. your experimental Structure Factor ("SF") file (indicate its format too).
3. If you do not remember what suite was used to process your data, this server can guess it for you. Simply input your SF file and check the "Guess SF File Format?" box in the Input form. This action will override any experimental data checks you request.

The extension/format of the SF file depends on the software you used to process your data. We accept a variety of popular formats, including mmCIF (macromolecular CIF), MTZ, HKL/SCALEPACK, CNS/CNX/XPLOR, d*TREK, SAINT, SHELX, TNT, XSCALE, and CIF (small molecule CIF). You can use mmCIF files generated by pdb_extract as input as well.

NOTE:

• If you used either the TNT or SHELX suites to process your data, then indicate whether the structure factors were calculated as amplitudes (F) or intensities (I) by filling in the radio button beside the correct option.
• If your data was processed using a suite not found in our list, then select OTHER. Make sure that your SF file contains labels for each column as described below. Also indicate if the structure factors were calculated in terms of amplitudes (F) or intensities (I). Since our tools expect a certain format, this information must be supplied by the user.

Examples of input files:

 Coordinate Files:              final_refine.pdb    File Type: PDB  

 Structure Factor files:           refine-sf.cv     File Type: CNS  

 				     dataset.mtz    File Type: MTZ  

---

Various Examples of the SF File Format

Most reflection/structure factor data are organized into at minimum 5 columns (see examples below). The default column assignments used by most programs are:

H  K  L  F(or I)  SigF(or SigI or status)  ...and floating Free_R Flag

with at least one space in between each column. These column labels might not be displayed depending on the program's particular format, but would be displayed in an mtz_dump output.

Below are examples of representative structure factor files, in case you want to check for yourself.

• the CCP4 MTZ format.
• Correspondence of MTZ to mmCIF tokens

The first three characters must be 'MTZ' then followed by a space. The size should be close to 4*(number of items)*(number of columns).

• the CNS/CNX/X-PLOR/ format 1
• the CNS/CNX/X-PLOR/ format 2
• the CNS/CNX/X-PLOR/ format 3
• the CNS/CNX/X-PLOR/ format 4
• the CNS/CNX/X-PLOR/ format 5
• the CNS/CNX/X-PLOR/ format 6


• the SHELX format 1
• the SHELX format 2


• the TNT format 1
• the TNT format 2


• the macro-molecular mmCIF format (PDB user)
• the small molecular CIF format (SHELX user)


• the HKL/SCALEPACK format 1
• the HKL/SCALEPACK format 2
• the HKL/SCALEPACK format 3
• the HKL/SCALEPACK format 4


• the d*TREK- format 1
• the d*TREK- format 2
• the d*TREK- format 3


• the XSCALE format 1
• the XSCALE format 2
• the XSCALE format 3


• the SAINT format 1


• the OTHER format 1
• the OTHER format 2