|autoSHARP User Manual||previous next|
|Copyright||© 2001-2006 by Global Phasing Limited|
|All rights reserved.|
|This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.|
|Documentation||(2001-2006) Clemens Vonrhein|
These contain at least a structure factor amplitude FMID and its associated standard deviation SMID. If anomalous data is present it will have the additional columns for the anomalous difference DANO and its associated standard deviation SANO. A column with a ISYM flag should also be present.
These come directly out of SCALEPACK using the keyword 'MERGE" (default) and optionally 'ANOMALOUS'. It contains h, k, l, I, sigma(I) or h, k, l, I+, sigma(I+), I-, sigma(I-) in format (3I4, 4F8.1).
These come directly out of SCALEPACK using the keyword 'NOMERGE' and 'original indices' or 'no partials'. See SCALEPACK documentation for format (or CCP4 program combat).
This contains H, K, L, F2, σ(F2) per line (i.e. HKLF 4 format).
The first line starts with >, second line is empty, following lines contain single-letter amino acid code terminated by an asterisk ('*').
>1TIG in C2 plus 4+2 missing residues KQKVINVKEVRLSP TIEEHDFNTK LRNARKFLEK GDKVKATIRF KGRAITHKEI GQRVLDRLSE ACADIAVVET APKMDGRNMF LVLAPKNDNK*
Our own format: the first 4 characters have to be 'ATOM', followed by the atomic symbol (first letter upper case, following letters lower case) and the fractional coordinates for x, y and z (in free format).
ATOM Se 0.123 0.234 0.345 ATOM Se 0.333 0.44444 0.1
Alternatively, a standard PDB file can be given (orthogonal coordinates using orthogonalisation code 1 as described in coordconv). make sure to have the correct atom name in columns 13-16: the atomic type needs to be right-justified in columns 13-14 (all upper-case).
Only after you have copied all necessary files to these locations will they be visible in your browser (you might need to press the "Reload" button). Also make sure that the permissions on these files is correct:
% chmod 0644 somefile
If you feel the need for other file formats to be implemented - please feel free to get in contact with us (best with an example file attached to your email).
These input forms are started from the main SHARP Control Panel. You can either start autoSHARP based on a previous run (e.g. if you just want to change a few parameters) or from scratch (i.e. based on "None").
Once you submit the job you can look at the results through one main HTML document (called LISTautoSHARP.html). You need to hit the "Reload" button on your browser from time to time to get the latest version of this document. From this document you can see more details about the various steps performed through the "details" link. This will present another HTML document that (finally) will contain a table of contents at the top, all important information and further links to the detailed output of various programs. Again, you need to hit "Reload" from time to time.
Each autoSHARP job is started in its own subdirectory within your sharpfiles/logfiles directory structure. This subdirectory will contain the main LISTautoSHARP.html file.If you requested to do heavy atom refinement and phasing, at least one additional subdirectory will be created (again, within your sharpfiles/logfiles directory structure and with the run number incremented by one). This will contain a LIST.html file of the first SHARP run (heavy atom refinement and phasing). If the automated checking of the various residual maps didn't result in the addition or deletion of heavy atom sites after the first SHARP run, only one additional (phasing only) SHARP run is necessary to get phases in the inverted hand. If, however, additional heavy atom sites were detected (or wrong heavy atom sites removed) one further refinement and phasing run of SHARP is done for the original hand.
So you can end up with a directory structure like this:
sharpfiles/logfiles/<identifier><run> -> LISTautoSHARP.html <identifier><run+1> -> first SHARP run: initial; refinement and phasing <identifier><run+2> -> second SHARP run: further refinement or inverted hand phasing <identifier><run+3> -> last SHARP run: inverted hand phasing if necessaryNote: the last but one SHARP run (referred to as "original" hand) and the last SHARP run ("inverted" hand) will have the same heavy atom model (apart from the inversion of coordinates).
Anyway, all the necessary files/directories are available through the main LISTautoSHARP.html file.