SHARP User Manual | previous |
Appendix 3 |
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) Claus Flensburg, Marc Schiltz, Clemens Vonrhein |
Contact | sharp-develop@GlobalPhasing.com |
Note : you also might to have a look at Appendix 2: How to use SHARP under UNIX
The input for various keywords has always to be on a single line. Furthermore, most keywords require exact spelling (no mixing of upper- and lower-case letters). The numerical values can be free format. Also, white space is ignored.
The refinement of each refinable parameter can be specifically switched on or off using the REFINE or NOREFINE flag following the parameter value(s). These flags will only have an effect, if the MODE keyword specifies that refinement is requested.
The default for each parameter is NOREFINE.
The estimation of each parameter can be specifically switched on or off using the ESTIMATE or NOESTIMATE flag following the REFINE/NOREFINE flag. These flags will only have an effect, if the MODE keyword specifies that estimation is to be done.
The default for each parameter is NOESTIMATE.
This points to the directory where the MTZ file is expected. It usually is something like /home/user/sharpfiles/datafiles (or relative to the main SHARP/autoSHARP installation.
Name of the MTZ file (in DATAFILES). This should contain all columns (and optionally the Hendrickson-Lattmann coefficients HLA ... HLD for external phase information).
You can override the DATAFILES/OBSFILE keywords by putting a file named REFL01.mtz into the current directory.
Just a string describing the calculation you want SHARP to do - handy to keep track of several runs with same identifier.
Can be one or several of:
All parameters defined as ESTIMATE will be estimated as a first step.
Maximum likelihood refinement of all parameters defined as REFINE.
Calculation of log-likelihood gradient maps.
Calculation of electron density (phases).
Calculation of Luzzati tables a la SIGMAA. Requires columns: Fn, Fmod, and, PHImod in the reflection file.
Give the space-group name: make sure to use
Cell parameters (all 6 values have to be given) in units of Å and degrees.
The syntax of the CYCLES card is:
CYCLES NumCycles iCycBeg iCycEnd |
The syntax of the REJECT card is:
REJECT s q |
The syntax of the SPARSE card within the SIN file is:
SPARSE Sparse_cut |
The default is:
SPARSE -8.0
The syntax is:
WEED I1 Q1 Q2 |
If I1 is non-zero weeding is switched on. Q1 is an absolute threshold (weed_t1) and Q2 is a factor to multiply the standard uncertainty of the mean of the scores to construct the relative threshold weed_t2, with
weed_t2 = <score> - Q2 * Sigma(<score>).
The default is to do weeding with thresholds of 0.50 and 3.00 for
Q1 and Q2,
respectively, ie.
WEED 1 0.50 3.00
For each BIG cycle it is possible to switch on/off classes of variables using the STRATEGY card. The classes are:
Description | Variable(s) | Class Number | Value |
---|---|---|---|
Scaling | SCAL_K SCAL_B SCAL_B6_ADD |
1 | 1 |
Non-isomorphism | NISO_BGLO NISO_BLOC NISO_CLOC NANO_BGLO NANO_BLOC NANO_CLOC |
2 | 2 |
Occupancy | HAT_OCC | 3 | 4 |
Coordinates | X, Y, Z | 4 | 8 |
B-factors | HAT_B HAT_B6_ADD |
5 | 16 |
Scattering factors | ATOM_f' ATOM_f" |
6 | 32 |
Others | 7 | 64 |
The syntax of the STRATEGY card is as follows:
STRATEGY I1 I2 I3 ... In |
For each BIG cycle you can construct the sum of the Class Values (see table above) for the variable classes which are to be optimised in that BIG cycle and put it on the STRATEGY card. Some examples:
BIG cycle 1 : | Scaling, Non-isomorphism, Occupancy |
BIG cycle 2 : | Scaling, Non-isomorphism, Occupancy, Coordinates |
BIG cycle 3 : | Scaling, Non-isomorphism, Occupancy, Coordinates, B-factors, Scattering factors |
BIG cycle 1 : | Scaling, Non-isomorphism, Occupancy |
BIG cycle 2 : | Scaling, Non-isomorphism, Occupancy, Coordinates |
BIG cycle 3 : | Scaling, Non-isomorphism, Occupancy, B-factors |
BIG cycle 4 : | Scaling, Non-isomorphism, Occupancy, Coordinates, B-factors, Scattering factors |
BIG cycle 1 : | Nothing (this BIG cycle will be skipped) |
BIG cycle 2 : | Scaling, Non-isomorphism, Occupancy |
BIG cycle 3 : | Scaling, Non-isomorphism, Occupancy, Coordinates, B-factors, Scattering factors |
The syntax is:
PRINT_HESS I1 |
The default is not to print the full Hessian (and eigenvectors)
PRINT_HESS 0
The syntax is:
BOX_CONSTR_F' I1 QAbs QRel |
If the variable I1 is non zero the f's will be constrained to be within the bounds:
MIN(f' - |f'|*QRel, f' - QAbs) and MAX(f' + |f'|*QRel, f' + QAbs)computed with the value of f' at the start of each BIG cycle. The default is to use the card:
BOX_CONSTR_F' 1 2.0 0.5
The syntax is:
BOX_CONSTR_XYZ I1 Q1 |
If the variable I1 is non zero each coordinate will be boxed within: initial value +- delta, where
delta = Q1 * Lowest_HiRes / Cell_parameterwhere Lowest_HiRes is the lowest high-resolution limit among all Batches and Cell_parameter is A for X, B for Y, C for Z.
The default is to box coordinates using:
BOX_CONSTR_XYZ 1 0.7071
The syntax of the SPHCLUSTER card (for SHARP versions 2.1.0 and above) within the SIN file is:
SPHCLUSTER TAG d1 d2 ... dN |
There has to be a SPHCLUSTER card for each element type in a cluster.
Use one G-Site to specify the location of the centre of the cluster.
At the C-site level you specify the actual scatter type of the cluster component and add: SPHCLUSTER TAG to specify what cluster component this C-site/G-site belongs to. Eg.
C-SITES { C-SITE-01 G-SITE-01 Ta SPHCLUSTER Ta6Br12:Ta C-SITE-02 G-SITE-01 Br SPHCLUSTER Ta6Br12:Br }
Optimisation of all the usual atomic parameters are allowed for a cluster component.
Note : Since Sushi does not (yet) handle the Spherical cluster keywords properly, you will have to run SHARP either as described in Appendix 2: How to use SHARP under UNIX or use the following recommended procedure:
A database of pre-defined clusters is available in the file $BDG_home/database/sphcluster. Any cluster defined in this database can directly be used. If the user wants to create their own database of cluster definitions, the environment variable SPHCLUSTER can be set to a database file with the same format as $BDG_home/database/sphcluster:
# Comment line TAG N d1 d2 ... dN(TAG and d1 to dN have same meaning as above)
The syntax is:
ABSSCALE_MODE MODE |
This card is used to switch between different algorithms to determine an absolute scale. MODE can be either WILSON or E2PROTEIN. See: Morris & Bricogne for more details.
Default is to use the Wilson mode.
The syntax is:
ABSSCALE_RESOL QLow [QHigh] |
This card sets the resolution limits for the determination of an absolute scale. If only one arguments is present it is assumed to be QLow.
This card specifies the form of the prior to be used during SHARP computations. The syntax is:
PRIOR Type |
If Type is EXTERNAL the reflection file MUST contain columns with the following names: PriorA, PriorB, PriorV11, PriorV12, and, PriorV22.
If Type is SIGMAZ the reflection file MUST contain columns with the following names: Fn, Fmod, and, PHImod.
Cards to specify a particular prior for only some of the MODEs have the following form:
The default is to use the Wilson prior for all computations.