X-GEN Manual, Section 5 | UPARAMS (crystal and detector parameters) | File Formats |
The UPARAMS file (name.upr) is a binary file containing information on the unit cell, orientational, and detector parameters for a particular data run. The information in the UPARAMS file is derived from indexing and refinement in refine1, refine, or refall. The format is as follows:
typedef struct { float xlambda; /* wavelength in Angstroms */ float xrec[3][3]; /* recip-space unit cell, unitless */ float xx0, xy0; /* translational (X,Y) offsets in cm */ float xplated; /* sample-to-detector dist. in cm */ float xpltd2; /* square of the above */ float xareal[3][3]; /* real-space unit cell in Angstroms */ float xtilt; /* tilt angle in radians */ float xctilt, xstilt; /* cosine and sine of tilt */ float xfrmsize; /* stepsize between images in radians*/ float xgam[3]; /* gamma (mosaicity) parameters */ float xswing; /* detector 2-theta angle, radians */ flaot xssw, xcsw; /* sine, cosine of xswing */ float xabc[3]; /* real-space unit cell lengths, A */ float xang[3]; /* real-space unit cell angles, deg */ float xerrind; /* error limit in index */ float xerrx, xerry; /* error limits in (X,Y), pixels */ float xerrphi; /* error limit in omega in frames */ float xresmin; /* low- and high-res limit, Angstroms*/ char xisref[20]; /* turn on&off refinement of params */ char xdir[3][5]; /* no longer used */ char xcmd; /* most recent refine command */ float xdelchi; /* chi Euler angle, degrees */ float xdelphi; /* phi Euler angle, degrees */ float xdelom; /* omega Euler angle, degrees */ short xisys; /* crystal system (1-7) */ short xispgp; /* Intl. Tables spacegroup # (1-230) */ float xstart[3]; /* start of current run in degrees */ char xmoveax; /* which axis is moving */ char xtemp; /* temp in Celsius (min=-128) */ char xrunno; /* nominal run number */ char xchamno; /* nominal detector number */ short xdetwid; /* # of pixels across detector */ short xdetht; /* # of pixels down detector */ short xdtype; /* integer detector type value */ short xversion; /* X-GEN version number * 100 */ } REFPARS; /* total: 256 bytes*/
The tilt angle, "xtilt," is defined as the angle between the rotation axis and the nominal vertical dimension of the detector. The gamma parameters are those described in the ancient but honorable analyses originally developed at Harvard for film data collection on viruses. The error limits are the values outside of which reflections will not included in the refinement. Thus if |Xob - Xpred| > xerrx, the reflection will not be used in refinement. The xisref values ('Y' and 'N') define whether a particular parameter is to be adjusted on a cycle of refinement. isref[0] corresponds to the unit cell length a, and so on. xisys is the crystal system: 1 is triclinic, 2 is monoclinic, 3 is orthorhombic, 4 is tetragonal, 5 is cubic, 6 is trigonal or hexaongal, and 7 is rhombohedral. The temperature is of limited utility since it doesn't go below -127. The software version number for X-GEN 5.4.8 will be 548.
The refinement functionalities rewrite the contents of the UPARAMS file rather than writing out new versions. In "integrate" the results of each on-the-fly refinement are written to a file whose name is derived, rather clumsily, from the frame number at which the refinement is conducted.
Usage: | $WORK/ |
Written from: | refine,
refine1, refall, integrate |
Edited in: | All of the above |
Read in: | All of the above and "reduce". |
Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.