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/<idname>.upr
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.