CCP4 wiki - User contributions [en]

SMV file format

2017-02-22T22:50:50Z

Hattne: Number of possible beam center conventions is 4 * 2 = 8.

The SMV file format is a broad standard x-ray diffraction image file format that appeared with the first CCD-based x-ray detectors. SMV stands for Super Marty View, a program written by Dr. Martin "Marty" Stanton to display the images form the original SBC CCD detector. The format is largely informal, the only rigid rule is that the file header is text and begins with the string: "{\nHEADER_BYTES=", where \n is the newline character (ASCII decimal code 13). This string must be followed with an ASCII number indicating the number of bytes in the header before the start of the image data. The header itself is generally expected to be all text and describe the nature of this image data in a keyword=value type format. The most common SMV header is 512 bytes. So common in fact that many data processing programs assume that it is without reading the HEADER_BYTES entry. An example of such a 512-byte header is given here:

<pre>{
HEADER_BYTES= 512;
DIM=2;
BYTE_ORDER=little_endian;
TYPE=unsigned_short;
SIZE1=3072;
SIZE2=3072;
PIXEL_SIZE=0.102592;
BIN=2x2;
BIN_TYPE=HW;
ADC=fast;
CREV=1;
BEAMLINE=ALS831;
DETECTOR_SN=926;
DATE=Thu Apr 17 07:45:15 2008;
TIME=0.674101;
ACC_TIME=2860;
DISTANCE=150.05;
TWOTHETA=0.00;
PHI=0.000;
OSC_START=0.000;
OSC_RANGE=1.000;
WAVELENGTH=1.115872;
BEAM_CENTER_X=156.27;
BEAM_CENTER_Y=156.52;
DENZO_X_BEAM=158.64;
DENZO_Y_BEAM=156.27;
}
</pre>

== Description of common keywords: ==
* DIM - indicates that the image is two-dimensional. No known beamlines produce other-dimensional SMV images.
* BYTE_ORDER - can be either little_endian or big_endian. No other values are known to be in use. This reflects the byte ordering of the image data. Big endian implies that the first byte of a 16-bit number is the most significant byte. Little endian implies the opposite. For more information, see [http://en.wikipedia.org/wiki/Endianness]
* TYPE - all known SMV images use the unsigned short integer (16 bit) value of TYPE.
* SIZE1 - number of pixels along each edge of the image. It is unclear and unimportant which of SIZE1 or SIZE2 is X or Y as all known SMV image formats are square.
* PIXEL_SIZE - size of a pixel. All known formats provide this number in millimeters.
* BIN - degree of pixel binning (averaging) used when reading out the CCD. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* BIN_TYPE - introduced for the ADSC Quantum 315r detectors to indicate that the binning was done on the hardware level, as opposed to the software level. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* ADC - indicates the mode of the analog-to-digital converter used to read out the image.
* CREV - introduced by ADSC to indicate the version number of the SMV header style. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* BEAMLINE - introduced at the Advanced Light Source to indicate which beamline was used to collect the data.
* DETECTOR_SN - serial number of the ADSC detector used to collect the image. Useful for determining which beamline was used to collect the data, but not with 100% reliability as detectors can move from beamline to beamline.
* DATE - a common, but unfortunately not universal entry to indicate when the image was collected. There is no standard to the nature of this format, but it is usually a Unix date.
* TIME - exposure time of the image in seconds. Sometimes this can be half the exposure time if the image was dezingered, but confusing records like this are discouraged.
* ACC_TIME - number of milliseconds between the start and stop of electron accumulation on the CCD. This is useful for determining an appropriate dark current.
* DISTANCE - the sample-to-detector distance. All known SMV file formats give this in millimeters. Although this is generally the distance along a line normal to the detector surface, there is no universal standard for this. It could also mean the distance that would be traveled by the direct beam before hitting the surface of the detector.
* TWOTHETA - detector angle relative to the normal-to-beam orientation.
* PHI - starting value of spindle rotation motor for this image.
* OSC_START - starting value of spindle rotation motor for this image.
* OSC_RANGE - change in value of spindle rotation motor for this image.
* WAVELENGTH - X-ray wavelength used to obtain this image. All known SMV file formats give this in Angstrom.
* BEAM_CENTER_X - position on the detector face that would be hit by the direct x-ray beam if the beamstop were removed. Most beamlines give this in millimeters, but some at ESRF give it in pixel units. Unfortunately, there are also eight possible conventions for representing the beam center (four corners to use as 0,0, and two axes to assign to either "X" or "Y"), and nearly all of these are used by one program or another. At the Advanced Light Source and Stanford Synchrotron Radiation Lab these values are such as to give the correct beam center display in the program ADXV (provided by ADSC).
* DENZO_X_BEAM - introduced at the Advanced Light Source to indicate the direct beam position to enter into the data processing program denzo or mosflm, as these programs coincidentally use the same beam center convention. This was an attempt to avoid confusion by specifying the convention explicitly.

== See also ==

[[Crystallographic data file formats]]

SMV file format

2013-01-25T11:02:36Z

Hattne: Corrected typo.

The SMV file format is a broad standard x-ray diffraction image file format that appeared with the first CCD-based x-ray detectors. SMV stands for Super Marty View, a program written by Dr. Martin "Marty" Stanton to display the images form the original SBC CCD detector. The format is largely informal, the only rigid rule is that the file header is text and begins with the string: "{\nHEADER_BYTES=", where \n is the newline character (ASCII decimal code 13). This string must be followed with an ASCII number indicating the number of bytes in the header before the start of the image data. The header itself is generally expected to be all text and describe the nature of this image data in a keyword=value type format. The most common SMV header is 512 bytes. So common in fact that many data processing programs assume that it is without reading the HEADER_BYTES entry. An example of such a 512-byte header is given here:

<pre>{
HEADER_BYTES= 512;
DIM=2;
BYTE_ORDER=little_endian;
TYPE=unsigned_short;
SIZE1=3072;
SIZE2=3072;
PIXEL_SIZE=0.102592;
BIN=2x2;
BIN_TYPE=HW;
ADC=fast;
CREV=1;
BEAMLINE=ALS831;
DETECTOR_SN=926;
DATE=Thu Apr 17 07:45:15 2008;
TIME=0.674101;
ACC_TIME=2860;
DISTANCE=150.05;
TWOTHETA=0.00;
PHI=0.000;
OSC_START=0.000;
OSC_RANGE=1.000;
WAVELENGTH=1.115872;
BEAM_CENTER_X=156.27;
BEAM_CENTER_Y=156.52;
DENZO_X_BEAM=158.64;
DENZO_Y_BEAM=156.27;
}
</pre>

== Description of common keywords: ==
* DIM - indicates that the image is two-dimensional. No known beamlines produce other-dimensional SMV images.
* BYTE_ORDER - can be either little_endian or big_endian. No other values are known to be in use. This reflects the byte ordering of the image data. Big endian implies that the first byte of a 16-bit number is the most significant byte. Little endian implies the opposite. For more information, see [http://en.wikipedia.org/wiki/Endianness]
* TYPE - all known SMV images use the unsigned short integer (16 bit) value of TYPE.
* SIZE1 - number of pixels along each edge of the image. It is unclear and unimportant which of SIZE1 or SIZE2 is X or Y as all known SMV image formats are square.
* PIXEL_SIZE - size of a pixel. All known formats provide this number in millimeters.
* BIN - degree of pixel binning (averaging) used when reading out the CCD. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* BIN_TYPE - introduced for the ADSC Quantum 315r detectors to indicate that the binning was done on the hardware level, as opposed to the software level. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* ADC - indicates the mode of the analog-to-digital converter used to read out the image.
* CREV - introduced by ADSC to indicate the version number of the SMV header style. Some image processing programs need to know this value in order to estimate the detector read-out noise.
* BEAMLINE - introduced at the Advanced Light Source to indicate which beamline was used to collect the data.
* DETECTOR_SN - serial number of the ADSC detector used to collect the image. Useful for determining which beamline was used to collect the data, but not with 100% reliability as detectors can move from beamline to beamline.
* DATE - a common, but unfortunately not universal entry to indicate when the image was collected. There is no standard to the nature of this format, but it is usually a Unix date.
* TIME - exposure time of the image in seconds. Sometimes this can be half the exposure time if the image was dezingered, but confusing records like this are discouraged.
* ACC_TIME - number of milliseconds between the start and stop of electron accumulation on the CCD. This is useful for determining an appropriate dark current.
* DISTANCE - the sample-to-detector distance. All known SMV file formats give this in millimeters. Although this is generally the distance along a line normal to the detector surface, there is no universal standard for this. It could also mean the distance that would be traveled by the direct beam before hitting the surface of the detector.
* TWOTHETA - detector angle relative to the normal-to-beam orientation.
* PHI - starting value of spindle rotation motor for this image.
* OSC_START - starting value of spindle rotation motor for this image.
* OSC_RANGE - change in value of spindle rotation motor for this image.
* WAVELENGTH - X-ray wavelength used to obtain this image. All known SMV file formats give this in Angstrom.
* BEAM_CENTER_X - position on the detector face that would be hit by the direct x-ray beam if the beamstop were removed. Most beamlines give this in millimeters, but some at ESRF give it in pixel units. Unfortunately, there are also 16 possible conventions for representing the beam center (4 corners to use as 0,0, and 2 axes to assign to either "X" or "Y"), and nearly all of these are used by one program or another. At the Advanced Light Source and Stanford Synchrotron Radiation Lab these values are such as to give the correct beam center display in the program ADXV (provided by ADSC).
* DENZO_X_BEAM - introduced at the Advanced Light Source to indicate the direct beam position to enter into the data processing program denzo or mosflm, as these programs coincidentally use the same beam center convention. This was an attempt to avoid confusion by specifying the convention explicitly.

== See also ==

[[Crystallographic data file formats]]

Mmdb

2010-09-07T14:50:32Z

Hattne: Added working link to mmdb documentation as provided by Gerard Kleywegt on ccp4-dev.

== What is mmdb? ==

MMDB is a macromolecular coordinate library, written by Eugene Krissinel primarily for use by CCP4 group. The Coordinate Library is designed to assist CCP4 developers in working with coordinate files.

The Library features work with the primary file formats of the Protein Data Bank (PDB), the PDB file format and the mmCIF file format.

The Library provides various high-level tools for working with coordinate files, which include not only reading and writing, but also orthogonal-fractional coordinate transforms, generation of symmetry mates, editing the molecular structure and some others. The Library is supposed as a general low-level tool for unifying the coordinate-related operations.

The [[Clipper]]-MMDB interface package provides an interface to allow MMDB models to interact with other types of crystallographic data as part of a structure solution application.

== How to install mmdb? ==

The easiest way for users of Linux distros is to install the Fedora 9 RPM package ([https://www.redhat.com/archives/fedora-package-announce/2008-November/msg00262.html announcement]). For Apple machines, this would probably be http://pdb.finkproject.org/pdb/package.php/mmdb .

== How to use it? ==
Link your application with ...

== Example: a typical problem and its solution with mmdb ==
What is the mmdb string for all atoms in the A conformation of residue 30 in the B chain? Answer: "//B/30/*:A"

== Documentation ==
* http://www.ebi.ac.uk/~keb/cldoc/ and http://msd.ebi.ac.uk/~keb/cldoc/ are both broken.
* [http://www.ebi.ac.uk/pdbe/docs/cldoc/ CCP4 Coordinate Library Project] at the European Bioinformatics Institute