Once you have specified a descriptor file on the command line (at the very least), exam will wait for your commands. The commands can be abbreviated to the minimum unambiguous string but obviously, file names cannot be abbreviated. There is no punctuation, you can string as many commands as will fit on a line. This is convenient for command pipes (if you are using UNIX). For example, the reporting feature (see below) will write the output on the standard output stream (normally the screen). The following is a C-Shell example where the reports are saved in a file:
echo move 2 rep bonds mov 3 rep nonb | ( exam -d desfile -a arcfile > repfile ) >& /dev/null
In this example, several commands to exam are strung together. The commands will cause the bond report to be created for the second archive record. This is followed by a report of the non-bond records for the third archive record. The commands are echoed to the standard output by echo and is piped to the standard input of the exam command where a descriptor file desfile and an archive file arcfile have been specified. The reports which would have gone to the standard output is redirected to a file repfile instead. With a bit more effort we have taken pains to separate the standard error output and discarded it (into the system's black hole /dev/null). The standard error output contains prompt strings and messages from exam which would be a distraction if it is mixed with the reports.
add_to_archive
Copy the current archive record to the new archive file. See open_archive about starting a new archive. See also the command arcedit which is a more convenient way to edit archive files.
move_to i
Load the i -th archive record into memory. All subsequent commands will apply to this record until a new record is loaded. If i exceeds the total number of records in the archive, the last record will be loaded instead.
bond_file bondfile
From the current archive record, write out the input files for a very old version of ribbons. Name the files starting with the string bondfile, with appropriate file name extensions. This supports an extremely old version of ribbons (called circles and spheres) and is therefore completely out-of-date.
coordinate_file arcfile
From the current archive record, write a new archive to a file named arcfile containing only this record.
pdb_file pdbfile
From the current archive record, write a PDB file named pdbfile. This is possible only if your descriptor contains the name record or you have specified a name dictionary file on the exam command line. See the name and type records in the reference for the descriptor file format. Or see the exam command reference for the command line options to read in the dictionary file.
macmolecule molefile
From the current archive record, write an input file named molefile for the molecular display program Macmolecule. Macmodel is a very old Macintosh program from the University of Arizona. There is a current version but it is not known if the result of this command is in the correct format for the new version of the program.
ribbons_files name
From the current archive record, write input files for the ribbons molecular display program. This will produce five files with names starting with name and with appropriate terminations. Be careful, make sure you do not have files starting with name or you may write over these files.
open_archive arcfile
Close the current archive file (if one was open) and open the archive file arcfile. Then read the first archive record into memory. The archive file must exist and must be compatible with the descriptor.
start_archive arcfile
Create a new archive file named arcfile and write the file header. Records can then be added to this file see add_to_archive. You can pick and choose records from different archive files (provided they are compatible) and add them to this file. See arcedit which is a program specifically designed to edit archive files.
color_read color
Read in a color template file named color. This file specifies the radius and color of atoms and bonds for the ribbons_files and draw commands. A template can be created using the color_write command. Once you are in ribbons, you will be able to change colors (and other display characteristics).
color_write color
Write a color template file named color. In the template, the atoms and bonds will be given a default color number. The atoms and bonds will be given a radius of 1Å plus a very small fraction where the fraction runs progressively from 1 to the number of atoms in the system. This provides a convenient way to locate a particular atom. (Otherwise you have to count the lines.) Once you have a color file, you can edit it to specify colors and radii for each atom and bond. The color numbers and their color are listed as comments on top of the file. Note that this file is not a ribbons feature. Only exam knows how to deal with this format.
contra_read pffile
Read in a postfix file pffile for CONTRA-MD.
report x
Write a summary of the x term of the potential function. The output typically consist of the atoms that are involved in the term, the equilibrium parameters and the prevailing values. x can be one of the following: amberhb, angles, bonds, energies, gradients, morse, noe, studs, torsions, nonbonds, electrostatics, vanderwaals, internal_coordinates, improper_torsions, contra. The reports appear on the standard output which can be lengthy. The example at the top of this page shows how to redirect the reports to a file.
report close_contacts dmin
Print a list of all pairs of atoms that are within a distance dminÅ of each other. This can produce a very long report.
report vlat
Report for each atom, the voxel indices, the weight, the energy and a reconstructed density. The voxel indices are three numbers indicating the voxel number along the three directions in which the atom is located. If any of the indices contain an asterisk, it indicates that the atom lies outside the unit cell. The reported energy also gives an indication of how optimally the atom has been placed in the vector lattice: the closer the energy is to the minimum the better is the atom packed into the lattice. The electron density is reconstructed from the descriptor record for voxels that have negative energies. It is not possible to reconstruct densities from positive energies and an * is printed for these voxels.
report radius_of_gyration
Not implemented.
distance atomi atomj
Print the distance in Å between the atoms atomi and atomj for the current archive record. The atom numbers must be within range, i.e., from 1 to the number of atoms in the system.
angle atomi atomj atomk
Print the angle spanned by the atoms atomi, atomj and atomk with atomj at the vertex.
crossangle atomi atomj atomk atoml
Print the angle between two vectors. The first vector runs from atomi to atomj and the second vector runs from atomk to atoml.
torsion atomi atomj atomk atoml
Print the torsion angle spanned by the atoms atomi, atomj, atomk and atoml. This is a signed quantity. Reversing the order of the atom numbers should reverse the sign. Reordering the atom numbers will produce a different torsion angle.
set tempfilename name
Set the initial part of the temporary input files created in the draw command to name. The preset value is YAMMPEXAMTEMP. Normally you would not need to set this but if you are strange enough to have files starting with this string, set a new name!
set graphicstyle which
Set the default display program to either ribbons or circles. The default setting is ribbons and circles is a very old version of ribbons and should no longer be available.
set selectrecord mode
The preset value of mode is current which means that only the properties of the current archive record will be reported. If mode is all, then the properties of all archive records all be reported. For example, to report the distance between atoms 3 and 25 for all time steps of a molecular dynamics trajectory, type "set selectrecord all dist 3 25 set selectrecord current". The last part of the command is a precaution to prevent accidental reporting of all records in later commands.
draw
With the current archive record, create temporary input files and call the default display program. The default display program is set in set graphicstyle. When you quit from the display program, the input files are removed. The names of these files start with the string specified on set tempfilename. If you do not quit the display program or exam properly, the temporary files will not be deleted; you can go ahead and delete them manually.
help
Print a listing of all commands.
status
Report the name of the current descriptor file, the current archive file and which archive record is currently in memory.
quit
Quit the exam program. You can also enter an end-of-file mark (Control-D) in UNIX. This is not needed in a command pipe.
xmd3 has a command set that is very similar to exam. See the exam reference for the following commands:
mod1_file coof
M
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S -- C
C
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S -- . -- M
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The current coordinates is transformed and written to coof. In the 3DNA model, each base pair of DNA is modeled by three atoms, C which is located in the center of the base pair, M an atom located in the major groove 2.5Å from C and S an atom located on one side of the base pair 5Å from C such that S-C-M forms a right angle. In this transformation, C is moved to the position formerly occupied by M and M is moved to the other side of S 5Å from the old position of C. This forms a more symmetrical figure and the purpose of producing such an archive file is for a better looking display. |
set granularity G
This sets the granularity to G base pairs. This is a constant used in many calculations. It is that number of base pairs that is to be considered as a single unit. The preset value is 5. The allowed value is from one to one base pair fewer than half the total number of base pairs.
set writhemethod M
set writherounds R
set writhesample S
This sets the method to be used to calculate the Writhing number and the parameters of one of the method. The preset value of M is gauss and the other allowable value is average. When M equals gauss, the Writhing number is calculated by evaluating the Gauss integral which is relatively fast. When M equals average, the Writhing number is calculated by enumerating apparent cross-overs in the backbone trajectory. This is calculated as the average over R rounds and each round consists of S projections over random directions. This method of calculating the Writhing number is slow and inaccurate. The preset value of R is 2 and of S is 100 which is far too small for all but the smallest molecules. However, there are rare situations where the Average method works (with appropriately large values for R and S) while the Gauss method fails. R and S have no effect when the Gauss method is used.
set loopcross Q
set loopexclude X
set loopratio L
Set the parameters for loop tip calculations (see report loops). The structure of the model DNA is analyzed to determine the number of loops. (For example a simple interwound DNA has two loops at the end of the supercoil and if there is a single branch in the interwound DNA, there will be three loops.) As part of this calculation the path of the DNA is divided into segments that are at least XG/2 base pairs long, where G is the granularity (see set granularity). The preset value of X is 20. A loop, by definition, is bounded by a pseudo-node (an apparent crossing of the DNA backbone). There are several criteria for a proper pseudo-node and one of this is the crossing angle; this has to be at least Q. The preset value of Q is 5 degrees. Once a loop is found a curvature criterion is applied. The ratio of the apparent to actual length of the segment must be below L. The apparent length of the segment is the straight line distance between the two ends of the segment. The actual length of the segment is the distance of the two ends traced along the curved path of the DNA backbone. The preset value of L is 0.5.
shift_bases Nbp
The base pairs are circularly rotated by Nbp. Base pair 1 is moved to 1+Nbp, base pair 2 to 2+Nbp, and so on. The base pairs displaced at the end of the sequence is moved to occupy the positions vacated by the leading Nbp base pairs. Once you have done this, you would want to write out the transformed coordinates to a new archive file. See coordinate_file.
twist_bases T
The base pairs are all evenly twisted by T degrees. The increment is with respect to the new rotated positions of the previous base pairs. Therefore, base pair N would have been twisted a total of NT degrees. Once you have done this, you would want to write out the modified coordinates to a new archive file. See coordinate_file.
report energies
Report the energies categorized into a stretching component (rise), two bending components (roll and tilt) and a twisting component (twist). The remaining internal energy is lumped together as a constraint component.
report helical_coordinates
report rise
report roll
report tilt
report twist
Report the helical coordinates. The first command will report all four helical coordinates and is equivalent to issuing the four remaining commands that follow.
report loops
Report the loop tips. The loop tips are the base pairs that are at the top or tip of loops. A simple interwound circular DNA has two loops and therefore two loop tips. A branched interwound DNA would have three loop tips and so on. This calculation is controlled by user controlled parameters.
report linking_number
report writhing_number
In the first command, the linking number and the radius of gyration are reported. The linking number is calculated by projecting and enumerating pseudo-nodes. This is done for three orthogonal projections and all three numbers are reported. The three numbers should agree in most situations. When there is a disagreement use the number that appears twice. If that is not possible one or two of the numbers contains a half fraction. Take an average of all three numbers noting that the linking number is always a whole number. In the second command the writhing number, the linking number and the radius of gyration are all reported. The calculation of the writhing number is user controlled. See the writhe parameters.
report min_cis bpi
report all_cis bpi
These commands report the closest physical neighbors to base pair bpi. Obviously, the closest neighbors to a base pair in a circular DNA are the base pair immediately before (bpi-1) and the base pair that immediately follows it (bpi+1). Instead, the immediate neighbors, G base pairs from either side of bpi, are excluded from consideration. G is the granularity (see set granularity). In report min_cis bpi, the nearest neighbor to bpi is reported. If this is just bpi +G+1 or bpi -G-1, i.e., the base pairs just outside the exclusion zone, then the outcome is not meaningful. The default value of G is also too small (5 base pairs at 3.4Å apart is 17Å which is much less than the closest approach of two double stranded DNA). With report all_cis bpi, all distances from bpi to immediate neighbors except for the 2G excluded immediate neighbors are reported. In both commands a ratio is also reported; this is the ratio of the actual distance to the straight line distance.
report orientation bpi
The orientation of the major groove at base pair bpi is reported in degrees. The orientation is calculated for a segment centered at base pair bpi that is extended by G base pairs on either side where G is the granularity. G can set in the set granularity command. The orientation is the angle between the vector from the center atom to the major groove atom of the 3DNA model and the plane formed by the curved segment. Thus orientation is undefined when the segment is perfectly straight. One could increase the granularity to increase the size of the segment but eventually the segment will be unrealistically large. A reliable orientation is obtained if the angle does not change (much) as the granularity is varied about the initial setting.
report curvature bpi
The curvature at base pair bpi is reported as the ratio between the apparent and actual length of a segment centered at base pair bpi. The segment runs from bpi -G to bpi +G where G is the granularity. The apparent length is the distance in a straight line between base pairs bpi -G and bpi +G. The actual length is the contour length between these two base pairs, i.e., the sum of the rise distance between the two base pairs following the curved path of the DNA. Thus the ratio runs from nearly zero (maximum curvature) to a maximum value of 1 (straight). G can set in the set granularity command.
(Under Construction)
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