2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

DialX

DialX makes dials plots from X-PLOR trajectories. The output is Encapsulated Postscript. The program was written by Tom Simonson in 1991.

As written, the input file DialX.inp will include all the dihedrals in the structure. It will automatically take into account the connectivity of the chain, leaving out missing phi, psi or omega angles from the final plot. 'Static' structures (e.g. Xray.pdb) can be overlaid on each dial in the form of radial segments; typically this is the Xray structure overlaid on the time series for comparison. Additional 'static' structures can be included (up to 15). If you want only a subset of residues to be plotted, modify the Xplor file in the fairly obvious way, that is modify the two loop statements:

             'for $i in id (name CA) loop li'

If you have more than one Xplor segment in your structure, and residues in the different segments have identical resid's you will have to make a couple of simple changes to DialX.inp.

To run DialX in the CSB core you require five (5) files:

Supplied by user:

PDB coordinate file (filename.pdb)

X-PLOR trajectory file (filename.crd)

X-PLOR structure file (filename.psf [edited])

From the installation:

DialX input file (DialX.inp [edited])

X-PLOR command file: (xplor.dialx)

An example containing the above files can be obtained by copying them from:

/srv/local/dialx/example/

To run the example submit a batch job to the queue with a command such as:

qsub -q short-pro xplor.dialx

Your output will be in a file called dialx.eps. You may view it with ghostview or print it directly.

To run DialX with your files you must edit the DialX.inp and filename.psf files.

In the DialX.inp file edit the following as appropriate:

!---------------------------
! user files and parameters
!---------------------------
evaluate ($coor="il8_template.pdb")
evaluate ($struc="dials.psf")
evaluate ($traj="tad.crd")
evaluate ($begin=1)
evaluate ($stop=400)
evaluate ($skip=1)
evaluate ($outp="dials.data")

and in the filename.psf file take the structure file you used to produce the trajectory; edit it to remove all dihedral angles. I.e. put NPHI to zero and remove the subsequent list of dihedrals. Be careful to preserve the format of the file--- e.g. it should look something like this:

 .
 .
 .
 1199 1198 1200 1202 1201 1203 1205 1204 1206
 1208 1207 1209

 0 !NPHI: dihedrals
 
 
 202 !NIMPHI: impropers
 1 4 3 6 14 17 16 19
 20 22 21 23 3 14 4 5
 .
 .
 . 

Note that there are TWO empty lines after the 'NPHI' line. If you only leave one you will get a nasty error message.

Then do the same as in the example above to run the program.