| [fraction] |
is (real number) the fraction of the atoms that will be considered
explicitly on the fit (that is, that will automatically be chosen
by the method as the best aligned atoms). Use any real number
between 0 and 1. For example: [fraction] = 0.7 for 70% of the atoms.
|
| align.pdb |
This is the PDB file which will containt the aligned trajectory. |
| file1.pdb etc. |
These are the PDB files that contain the trajectory
to the aligned. Each PDB file may contain more than one
frame of the trajectory, and the files will be considered
as a sequential trajectory in the input order. In each PDB
file, the frames must be separated by "END" or "ENDMDL".
These files must always be the LAST input options of the command
line.
|
| Optional: | |
| -rmsf rmsf.dat |
A file, in the example called 'rmsf.dat', is created containing
the Root Mean Square Fluctuations (RMSF) of the selection atoms.
|
| -atoms N CA ... |
By default, MDLovoFit considers only CA atoms for alignment. You can change
this with this keyword, by selecting the atom names (see the -atomsfile option for
more sofisticated selections).
|
| -atomsfile file.pdb |
This file determines which are the atoms that will be considered for
alignment (default: CA). Atoms with zero occupancy will not be considered,
and atoms with 1.00 occupancy will be considered. You can create a file
with sofisticated selections using VMD, for example. For more simple selections,
see the -atoms option above.
|
| -ntrial [integer] |
The number of different initial correspondences. Larger ntrial
improves the chances that the global minimizer of the RMSD
is obtained. The computational time is proportional to the
number of trials. The default value is 100.
|
| -iref [integer] |
Frame to be considered as the reference frame for the alignment
(default = 1).
|
| -perframe (or -pf) |
The fraction of best aligned atoms is computed
independently for each frame. Thus, the assignment of which are the
least and most mobile atoms changes from frame to frame. If this
option is not set, the average best assignment is kept and the
alignmnet of this set is repeated for every frame.
|