PROFASI  Version 1.5
MimiqA : A swiss army knife for RMSD calculations

MimiqA is a command line RMSD calculator. The name stands for "Minimaler mittlerer quadratischer Abstand", which is German for "minimal mean square distance". The name does not contain the "square root", but the program returns values with the square root. MimiqA is implemented using PROFASI version 1.1 PDB Handling module. It is not crucial for the other parts of PROFASI to function, and is not as such a "Simulation" program. But it is an application with a lot of potential use in analyzing protein structures, that extend beyond the intended use of PROFASI simulation routines.

Usage:

$ mimiqa [OPTIONS] pdbfile_1:model:selections_in_file_1 pdbfile_2:model:selections_in_file_2

The program only supports a few options.

While on surface there are only a few options, the program is very flexible. The selections method hinted above, along with the filters passed through the "-u" option allow you to calculate almost any kind of RMSD you might need. We illustrate with a series of examples...

examples

$ mimiqa file1 file2

This suffices if the files contain only one model and one protein chain each, and the entire range of amino acids is to be used. This also assumes that you are interested in the RMSD with all heavy (non-hydrogen) atoms.

If you wish to perform RMSD over backbone atoms you would pass a "using" option...

$ mimiqa file1 file2 -u "+BB"

When an explicit "using" option is given, the default filter which chooses heavy atoms is removed and only the filter passed explicitly is used.

To get RMSD with backbone and Cbeta atoms, you would write,

$ mimiqa file1 file2 -u "+BB+CB"

All heavy atoms except those on the backbone ?

$ mimiqa file1 file2 -u "+HV-BB"

All carbon atoms ?

$ mimiqa file1 file2 -u "+@C"

All backbone atoms but excluding the parts in Proline residues ?

$ mimiqa file1 file2 -u "+BB-%PRO"

You get the idea. The full set of filter and other selection rules is given in ProFASi PDB handling: Selections and Filters .

To compare one given pdb file with a whole set of files, use

$ mimiqa nmr.pdb file1 file2 file3 file4 ...

where the dots above are only for effect!

A PDB file may have several chains. To use chain A in one file and chain B in the other, you would write,

$ mimiqa file1::A file2::B -u "+BB"

In case there are many chains, and none is selected, ALL will be used.

By default, the full range of amino acids in every chain are used. If one chain is bigger than the other, the smaller one will be slid over the bigger one to find the position where the sequence of the smaller one matches. This sequence allignment is done, when the chains differ in size or in sequence. For chains with different sequences only the parts with overlapping sequence in the best possible allignment are used.

For a finer control over the range of residues over which to perform calculations, one provides the range along with the file name...

$ mimiqa file1::A,2,33 file2::B,32,63 -u "+BB"

It is possible to have discontinuous ranges...

$ mimiqa file1::A,2,13:A,56,61 file2::A,2,13:A,56,61 -u "+BB"

In the above case, residues 2 through 13 and 56 through 61 in the files will be used. When using disjoint ranges, the sequence allignment provided here should not be trusted. Instead, the user should carefully choose the segemnts from both files.

When a file has several models, one particular model can be optionally selected (default: first model)

$ mimiqa file1:3:A file2

Sometimes, it is necessary to compare structurally similar areas in two chains, which have different sequences. Normally, mimiqa would complain about the sequence mismatch, and attempt a sequence alignment. All mismatched parts are ignored. But if we want to use the mismatched parts, say, to calculate backbone RMSD, consisting of atoms common to all residue types, it is convenient to be able to switch-off sequence alignment. The user then takes care of providing an exact range for each structure, and asks PROFASI to not bother with alignment. This is done by passing an option "-no".

$ mimiqa -u "+BB" -no mol1.pdb::A,2,25 mol1_mutant.pdb::A,2,25

This finds the backbone RMSD in the specified region, without looking at the sequences.

Additional notes


PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2