The checkboxes on the PARVATI submission long form allow you to select or deselect various features of the analysis. Short form options are shown in red.

Include uploaded text file in output

The PARVATI output usually begins with general introductory text. This option allows you to replace this with a file of your choice, probably containing information about the structure refinement being analyzed.

Neighboring atom ellipsoid similarity check

The quantity S(u,v) is a measure of the similarity of the thermal ellipsoids of atoms U and V [Merritt, 1999b]. Values greater than 1 indicate that the two ellipsoids are more similar to each other than either one is to a 'random' ellipsoid. Values less than 1 indicate that the ellipsoids are less similar to each other than either is to a purely isotropic model. Since one expects the vibrational modes of bonded atoms to be similar, a low value of S(u,v) for a pair of bonded atoms is suspicious. Note that this test compares the overall shape of the ellipsoids, not just their along-bond components (DELU in shelxl, RBON in refmac). It is also not quite the same as the similarity tests SIMU in shelxl, BFAC in refmac.

Treat nucleic acids separately

PDB standard residue names A C T G U I +A +C +T +G +U +I are tabulated and graphed in a separate category from other residues. Not extensively tested!

Label plots

This option writes the code name into the upper left corner of all plots. If you deselect this option, the code name will still be used to identify your coordinate set in the output text, but will not appear in the plots.

Fix y axis range of anisotropy plot

By default the program will scale the y axis of the final summary plot to fit the anisotropy distribution of the input model. If you are comparing PARVATI runs on different models, however, you may want to force the y axis always to have the same maximum value so that the plots are comparable.

Shelxl-style chains

The shelxl refinement program does not allow use of alphanumeric chain identifiers. So multiple protein chains are often handled by assigning residue numbers 1001-1999 to chain A, 2001-2999 to chain B, and so on. Selecting this option in the short form causes PARVATI to treat residues differing by a multiple of 1000 as equivalent residues in different chains. Residue 1023 is treated as residue 23 of chain 1, residue 2023 is treated as residue 23 of chain 2, and so on. The only difference this really makes is that it allows the plots of per-residue properties to place multiple chains in register with each other. The long form allows you to specify both a starting residue number and a chain offset. For example choosing start 1000 and offset 200 would assign residues 1000-199 to chain 1, 1200-399 to chain 2, etc.

Rogues Gallery

PARVATI normally displays rastep pictures of up to 12 residues containing atoms with large anisotropy. If you don't want to see the pictures, you can deselect this option in the short form. In the long form you can specify the maximum number of suspect residues drawn, the size of the images, and the rastep option used to draw the pictures.

Rastep figure of full molecule

PARVATI uses rastep to create a color-coded thermal ellipsoid represenation of your entire protein model. In the long form you can choose the color coding or disable figure generation altogether.