SUPCW
On launching supcw, the prompt will ask you the number of models to be analyzed. If you enter 1, it will also ask you if you want to save the results in a file, but for more than one model the save-to-a-file option is automatic, and a filename will be asked anyway. If you choose more than one model, you will be prompted to choose between "sequential" files of not. If you choose sequential files, you will be later asked to enter a common prefix for the filenames, and a starting and ending number. In this way, if you have generated, say, a number of random string-of-beads models, you can analyze them sequentially, and at the end SUPCW will also calculate the mean values of all the parameters. For the Windows version, SUPCWIN, we strongly advise to save the results in a file anyway, as the DOS screen does not have scroll capabilities! Next, a conversion factor is asked, because the units of the program are nanometers. Therefore, if yor beads are angstrom-sized, such as the ones generated by SOMO, enter 0.1, if they are micron-sized enter 1000. Next, it is asked to which point the parameters are to be referred to in the computations, cartesian origin or diffusion center. For most work, these numbers will not differ appreciabily. We always refer the computations to the diffusion center. Stick or slip boundary conditions are then asked. For beads larger than atoms, sticky boundary conditions usually apply.
Volume correction: this is a correction required in order to properly calculate the rotational diffusion coefficients, and it is usually taken as the sum of the volumes of the beads. The automatic feature in SUPCW does just this, but there is also the possibility of introducing a different volume correction. Mass correction: as above. The mass is needed to properly calculate the intrinsic viscosity, and if the masses of each bead are properly stored in the rmc file, SUPCW will just use them. Beads to be included in the computation: this is a feature introduced for models generated directly from atomic coordinates of pdb structures, such as those produced by SOMO. It turns out that in such a case the beads representing aminoacids placed in the core of the protein are not contributing very much to the hydrodynamic properties (because they are not on the surface), and so they can be left out of the computations, which allows for a superior speed and also permits bigger structures to be analyzed. However, those beads are still needed for the computation of the radius of gyration and MAY be required for the the volume correction. Therefore, SOMO color-codes "6" such beads and SUPCW, if prompted, will NOT use them for the hydrodynamic computation part. Our recent work suggest that those beads in SOMO-derived models should NOT be included in the volume correction for neither the rotational diffusion coefficient nor the intrinsic viscosity, so "0" should be entered when the four options are presented. For low-resolution bead models, choose all beads.
Next, the model(s) filename will be asked, and the total number of beads in the chosen file will be displayed. At this point, you can choose to analyze the whole model, or a part of it, by entering the starting and the ending bead. For multiple, non-sequential files, this question is asked for each file. A note on the BEAMS file format: each model is made of two files, one containing an "header" and the X,Y,Z coordinates, the other containing the radius, mass and color of each bead (rmc file). The header (first line) of the first file contains two to four fields, which are: 1-number of the beads in the model 2-a "flag", whose value can be a positive number, or 0, -1, -2, -3. If the value is a positive number, then all the beads have the same radius (that number!), no more fields are present in the file, and the second file doesn't exist. If the value is 0, then there is another field which contains the filename of the second file (the rmc file). If the value is -1, then in the rmc file a fourth column is present, which contains another set of values for the radii (this is done in the case one wants to have beads containing the water of hydration and also keep track of their unhydrated volumes). If the flag is -2, then after the filename field there is another number, which is the partial specific volume of the model, used by BEAMS to compute the sedimentation coefficient of the model. Finally, if the flag is -3, then both options (unhydrated radii and psv) are active. Anyway, for MOST pourposes, only the 0 value of this flag will be used. 3-rmc filename (if the flag is <= 0) 4-psv value (if the flag is = -2 or -3)
At this point, the program starts. First, the model is automatically "normalized", that is, a principal axix transformation (PAT) is applied in order to align the longest dimension to the X -axis, the second one to the Y-axis, and the shortest to the Z-axis. SUPCW does this by calling the executable "pat". This is needed for proper evaluation of the rotational diffusion matrix. All the parameters are then displayed on screen, and at the end you have three choices: To exit To view the diffusion matrices To store the bead model (if you want to have the "normalized" version, or if only part of the model has been analyzed, and you want to save it). For further informations or questions, e-mail mattia.rocco@istge.it