HYDROMIC

Version 7c, February 2006

J. García de la Torre, J.M. Valpuesta and J.L. Carrascosa, "HYDROMIC: Prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron-microscopy images" Eur. Biophys. J., 30, 457-462 (2001).

HYDROMIC is a computer program for the calculation of solution properties of macromolecular or supramolecular structures determined by cryo-electron microscopy or related techniques. The structure is taken from a structural file which can be in several formats: spider , MRC, formatted, etc. HYDROMIC reads the structural file, builds from it an appropriate hydrodynamic model, and proceeds with the calculation of properties, including hydrodynamic coefficients, scattering-related quantities, etc.

For more details, see the HYDROMIC User Guide

Files for download:

FILE TYPE DESCRIPTION
hydromic.pdf PDF Paper on HYDROMIC
hydromic7c.pdf PDF User Guide
hydromic7cmsd.exe Executable MS DOS/Windows
hydromic.dat ASCII Sample of main input file
apo_cct.spi Binary Spider file (Silicon Graphics format)
apo_cct-lnx.spi Binary Spider file (DEC/Linux format)
apo_cct.mrc Binary MRC file
apo_cct-37-spi.res ASCII Results for the 1st case in run
apo_cct-37-mrc.res ASCII Results for the 2nd case in run
apo_cct-37-spi-she.bea ASCII (PDB) Visualization of shell model (RasMol)

Linux users: SORRY! The linux executable is not available as yet; I had the n-th problem reading binary files! But the problem has been identified and can be solved. The Linux version will be ready very soon: Just keep watching!

The spider file (Silicon Graphics) apo_cct.spi was translated into apo_cct.mrc (MRC format), and this in turn transformed into another spider file (Linux) apo_cct-lnx.spi, using em2em for these format transformations

The sample execution contains two cases, for the same protein, but the first with fixed NSIG, SIGMAMAX, SIGMAMIN, and the second one with "automatic sigmas", NSIG=-1, see Users' Guide. As the sigmas used in the two cases do not coincide, the results are slighlty different due to the uncertainties introduced by the shell-model extrapolation in the final results. different due to the uncertainties Note that the sample input file contains two cases

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