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Dear Jeff, 1. I used Steinkellner at al. (2009), BMC Bioinformatics 10, 32. http://www.ncbi.nlm.nih.gov/pubmed/19166624 a year ago and run into trouble. With the help of the authors it was solved. /It seems that the third party pre-compiled program "msms" has an issue on your machine. (Segmentation fault (core dumped)) Have you tried the VASCo.py -testrun ? If the same error occurs there a re-installation or an exchange of the msms program (located at the installation directory "/ppix_modules/cprogr/unix/msms/msms255i86Linux.5" to a newer version (from //http://mgltools.scripps.edu/downloads//) pre-compiled especially for your environment may solve the problem. (if you do not want to change the code itself in the VASCo.p file you also would have to rename the msms binary to the same name like in the directory "msms255i86Linux.5"). / 2. Another possibility is this (cut and pasted from the material and methods of the paper I am currently writing. /Protein structure properties analysis was done as described in Fusco et al. (Fusco, Barnum et al. 2014). Firstly, given a protein 3D structure, residues that have at least 2.5 A 2 of surface// //exposed to solvent are identified. This is done by using pymol. Once these residues are found sSCE and Pol are calculated using the values reported in Table 3 of Cieslik et al. (Cieslik and Derewenda// // //2009) (last column), and the sGRAVY (surface grand average of hydropathy) using the values reported in Table 2 Kyte et al. (Kyte and Doolittle 1982) (first column). For this you need a python script. /Many thanks to the authors of this publication. On 05/20/2016 12:11 PM, Fabio Dall'Antonia wrote: > Dear Jeff, > > you might be interested in the following publication regarding the > mapping of hydrophobicity scores onto protein surfaces - which is more > or less what you want, if I understood the question correctly > > Steinkellner at al. (2009), BMC Bioinformatics 10, 32. > http://www.ncbi.nlm.nih.gov/pubmed/19166624 > > The hydrophobicity aspect of this work is mainly based on > Ghose-Crippen parameters: > > Ghose & Crippen (1986). J. Comp. Chem. 7, 565. > > Best > Fabio > > >> CCP4, >> >> I am interested in calculating differences in hydrophobicity between two >> proteins as a function of surface area. Any suggestions? >> >> In short, I am hoping to find a way to calculate the % of a proteins >> surface area that is not charged (or within some sort of threshold >> assigned by an electrostatics program like APBS). Alternatively, are >> there any user friendly tools available that can calculate a proteins >> partition coefficient? >> >> Best, >> Jeff >> >> -- >> Dr. rer. nat. Fabio Dall'Antonia >> European Molecular Biology Laboratory c/o DESY >> Notkestraße 85, Bldg. 25a >> D-22607 Hamburg >> >> phone: +49 (0)40 89902-178 >> fax: +49 (0)40 89902-149 >> e-mail:[log in to unmask] > > > > -- > Dr. rer. nat. Fabio Dall'Antonia > European Molecular Biology Laboratory c/o DESY > Notkestraße 85, Bldg. 25a > D-22607 Hamburg > > phone: +49 (0)40 89902-178 > fax: +49 (0)40 89902-149 > e-mail:[log in to unmask]