Hello Dan, Yes there is an application free of charge found at http://www.yasara.org/index.html that will do what you would like and much more, e.g. superpose (recently somebody asked about this as well), align, etc. This is an excellent application full of good features developed by U. Graz -Austria- and Radbound Nijmegen -Netherlands-. In addition, up to date I have not seen another application with prettier rendering than this one. Only thing to do is to register and ask for the application. For example I took 1c8d (must download the file to local disc because I have not seen a direct link import function to RCSB as in spdbv) and although I do not know from where you look at the cavity, I measure the distance where it looked narrowest between N-Asp240 and N-Thr476 with "Analyze Geometry" and obtained 168,91 nm, N-Gly242 and N-Asp 475 = 164,06 nm and N-Gly242 and N-Asp477 = 193,66 nm; it took less than 10 minutes. Worth trying it! Hope this helps, Ricardo A. Correa C. Molecular Biology Amateur Trans-Laboratory Chemical Analysis Service Provider Rue François Stroobant 41 1050 Brussels - Belgium e-mail : trans.lab at skynet.be TEL./FAX : 32 (0)2 345 97 41 GSM : 32 (0)477 42 88 94 -----Original Message----- From: molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org [mailto:molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org] On Behalf Of Dan Bolser Sent: 20 April 2006 13:58 To: molvis-list at bioinformatics.org Subject: [Molvis-list] Measuring viruses (and other viral-like things)? Hi, I am trying to get some rough estimates for the overall diameter and cavity size of the following 5 structures... 1c8d (diameter = ~200A from the literature) 1stm 1hqk 1jh5 (diameter = ~ 200A from the literature) 1c8n (diameter = ~ 280A from the literature) Specifically 1stm and 1hqk, for which I can't find an estimate in the literature (admittedly only after a quick look). I decided to tried using Rasmol, starting with 1c8d. I quickly found that I couldn't get the structures from the PQS, which showed the correct structure (60-mer) but the link to the file was broken. Conversely, the pdb-beta site appeared not to know about the correct biological assembly (showing only the ASU), but gave me the correct (60 subunit file) anyway. Using the 'pick distance' feature in Rasmol proved to be a bit buggy, sometimes returning a 'nan' distance at the terminal (apparently labeled correctly on the structure) but worse, sometimes returning a distance that seemed far too small (giving values in the range of 30 to 60 A instead of 100 to 200 A by eye). Computationally what I would like to do is fit a sphere (or an ellipse, whichever is smaller) to the structure and minimize the size of the sphere to enclose something like 95-99% of the atoms. Is there any tool that I can use to do this? I am not even sure if this description makes sense, but I want to avoid just returning the maximum distance between any two atoms, which probably isn't a fair 'rough estimate' of the diameter of the above molecules. Does anyone happen to know (approximately) the external and internal diameter of these molecules? Or a (free) package that lets me find them? Thanks for any suggestions, Dan. _______________________________________________ Molvis-list mailing list Molvis-list at bioinformatics.org https://bioinformatics.org/mailman/listinfo/molvis-list