Hi Dan, For cavity-type analysis you may want to use castP (web interface): http://cast.engr.uic.edu/cast/ or the far more advanced volbl algorithm that is behind castP (linux/unix): http://biogeometry.duke.edu/software/alphashapes/ See additional relevant links in a course I once gave: http://bioportal.weizmann.ac.il/course/3dbioinfo/links.html Cheers, ilan -- Ilan Samish, Ph.D. Dept of Biochemistry & Biophysics School of Medicine & Dept of Chemistry 231 South 34th Street University of Pennsylvania Philadelphia, PA 19104-6323 Office: Chemistry, 261 Cret Wing Tel (Saven Lab): (215) 898 2025 Tel (DeGrado Lab):(215) 898 2322 Mobile: (267) 334 5917 Fax: (215) 573 6416 E-mail: samish at sas.upenn.edu > > -----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 > > > _______________________________________________ > Molvis-list mailing list > Molvis-list at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/molvis-list > > >