Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

2011-03-23 Thread Franz Gruswitz
Though I like our program HOLLOW for visualization, I think the tool for this job is MOLE (http://mole.chemi.muni.cz). You can use the online version to quickly generate two trajectories out from the center of the channel. MOLE has some mathematical advantages over HOLE or Caver. You then merge

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

2011-03-23 Thread Regina Kettering
Bert; I have found the online gui 3V to be very useful in calculating channel dimensions. It outputs the volume and surface area of the pore, along with a surface representation that can be visualized in Chimera or PyMOL. You can either specify a specific pore or search for pores within a giv

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

2011-03-23 Thread Parthasarathy Sampathkumar
Dear Bert, You could try the program Hole from http://www.ncbi.nlm.nih.gov/pubmed/9195488 J Mol Graph. 1996 Dec;14(6):354-60, 376. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Smart OS

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

2011-03-23 Thread Jürgen Bosch
Try the program Hollow. Or visit USF and find the cavity script. There's also Carver out there but I never got it really to work for my purposes, but it's been written for channels. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochem

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

2011-03-23 Thread Matthew Franklin
On 3/23/11 9:02 AM, Van Den Berg, Bert wrote: Hello all, Does anyone know how to get values for pore sizes of membrane channels? I'm not interested in A x B angstrom values measured between atom centers and assuming a regular pore shape, but a "real-life" value of either surface area at the n