Hi, I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity. Thanks, best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, There's no "fill cavities" tool. I was trying to think of some clever way to do it with a mask, but even if you had the void space filled and vice versa, it doesn't seem to simplify checking size selectivity. As far as I know, you would still need to place a couple of markers across from each other where there seems to be a constriction and measure the distance between them. That would be tedious and highly dependent on your skills at placing markers. Maybe other people have ideas, or suggestions of other programs that might be useful. As you probably know, most of the channel analysis tools work on atomic structures (.... Hole, MoleOnline, Caver, 3V, MolAxis...). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 16, 2021, at 1:10 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity. Thanks, best, Dieter
participants (2)
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Dieter Blaas -
Elaine Meng