I guess you could expand your structure using SYMEXP and measure across the solvent channels in PyMOL using the Measure tool?
Nevertheless, I don't think this sort of exercise is very useful. Crystal soaking is a highly empirical procedure, which in most cases is based on pure trial-and-error. Let's say you find that the channels are 2 Å too small for your molecule to pass. Would you then not do the soak experiment? I think protein crystals are much more dynamic and flexible than we tend to think. Many crystallographers have experienced crystals cracking during a soak experiment and still have been able to collect useful data. I guess this means that the molecules can flex quite a bit and still regain crystal contacts... We once managed to soak an entire protein (IF1) into crystals of the small ribosomal subunit. Amazingly, it worked. If we had thought too much about this experiment beforehand, we probably wouldn't have done it... So, my advice: Stop thinking and just do the experiment. Ditlev --- Ditlev E. Brodersen Lektor, Associate Professor Department of Molecular Biology and Genetics, Aarhus University Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark Phone: +45 21669001 Lab home page: www.bioxray.au.dk/~deb<http://www.bioxray.au.dk/~deb> Educational IT portal: curriculearn.dk On 30 Sep 2018, at 20.58, Murpholino Peligro <[email protected]<mailto:[email protected]>> wrote: Dear all. I wonder If any of you know how to calculate the radius along a distance for a bulk solvent channel in a protein crystal. I can see there is a plethora of programs* to find channels, pores, clefts and all the related holes within a protein, but how can I take a look at this for the solvent? Any tips or suggestions are welcome. Ps Let's say I want to know if molecule A can diffuse into the protein crystal. Thanks *caver, hole, mole, molaxis, porewalker, hollow just no name a few ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
