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Thanks. I will follow your suggestions. The program does look a lot like what I need. I feel like this should be on the ccp4 suite...right? :) El dom., 30 de sep. de 2018 a la(s) 17:03, Mitchell D. Miller ( [log in to unmask]) escribió: > As Ditlev points out, measuring the channels ignores the flexibility / > dynamic nature of proteins in crystals. Also, if you have any disordered > tag residues or loops, they also occupy space in the solvent channels. That > said, I have found the Doug Juers' lab's program map_channels very useful > for characterizing the dimensions of the solvent channels in a crystal. See > http://people.whitman.edu/~juersdh/Channel_Mapping.shtml > > D. H. Juers and J. Ruffin. MAP_CHANNELS: a computation tool to aid in > the visualization and characterization of solvent channels in > macromolecular crystals. J. Appl. Crystallogr. (2014). 47, 2105-2108. > https://dx.doi.org/10.1107/S160057671402281X > > https://www.researchgate.net/publication/269041287_MAP-CHANNELS_A_computation_tool_to_aid_in_the_visualization_and_characterization_of_solvent_channels_in_macromolecular_crystals > > Regards, > Mitch > > > > Quoting Ditlev Egeskov Brodersen <[log in to unmask]>: > > > 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 > > <[log in to unmask]<mailto:[log in to unmask]>> 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 > > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1