To get a rough idea of the solvent channels, one could use coot. By displaying the symmetry molecules as Ca traces (an option hidden in the symmetry menu under "symmetry by molecule") one can set a large radius (100Å) and still rotate the display. A more accurate display can be obtained by generating a number of symmetry mates and reading them in pymol. Even in surface mode, pymol can handle quite a few complete protein molecules without getting excessively slow.
However, it is just as important (or even more important) to examine whether the putative binding site is free and not involved in crystal contacts and whether enough room is available to accommodate the ligand. To be absolutely sure, the gold standard is of course still cocrystallization and with 96-well plates and crystallization robots it is not prohibitively difficult. I agree with Jacob Keller, in my experience, soaking is usually much faster than 10 hrs. unless some conformational change in the protein is necessary to let the ligand in the binding site. Nevertheless, we routinely soak overnight (24 hrs.). It is convenient and there is less risk that the structures end up in the twilight database. Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Bernhard Rupp Gesendet: Freitag, 27. Juni 2014 15:00 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Solvent channels Just a remark: diffusion is a slow and random-walk process. Particularly large molecules in viscous media (PEG anybody?) move (diffuse) slowly in solution. To simply extrapolate from the fact that the ligand is smaller than the solvent channels to the odds of the presence of a ligand is a risky proposition. Positive omit difference density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. The little movie below shows how slowly even a small aromatic dye molecule soaks into a crystal. Total time 10 hrs. http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv The literally hundreds of empty ligand structures collected in Twilight attest to that fact. http://journals.iucr.org/d/issues/2013/02/00/issconts.html Best, BR Science is a way of trying not to fool yourself: The first principle is that you must not fool yourself - and you are the easiest person to fool. R. Feynman, 1974 -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Friday, June 27, 2014 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Solvent channels Hi, I'm not aware of a program with an option to display channels in crystals but if you use any of the currently available molecular display program and ask to display symmetry-related molecules + adjacent unit cells, it should give you a good enough idea of the spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. Independently of the calculation, I would try soaking first and consult the calculations later (in the spirit of Rossmann's American method: shoot first ask later). Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reza Khayat [rkha...@ccny.cuny.edu] Sent: Friday, June 27, 2014 2:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Solvent channels Hi, I'd like to do some soaking experiments with a relatively large molecule. Can someone suggest a program/method to display the solvent channels of a crystal? We have the crystal structure. I'd like to see if the channels are large enough to allow the molecule to travel to the hypothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org =
