The other possibility of course is that the data is good, that this is an accurate experimental result and there really is a void, or at least a cavity where the mean bulk density is lower than in bulk water. One way to test the void theory would be to fill the cavity with O atoms of zero (or very small, say 0.01) occupancy. Hopefully (!) that will prevent Refmac filling the cavity with bulk solvent. One could then try giving these O atoms large B factors, say 200, to smear them out, and then increase the occupancies to titrate the actual bulk density.
There was a paper by Brian Mathews group (sorry I don't have the reference) on a high pressure form of lysozyme where they found a large hydrophobic void (I think sufficient to contain something like 5 waters). Bulk water could only be compelled to enter the void by application of very high external pressure. Interesting! Cheers -- Ian > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Dirk Kostrewa > Sent: 02 June 2009 10:13 > To: CCP4BB > Subject: Re: [ccp4bb] solvent mask with refmac > > Dear Ana-Maria, > > in my experience, mask bulk solvent artifacts can only occur at narrow > channels, where the mask radius is too big to define the channel as > belonging to the bulk solvent region, leaving it "empty" and thus > resulting in positive (!) difference density. Changing from simple scaling > to Babinet scaling is an important check to exclude mask bulk solvent > artifacts, but there, you have to uncheck the "calculate contribution from > the solvent region", because this is done by the Babinet scaling, already. > However, in your case, you have negative difference density in a, as you > say, big cavity. This will be certainly filled with bulk solvent density. > One possible reason for a negative difference density are underestimated > magnitudes of |Fobs| at very low resolution, either because they are > weakened by the beam-stop (half-)shadow, or because they are overloads > that have been poorly extrapolated. A simple check for wrongly determined > low-resolution |Fobs| is to cut your low resolution data during refinement > at a somewhat higher resolution, say 20 A instead of 80 A, and see whether > the negative difference density disappears. If, yes, you should check your > data processing again. > > Best regards, > > Dirk. > > Am 02.06.2009 um 10:43 schrieb Ana-Maria Goncalves: > > > Dear BB, > > I'm refining a structure which presents a big hydrophobic cavity > where a strong residual difference negative density can be seen. I presume > that this is an effect of not having a proper solvent mask determined and > I was wondering if there is a way to provide a better mask description to > REFMAC. The resolution of the data is 1.6 A and I have already tried > changing from simple to Babinet scaling, without any improvement. Any > advice/suggestion would be very welcome. > > Many thanks, > Ana-Maria > > > > -- > Ana-Maria Goncalves > Macromolecular Crystallography Group > European Synchrotron Radiation Facility > B.P. 220, 6 rue Jules Horowitz > F-38043 GRENOBLE CEDEX > FRANCE > > Tel: +33 (0) 4.76.88.19.12 > Fax: +33 (0) 4.76.88.29.04 > > > > > ******************************************************* > Dirk Kostrewa > Gene Center, A 5.07 > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: [email protected] > ******************************************************* > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [email protected] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
