Dear Phenixers I've been helping a colleague with a dataset at ~3.8 Angstroms (phases and map from AutoSharp using SAD phasing). At the moment he has an incomplete polyALA model consisting of two chains related by NCS and a few extra sections. Refinement seems to proceed OK using phenix.refine version 1.4-3, but the resultant maps have blobs of negative density in the core of the protein. I am assuming that these are a side-effect of the bulk-solvent correction part of the refinement which is confusing the region where the protein sidechains would be as solvent. There are no corresponding negative peaks on the surface of protein, but some positive peaks where larger sidechains may be. Is this interpretation likely to be correct and if so, which parameter should be altered in the Bulk Solvent section of the input to allow for a bigger mask around the protein. I see that it isn't recommended to change the parameters, but the refinement.mask.solvent_radius=1.0 looks like an obvious candidate. If necessary, I can get an image made showing the maps. Thanks Andrew Purkiss-Trew This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.