Waight, Andrew schrieb:
Hello everyone I have a question for the experts.I am in the final stages of refining my model placing waters and whatnot. However when I refine my model against the pure scalepack output, I see some rather signifigant negative difference density peaks (3sigma) in a marginally important region of the protein. The strange thing is that there is no model built into this region. How can there be negative difference density when there is no model built there? It is obviously not a weighting problem because the structure factors are directly from the raw reflection list. Has anyone else ecperienced this phenomenon and what if any actions would you suggest. I have attached also a screenshot. Thanks for your advice everyone I have learned so much from reading this BB everyday.Drew ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
negative density may be due to missing bulk solvent. See http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#Bulk_solvent_correction_produces_difference_density for other explanations, and some remedies. HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".
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