Hi Eze - I’m glad to see you solved your problem.
On Jun 2, 2014, at 9:07 PM, Eze Chivi <ezech...@outlook.com.ar<mailto:ezech...@outlook.com.ar>> wrote: Thanks to everyone for the useful information. I refined my structure in the reduced form (using the method suggested by Pavel). Negative density disappeared, and also R/Rfree improved a little bit. I attach two example pictures. In parallel, I mutated Cys residues to Ala and re-refined again adding the simulated annealing option in phenix (Is this the way to make an omit map?). In the future, instead of mutating to Ala, you could try using the delete-residue-sidechain function, which prunes the side chain of the active residue back to CB. The function is bound to capital letter K (as “Kill Sidechain”) in Paul’s key bindings: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Pauls-key-bindings-for-coot. That way, the sequence will remain correct, and until you add the atoms back into your model, you will be able to remind yourself about them via Extensions > Modeling > Residues with Missing Atoms. Cheers, Jared Positive density appeared in the place of S atoms (another picture attached, the oxidized model is shown). It appears that radiation damage caused full reduction... Thank you again! Regards Ezequiel PS: This protein was crystalized before by my group (and other group) in oxidized form (several times), it is a single point mutant. Data were collected at SLS using a Pilatus Detector. <reduced1.jpg><reduced2.jpg><omit.jpg> -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ ------------------------------------------------------------ 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. =================================
