Hi All, I agree that this could be a problem, and it seems to be exactly similar to having inaccurate cell constants in crystallography. On both of these issues, I have wondered why not add these parameters to refinement as simple scale factors, even as an independent refinement step, since it's only three parameters? I have heard that it doesn't matter too much bottom line, but I would think it might matter in certain circumstances. The scale factors xyz would just be optimized to make the center of the observed bond length distribution equivalent to the dictionary one. Would be really easy to implement, I would think. JPK +++++++++++++++++++++++++++++++++++++++++++++++++ Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 +++++++++++++++++++++++++++++++++++++++++++++++++ The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Reza Khayat Sent: Sunday, July 8, 2018 4:38 PM To: Pavel Afonine ; anaa2 Cc: [email protected] Subject: Re: [phenixbb] Detrmining pixel size Hi, A 1.38Å vs 1.40Å pixel size will make a tremendous difference for complexes like viruses. Imagine an image reconstruction of a virus that is 200 pixels in diameter -pixels are an EM's readout, not distances. At 1.38Å/pixel this is a diameter of 276Å, but at 1.40Å/pixel this is a diameter of 280Å. A 2Å expansion is certainly biologically important. So an incorrect pixel size of 0.02Å will give the perception that a biologically important phenomenon has occurred. Thus, despite acceptable refinement statistics one can make incorrect conclusions based on incorrect pixel size. I'm dealing with this problem when comparing my image reconstructions from different scope to crystal structures. This problem is amplified as the virus size increases. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________________ From: [email protected] on behalf of Pavel Afonine Sent: Sunday, July 8, 2018 3:59 PM To: anaa2; PHENIX user mailing list Subject: Re: [phenixbb] Detrmining pixel size Hi Noor,

Does anyone know how to accurately determine the voxel size of an EM map? If you are slightly off (i.e. 1.38 compared to 1.40 pixel) does this affect real space refinement in PHENIX?

if it's not too much off then I would not expect much difference in results except map-model correlation (CC) may be worse.. This is because phenix.real_space_refine works such that no matter what fit to the map is the model geometry must stay within acceptable limits. Pavel _______________________________________________ phenixbb mailing list [email protected] https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=DwICAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=sdGNH7yvifjhJ3j93rli_lGL9crUWlSGxb2ybKnFUA8&s=7TPIP3GItfApCLU1NzT-1COlEvamhOa7QSfdnPl_ym4&e= Unsubscribe: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]