I the software used for that is PhotoBlot®
BR From: Phoebe A. Rice [mailto:pr...@uchicago.edu] Sent: Tuesday, March 21, 2017 17:19 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Positive densities map on selective residues on Coot or Pymol Thank you Bernard. I'd like to add that carving the density shown in a figure (especially without explicitly describing the carve radius used) is the moral equivalent of showing only 1mm of background above and below the band of interest in a western blot. Phoebe _____ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp [hofkristall...@gmail.com] Sent: Tuesday, March 21, 2017 3:29 AM To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol > and carve=2.0 means the mesh is created within 2.0 Å of the selected atoms. Adjust these values to suit. I would advise extreme care when employing such presentation features. They are useful for display purposes and only when their use is stated as such, but they also open a venue for cognitive biases. One might want to have a look at how creative use of these blob features until things suit can betray the true believer http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb070 9-795.pdf?dl=0 Best, BR The first principle is that you must not fool yourself and you are the easiest person to fool. Richard P. Feynman
