Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

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.

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

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

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

Hi Martin, I followed your instructions and everything works. Thank you for your illustration! On Mon, Mar 20, 2017 at 3:52 AM, Martin Montgomery wrote: > Hello, > > You need to tell pymol what to do with the map. > > Load your pdb file > Load the map > > create an

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

Hello, You need to tell pymol what to do with the map. Load your pdb file Load the map create an object with residues you wish to display the map around. You can use the create command to do this or you can click on all the residues that you want to use in the main window then go to the

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

I think CCP4MG does this very selectively? Eleanor Dodson On 17 March 2017 at 17:03, Xiao Lei wrote: > Dear All, > > Thanks for the information. > I tried the way suggested by pymol wiki, but pymol fail to display the > map. > This is what I did: Run Fft to generate

[ccp4bb] Positive densities map on selective residues on Coot or Pymol

Dear All, In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but I'd like to show the density on selective residues, not on the unselected part of structure, is there a way to do it? I am using WinCoot 0.81. In addition, could Pymol do it? Thanks ahead!