; To: b...@hofkristallamt.org <mailto:b...@hofkristallamt.org>;
> CCP4BB@JISCMAIL.AC.UK <mailto: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 den
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
hoebe
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
Subject: Re: [ccp4bb] Positive densities map on selective residues on Coot or
Pymol
> and carve=2.0 means the
> 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
fo
Hi Paul,
Thanks for the instructions! Works in my case.
On Mon, Mar 20, 2017 at 6:05 AM, Paul Emsley
wrote:
> On 17/03/17 14:41, Xiao Lei wrote:
> >
> > 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
> > o
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 object with residues you wish
On 17/03/17 14:41, Xiao Lei wrote:
> 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?
Yes. Extensions -> Maps -> Mask Map by Atom Selection...
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 objec
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 simple mapin ccp4i, input mt
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 simple mapin ccp4i, input mtz map
from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM. Add the
file extension .map.ccp4 to the genera
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!
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