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Dear Almuda,
I am afraid you misunderstood what I and others tried to tell you, so I will try to clarify it somewhat more:
-There is no need to generate a new map if you already have a nice one.
-A map is not generated at a certain sigma level, it is a collection of numbers specifying the value of the electron density at certain positions
in the unit cell.
-For contouring you need to specify a certain level, at which level the graphic program will draw its net.
-This level is often specified as sigma, and here is where the difficulty gets in: Coot and Pymol will determine themselves what the sigma level
of the map is, but apparently, they do it differently, so the same map, contoured at say 1.5 sigma, will look differently in Pymol and in Coot. It would be good if somebody (the developers?) could look into this.
What I do is to generate in Pymol a number of levels and select the one which gives the (in my eyes) best picture.
If you wish, I could send you the commands.
Best,
Herman
Von: Almudena Ponce Salvatierra [mailto:[log in to unmask]]
Gesendet: Mittwoch, 22. Juli 2015 13:05
An: Schreuder, Herman R&D/DE
Cc: [log in to unmask]
Betreff: Re: [ccp4bb] AW: [ccp4bb] off-topic: pymol map
Hi,
thanks everyone for replying. However the question was a bit different ...
- I already had my nice map, and I saved it in a pymol session.
- I don't remember the sigma level at which I generated it
- I wanted to know if I could figure this out without generating a new one and comparing by eye.
Anyway I think that the less time consuming option is just to generate a new map.
All the best,
Almudena.
2015-07-21 11:46 GMT+02:00 <[log in to unmask]>:
This is interesting! I noticed that for omit maps (the only maps for which I make pictures) I had to use much lower contour levels as in the past. I thought it was due to the maximum likelihood programs, but now
it seems that the contouring in Pymol is to blame.
Best,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Emilia C. Arturo (Emily)
Gesendet: Montag, 20. Juli 2015 21:30
An: [log in to unmask]
Betreff: Re: [ccp4bb] off-topic: pymol map
This is a hot topic, and the answer is not straightforward. It was recently discussed on this BB (and on the PyMOL users list); see:
[log in to unmask]" target="_blank">https:[log in to unmask]
Hope this helps,
Emily.
On Mon, Jul 20, 2015 at 9:57 AM, Jurgen Bosch <[log in to unmask]> wrote:
> Dear Almudena,
>
> isomesh map, mymap.map, 2.0, site, carve=1.6
>
> the 2.0 sets the sigma level of your map.
> See also here:
>
http://www.pymolwiki.org/index.php/Display_CCP4_Maps
>
> Jürgen
> ......................
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology Johns Hopkins Malaria
> Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-2926
> http://lupo.jhsph.edu
>
> On Jul 20, 2015, at 9:48 AM, Almudena Ponce Salvatierra
> <[log in to unmask]> wrote:
>
> Dear all,
>
> I have a pymol session in which I generated a map (isomesh... ) over
> my structure. Does any of you know how to display of find out at which
> sigma cutoff was it generated?
>
> Thanks a lot in advance.
>
> Best wishes,
>
> Almudena
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry Max Planck
> Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen
> Germany
>
>
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany