Hi Emilia and Steven,
(re-posting after accidentally replying to the coot mailing list)
After off-list discussion with Steven, I updated:
http://pymolwiki.org/index.php/Normalize_ccp4_maps
If the goal is to match the display in Coot, this is what I would do:
# load map into PyMOL but don't norm
Thomas,
> I tried to figure out the PyMOL vs. Coot normalization discrepancy a while
> ago. As far as I remember, PyMOL normalizes on the raw data array, while
> Coot normalizes across the unit cell. So if the data doesn't exactly cover
> the cell, the results might be different.
>
I posted the
Hi James,
carving and normalization in PyMOL are really independent things. Normalization
happens during map loading (if normalize_ccp4_maps is on). Carving happens
during mesh generation (it's an argument of the isomesh command) and is really
just a way to limit mesh display to an area of inte
Tim is making a very good point (as usual!) The RMSD of the whole
asymmetric unit is only a rough guide to a useful map contour - that
depends on the relative B values of the feature you want to display. It is
pretty obvious that features with lower than average B factors show up at
higher Sig leve
I have never trusted Pymol's "normalization" of maps, because it has
never been clear to me if it does the normalization before or after the
"carve". If it is after, then you have a serious interpretation
problem: the "1 sigma" level will be MUCH lower than if the rest of the
map were not set
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You are correct about this. The magnitude of this effect depends
on the amount of solvent in your crystal (which tends to be flatter)
but it rarely reaches a factor of two.
This does point out a serious flaw with contouring a map relative
to i
Hi Emilia et al.,
I tried to figure out the PyMOL vs. Coot normalization discrepancy a while ago.
As far as I remember, PyMOL normalizes on the raw data array, while Coot
normalizes across the unit cell. So if the data doesn't exactly cover the cell,
the results might be different.
Cheers,
T
>
>
>
>One cannot understand what is going on without knowing how this map
> was calculated. Maps calculated by the Electron Density Server have
> density in units of electron/A^3 if I recall, or at least its best
> effort to do so.
This is what I was looking for! (i.e. what the units are) T
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One cannot understand what is going on without knowing how this map
was calculated. Maps calculated by the Electron Density Server have
density in units of electron/A^3 if I recall, or at least its best
effort to do so. There are many problems wi
some later point. You don’t need to
remember to do that yourself.
Cheers,
Robbie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Emilia C.
Arturo (Emily)
Sent: Friday, May 29, 2015 22:16
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PyMOL v. Coot map 'level'
Hello.
I am struggling with an old question--old because I've found several
discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (
http://sourceforge.net/p/pymol/mailman/message/26496806/ and
http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions
about how to
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