mobile phone…
John
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
Sent: 10 September 2018 20:42
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for
Cryo-EM structures.
Hi Kevin,
a)
If your goal is merely
UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] Electron density maps for
Cryo-EM structures.
Hi Marin
I was about to comment on that too but then I realised that Pavel
is referring to the map _contours_ (which is what most people
using a map visualisation program like Coot actua
ontour level as you like.
>>
>>
>>
>> Of course, if the authors did not deposit their EM-map, you cannot
>> download it, but the same is true for X-ray structure factors.
>>
>>
>>
>> Happy viewing!
>>
>>
>>
>> Herm
the authors did not deposit their EM-map, you cannot download
> it, but the same is true for X-ray structure factors.
>
>
>
> Happy viewing!
>
>
>
> Herman
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>
>
>
>
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <mailto:
structure factors.
>
>
>
> Happy viewing!
>
>
>
> Herman
>
>
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> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Ian Tickle
> *Gesendet:* Montag, 10. September 2018 12:58
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betref
Dear Kevin,
Are you referring to "generating a map" from the model (PDB
coordinates) generated from tracing the chain in the ab-initio EM map?
Best wishes,
Natesh
On Mon, 10 Sep 2018 at 09:58, Kevin Jin wrote:
> Dear All,
>
> Is there any sever available to create electron density
download it,
but the same is true for X-ray structure factors.
Happy viewing!
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian
Tickle
Gesendet: Montag, 10. September 2018 12:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps
] Electron density maps for Cryo-EM structures.
Hi Marin
I was about to comment on that too but then I realised that Pavel is referring
to the map _contours_ (which is what most people using a map visualisation
program like Coot actually see). So the contoured map does represent an
iso
Great, thanks!
On Sun, Sep 9, 2018 at 9:49 PM Pavel Afonine wrote:
> P.S.: all questions are welcome of course, no labeling. It's just some of
> them are so orthogonal to common sense that answers my be such as well.
> Best,
> Pavel
>
> On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote:
>
>>
P.S.: all questions are welcome of course, no labeling. It's just some of
them are so orthogonal to common sense that answers my be such as well.
Best,
Pavel
On Sun, Sep 9, 2018 at 9:38 PM Pavel Afonine wrote:
> Hi,
>
> Is there any sever available to create electron density maps for cryo-em
>>
Hi,
Is there any sever available to create electron density maps for cryo-em
> structures?
>
The questions are nonsensical. Here is why:
1) In cryo-EM maps are not electron density maps but surfaces representing
electric potential.
2) Creating such a map is essentially carrying on from cryo-EM
Dear All,
Is there any sever available to create electron density maps for cryo-em
structures? Or, we should create the maps from mmCIF. I am particularly
interested in those cryo-em structures with high resolution, like 2.6~2.8A.
Please give me an education.
Thanks,
Kevin
Dear Pascal,
2009/8/10 Pascal Egea pas...@msg.ucsf.edu:
Dear All,
I am currently carrying the refinement of a structure and comparing the
results obtained in Refmac, Phenix and CNS.
While Phenix and Refmac write maps and their corresponding coefficients in
mtz format allowing display of
If you want to display CNS maps in Coot and have them on the right
scale, then you need to do one of two things. Either:
1. Don't use the map file, use the reflection file containing the map
coefficients, or
2. Change the setting in CNS which controls the extent of the output
map. Instead
I use this to get the same maps:
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover
http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff
I used zsh but I think it should work with current versions of bash.
mac minista wrote:
Dear all,
I have noticed
On Wed, 2007-02-14 at 07:59 -0800, mac minista wrote:
Dear all,
I have noticed that going from refmac 5 (script) to generate fo-fc and
2fo-fc maps in O / Pymol once and Coot in the other, the outcome is
not exactly the same electron density maps-I mean some differences are
seen. I have
Hi Mac,
I have noticed that going from refmac 5 (script) to generate fo-fc and
2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not
exactly the same electron density maps-I mean some differences are seen.
I have used the following columns in Coot (latest version): FOFCWT,
I am guessing it is a difference in normalization, but I would love to hear a
definitive answer from someone.
Steve
-Original Message-
From: CCP4 bulletin board on behalf of mac minista
Sent: Wed 2/14/2007 10:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] electron density maps
Hi,
thank you for your suggestions, the difference I am
seeing in the maps is mainly with the Fo-Fc maps i.e.
what appears in coot does not always appear in
O/Pymol. Here are the scripts for FFT and MAPMASK:
FFT
#!/bin/sh
set -e
fft hklin model.mtz mapout fofc_f.map eof
title fofc map
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