Good evening,
since I've been contacted off line several times about this, I'm posting
here the protocol to combine maps with 2 mtz files of original and
truncated data.
I went through this procedure as I wanted to include the maps, and this
was the tricky part of the procedure in my hands. This way, everyone can
look at the same maps when critically assessing a structure (especially
in the context of redo-ing and severe anisotropy).
In a new directory, put all 3 mtz files (original Intentisties, merged
staraniso reflections, maps from buster)
/PATH_TO-DIR/BUSTER/Refine45/autoPROC/.
aP_deposition_prep -p combine -r maps.mtz -f staraniso_output.mtz -a
Original_Intensities.mtz >aP_deposition_prep.log
It creates combine_all.cif
This file has everything but it has a “refln” naming issue.
To fix the “refln” issue:
cat combine_all.cif | sed -e "s/refln.F_sigma /refln.F_meas_sigma /g" -e
"s%[ ]* #.*from dataset.*%%g" | awk
'/^#/{if(s){print;next};c++;a[c]=$0;next}/^data/{print;if(s)next;s=1;for(i=1;i<=c;i++){print
a[i]}next}{print}' > combine_all_refln_fixed.cif
DONE.
Best
Vincent
ps: again, the credit of this script goes to the globalphasing team who
kindly helped when I asked them for help with it.
Le 01/06/2020 à 11:47, Clemens Vonrhein a écrit :
Dear all,
On Sat, May 30, 2020 at 03:40:53PM +0100, Eleanor Dodson wrote:
My pennysworth. If you find your maps look better after the
anisotroy correction use it, but it may be helpful to those wo want to mine
your data if you deposit the whole sphere..
Agree (which is what e.g. we provide when using STARANISO via autoPROC
[1]).
And in the same vein: those depositing isotropically truncated data
should consider also providing data to a higher diffraction limit to
give a potentially more accurate picture (if there is even a slight
indication of anisotropy - which there often is).
I find it very helpful even looking at an idealised (and therefore
simplified) picture of anisotropy as in
http://staraniso.globalphasing.org/anisotropy_about.html
We can consider
(1) for refinement:
(1a) green+red, i.e. spherical (i.e. isotropically) truncated
data
(1b) green+blue, i.e. anisotropycally truncated data
(2) for deposition:
(2a) green+red => full sphere, but dropping real observations
(blue)
(2b) green+blue => all observations, but not providing
insignificant/weak data (red) in all directions
(2c) a sphere to the "tip" of blue (i.e. anisotropic diffraction
limit) => all observations and all insignificant/weak data
Cheers
Clemens
[1] https://www.globalphasing.com/autoproc/ - which gives a mmCIF file
with (2a), (2b) and (2c) ready for deposition.
eleanor
On Sat, 30 May 2020 at 09:36, Robbie Joosten <robbie_joos...@hotmail.com>
wrote:
Hi Everyone,
I've been looking at some recent PDB entries that have much lower
spherical) completeness than reported in the coordinate file. One reason
for this is that the data were anisotropicly truncated, another reason is
some mess-up with the deposition of the reflection data. There is a lot of
discussion about the former practice and I don't want to go in to that, but
the second one is obviously an error. Now how do I distinguish these cases?
Sometimes, you can look at the reported number of reflections and compare
that to the deposited reflection file and you will find that something has
clearly gone wrong. However, the reported number of reflections is not
entirely reliable because of other issues so I'd rather not use it. If you
use PDBpeep (e.g. for 6rjy) you can see something is wrong, but that is
completely visual. Is there a tool in CCP4 that reports both spherical and
ellipsoidal completeness (on merged reflection data)? That would make it
easy to distinguish such cases.
Cheers,
Robbie
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
available at https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
--
Vincent Chaptal, PhD
Director of GdR APPICOM
Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.appicom.cnrs.fr
http://mmsb.cnrs.fr/en/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
