Dear Bernhard,
I just went through this process to deposit staraniso-corrected data
into the PDB.
I wanted to concatenate into a single mmcif the original intensities (so
that people can work with unmodified data), the modified ones from SA
(so that people can reproduce the refinement), and the final maps I was
working on (so people don't rely on new maps to question the model built
but we all work on the same thing).
I couldn't make it happen with the tools in ccp4, so I emailed Gerard
Bricogne, and together with the autoPROC team they worked out a solution
to concatenate everything.
I suggest that you ask them directly for the solution, maybe they would
want to implement something more robust for the increasing users working
with Staraniso. I can provide the workaround I have off list if needed.
All the best
Vincent
Le 16/07/2019 à 01:13, Bernhard Rupp a écrit :
Hmm….this is all a mess.
If the objective is that the users can generate the EXACT map the
depositor saw, I agree, the output of the Refmac mtz file with the map
coefficients would be good.
Alas, no can do, because the Fs are not the same as in the input file,
if I am understanding this correctly – reportedly Refmac does
something (which is?) to them before it dumps them into the output mtz.
So I deposit the SA file xyz-staraniso-merged-aniso _free.mtz to get
closer to the data I used to input into refmac. Bad boy:
(a) no can do, PDB no eat SA_flag. Maybe because the FreeR_flag is
added as a second data set to the xyz-staraniso-merged-aniso.mtz. Ok,
fixable.
(b) no should do, because we actually want unmerged untruncated and
unalterted I(obs) – which I agree - and with the XDS_whatever.HKL as
close as I can get it.
Seems we need a file description that includes all the desired items,
and a little program the can harvest all that in a single cif file. As
I put the ASCII XDS*.HKL
file into StarAniso, there seems to be the perfect pre-processing site
for all our desires. This SuperStar.mtz file then would additionally
need only the map coefficients for the reflections
actually used by Refmac to generate the map. Might well be that such
does already exist as some sort of intermediate file. PDB_REPROCESS
could take the unmerged HKL, process, and F-convert if desired,
PDB_REDO could use these data then (or the I’s/F’s from
SuperStar.mtz). I am sure this does not cover every conceivable
combination, but it’s worth a discussion. Not that it could ever move
through glacial committees….
In any case, I provide a link to the images for
REDO_THE_DARN_JOB_YOURSELF.
Cheers, BR
PS: About the deposition read errors on mmcif files later.
*From:* Ian Tickle <[email protected]>
*Sent:* Monday, July 15, 2019 3:00 PM
*To:* [email protected]
*Cc:* [email protected]
*Subject:* Re: [ccp4bb] SA_flag vs PDB
Hi Bernhard
Oh dear, yes that's quite possible.
But in any case we recommend _not_ to deposit the output from STARANISO:
http://staraniso.globalphasing.org/deposition_about.html
Cheers
-- Ian
Cheers
-- Ian
On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp <[email protected]
<mailto:[email protected]>> wrote:
Hi Fellows –
wondering if there is a particular reason the PDB cannot process a
mtz file that in addition to FreeR_flag includes a SA_Flag column
from StarAniso?
Can there be no more than one I column type because that is
automatically interpreted as the free flag??
Best, BR
------------------------------------------------------
Bernhard Rupp
Crystallographiae Vindicis Militum Ordo
http://www.hofkristallamt.org/
[email protected] <mailto:[email protected]>
+1 925 209 7429
+43 676 571 0536
------------------------------------------------------
Many plausible ideas vanish
at the presence of thought
------------------------------------------------------
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
--
Vincent Chaptal, PhD
MMSB -UMR5086
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
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
