Hi all,
I just submitted a PDB deposition where two of the deposition authors did
not have an ORCID and it went through fine. As long as the corresponding
author (ie the person submitting the PDB) and the PI has the ID I think it
will work.
Regards
Christine
On Tue, Apr 9, 2019 at 8:34 AM
Dear Sam,
As already pointed out by other CCP4bbers, I think trying to merge
non-overlapping resolution shells cannot lead to good data. In addition it is
very straight forward and fast to remove ice-rings during data processing with
either XDS or imosflm, as also already pointed out. And your
There are 3 lists of authors associated with a PDB deposition.
1. PDB entry authors - listed in audit_author in the public mmCIF / author
record in the legacy PDB format
2. citation authors - listed in citation_author in the public mmCIF / JRNL
record in the legacy PDB format
3. Contact
Dear CCP4bb,
We are seeking someone with a structural or biophysics background to join
our group. No industry experience necessary but ability to consume large
amounts of contemporary protein engineering literature is a must. Please
see the link below and sorry for the spam.
There is an option in xds to exclude typical ice ring regions. It was
usually in the XDS.INP but commented out by default. That should work as it
should work with the ice ring button in mosflm.
Cheers
Christian
On Tue, Apr 9, 2019 at 11:07 AM Harry Powell <
Hi SamDid you use the ice-ring exclusion option in iMosflm (a button that has an image like a snowflake)? It should exclude data in _narrow_ resolution rings (substantially less than 0.2Å!) around the ice rings, and can be set for any combination of indexing, refinement and integration. There
Dear all,
How can i build an oxidized HemeB molecule in my COOT structure? do you
have anybody a library from HemeB for me?
best regards...
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Dear all,
Did anyone observe that oneDep from EBI made ORCID mandatory for
deposition? What am I supposed to do if my collaborators do not want
to create ORCID? (especially with GDPR I do not want to create ORCID)
Just posting here so that some one will respond? my mails are going to
/dev/null?
I am wondering, are there any arguments that would suggest that ORCID is not in
line with GDPR requirements? You are disclosing your name etc to the PDB
anyway, does it matter if its through ORCID or not?
Tassos
> On Apr 9, 2019, at 14:04, V F wrote:
>
> Dear all,
> Did anyone observe that
Perhaps the poster is referring to the legality of creating an ORCID on behalf
of the collaborator?
That is how I interpreted it - but perhaps I over-interpreted...
Another thing that came to my mind, not everyone has to be an author of the PDB
structure. Often all the authors of the
Than it is easy enough. You mustn't create an ORCid for others, this could
indeed get you into GDPR trouble as you are sharing personal data without
consent.
So that leaves the practical bit. If deposition requires an ORCid and a
collaborator does not have an ORCid despite your requests, then
Hi,
While using mar2mtz command in linux ubuntu, we are getting the following
error.
mar2mtz: error while loading shared libraries: libccp4f.so.0: cannot open
shared object file: no such file or directory
Can anyone suggest how to proceed further.
Thanks
Raj
Hi,
While using mar2mtz command in linux ubuntu, we are getting the following
error.
mar2mtz: error while loading shared libraries: libccp4f.so.0: cannot open
shared object file: no such file or directory
Can anyone suggest how to proceed further.
Thanks
Hello again.
I agree the get-around strategy we took is not a good practice at all.
For our initial imosflm run we actually turned on 'exclude ice ring'
button. The following was reported in the log:
ICE RING SUMMARY:
reso ice_ring mean_I mean_Sigma Estimated_I Ratio Zscore Completeness
to be honest, I would want to be an author on the paper (especially in a
"glossy" :-)), but perhaps not on all the database entries...only the ones I
actively contributed to.
I agree being on the paper involves accepting responsibility for all the work,
and often it is impossible to really be
Very good point, and a good argument against the current trend of publications
in the glossies including everything from mice to omics to structure all in one
manuscript with one set of authors. Especially since it is being pointed out
more vociferously these days (as it should be) that
There is something to be said for not everyone being an author of the PDB entry
anyway.
If I were a non structural biologist who for example had made and tested some
essential knock-out mice for the paper, I might prefer not to be an author of
the PDB entry in case there was something wrong
On 09/04/2019, Mark J van Raaij wrote:
> Perhaps the poster is referring to the legality of creating an ORCID on
> behalf of the collaborator?
Yes that is what I meant. (English not my first language)!
> That is how I interpreted it - but perhaps I over-interpreted...
>
> Another thing that
I agree with Harry that an ice ring should never require you to process the
data in two separate runs, and hopefully this does not become a standard
approach..
How did you present those data to aimless so it could scale the two
datasets that have no overlap at all?
Johan
On Tue, 9 Apr
All these monomers listed in the monomer library are HEM look-alikes. Maybe
one of them is useful to you
Eleanor
HAS.cif: HAS NA FEsingle 2.0900.020
HAS.cif: HAS NB FEsingle 2.0900.020
HAS.cif: HAS NC FEsingle 2.090
(in case everyone assumes someone else already answered offline, which they
probably have)
In coot go to the region where you want to put the heme and do:
File:get monomer and type HEM in the box that pops up.
This gives plain old heme b (ferroprotoporphrin 9) like in Hb or cyt b
For heme C
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