Re: [ccp4bb] ORCID being mandatory for PDB depositions

[John Berrisford]

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 authors directly involved with the PDB deposition - with whom we 
communicate during deposition. Information collected about these authors is not 
made public. This information is stored internally within the wwPDB. 

ORCiD's are only required for the 3rd set and this information is not made 
public. We do provide the option of providing ORCiDs for groups 1 and 2, but it 
is not mandatory.

For more details please see the wwPDB policy on authorship:
https://www.wwpdb.org/documentation/policy#toc_authorship

For our privacy information please see
https://www.wwpdb.org/about/privacy

Both of these pages are linked from the OneDep deposition system. 


I hope this helps

Regards

John
PDBe

-Original Message-
From: CCP4 bulletin board  On Behalf Of V F
Sent: 09 April 2019 14:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ORCID being mandatory for PDB depositions

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 came to my mind, not everyone has to be an author 
> of the PDB structure. Often all the authors of the corresponding paper 
> are also on the PDB entry, and there is nothing wrong with that, but 
> if a
> (non-crystallographer?) collaborator really doesn't want an ORCID, he 
> or she doesn't have to be an author of the PDB entry.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology 
> Communications http://journals.iucr.org/f/
>
>
>> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>>
>> 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 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?
>>>
>>> Many thanks,
>>> VF
>>>
>>> 
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> #
>> ###
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] entry level scientist position in antibody engineering

[Andrew Waight]

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.

https://systimmune.com/proteinengineering.html



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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Christine Gee]

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 Mark J van Raaij 
wrote:

> 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 fully responsible, because it
> would imply checking (i.e. redoing) much of it, but at least in the paper
> byline it should say who did what, giving some "safety" if something turns
> out wrong with the omics or the mice, but the structure(s) being fine.
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
> On 9 Apr 2019, at 17:22, Phoebe A. Rice  wrote:
>
> 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
> accepting authorship implies accepting responsibility.
>
>- Phoebe
>
>
> *From: *CCP4 bulletin board  on behalf of Mark J
> van Raaij 
> *Reply-To: *Mark J van Raaij 
> *Date: *Tuesday, April 9, 2019 at 9:32 AM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] ORCID being mandatory for PDB depositions
>
> 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 with it (which I
> might not necessarily be able to judge).
> Similarly, as a structural biologist I might prefer not to be on the
> knock-out mice database entry in case there was something wrong or
> unethical in the way the mice were made...
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
> On 9 Apr 2019, at 14:49, Robbie Joosten 
> wrote:
>
> 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 that
> collaborator cannot be a depositor. Let the record show that this is not
> your fault as your hands are tied here.
>
> HTH,
> Robbie
>
> On Apr 9, 2019 14:33, V F  wrote:
>
> 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 came to my mind, not everyone has to be an author of
> the
> > PDB structure. Often all the authors of the corresponding paper are also
> on
> > the PDB entry, and there is nothing wrong with that, but if a
> > (non-crystallographer?) collaborator really doesn't want an ORCID, he or
> she
> > doesn't have to be an author of the PDB entry.
> >
> >
> > Mark J van Raaij
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > calle Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://wwwuser.cnb.csic.es/~mjvanraaij
> > Section Editor of Acta Crystallographica F, Structural Biology
> > Communications
> > http://journals.iucr.org/f/
> >
> >
> >> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>
> >>
> >> 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 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?
> 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Philippe BENAS]

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 I_obs and 
Sig_I_obs will be much more accurate.

HTH,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/





En date de : Mar 9.4.19, Sam Tang  a écrit :

 Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Mardi 9 avril 2019, 13h27
 
 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
 Ave_Completeness 3.88   yes    39933.04   
 3690.30     1398.21   28.56  10.44        0.48 
     nan 3.67   yes    44809.76   
 4257.56      778.04   57.59  10.34        0.58 
     nan 3.43   yes     7270.25   
  885.61      532.75   13.65   7.61        0.54 
     nan 2.66   yes     2070.19   
  488.66      156.09   13.26   3.92        0.46 
     nan
 
 A total of >2200 reflections were
 already omited. 
 The
 range of poor R seems to correlate to the range 3.8-3.6A. I
 am thus also thinking there may be other issues (not visibly
 identified on images) other than ice rings.
 We actually first merged the two
 datasets (high and low resolutions) in pointless before
 presenting to aimless.
 We are trying over other different
 strategies to see if we can get a better tackle. Will report
 again soon.
 
 Sam
 
 On Tue, 9 Apr 2019
 at 18:47, Johan Turkenburg <2a539df422fe-dmarc-requ...@jiscmail.ac.uk>
 wrote:
 
 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 2019
 at 10:07, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
 Hi Sam
 Did 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 should not be any need to process the
 data twice, once for the low resolution data and once for
 the high.
 
 Harry
 --
 Dr Harry
 Powell
 
 
 
 To unsubscribe from the CCP4BB list, click
 the following link:
 
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 
 
 
 
 On 8 Apr 2019, at 19:50, Sam Tang
 wrote:
 Hello everyone
 Thanks a lot for your input and
 advices. To report on how we tackled the issue
 - 
 (1) We used
 imosflm to integrate the data.   (2) We
 eventually integrated the data in two resolution ranges, say
 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add
 that indeed from the log file for our initial round the
 program had already identified some ice ring
 regions.
 Aimless
 statistics looked fine and we were able to get a MR solution
 which was refined to much better Rf/Rw.
 This is definitely not a smart
 solution because we effectively 'throw away' useful
 data between 3.5A-3.3A, but for the purpose of MR and
 refinement, it seems we have solved (or simply bypassed?)
 the problem.
 Suggestions on XDS/DIALS are
 appreciated. We are actually using this dataset as a test
 set for XDS/DIALS to deal with ice rings. Will further
 report if we've got anything interesting.
 Thanks again!
 Sam
 
 
 
 On Thu, 4 Apr 2019
 at 20:54, Clemens Vonrhein 
 wrote:
 Dear all,
 
 
 
 And if you want to process with XDS: autoPROC [1] will try
 to detect
 
 and exclude ice-rings automatically - if present [2].
 
 
 
 If you know that you have ice-rings you can force it [3] to
 exclude
 
 all known ice-rings ranges - but this might not be the best
 solution
 
 if you have "just" diffuse ice-rings (where the
 special treatment of
 
 background within DIALS might be better). Something to test
 and
 
 compare maybe?
 
 
 
 Cheers
 
 
 
 Clemens
 
 
 
 [1] https://www.globalphasing.com/autoproc/
 
     https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
 
 [2] 
https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
 
     https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
 
 [3] 
https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically
 
 
 
 On Thu, Apr 04, 

Re: [ccp4bb] (EXTERNAL) [ccp4bb] Heme b

[Edward A. Berry]

(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 that would be HEC

On 04/09/2019 07:05 AM, Sanaz Asadollahpour wrote:

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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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Mark J van Raaij]

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 fully responsible, because it would 
imply checking (i.e. redoing) much of it, but at least in the paper byline it 
should say who did what, giving some "safety" if something turns out wrong with 
the omics or the mice, but the structure(s) being fine.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Section Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/


> On 9 Apr 2019, at 17:22, Phoebe A. Rice  wrote:
> 
> 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 
> accepting authorship implies accepting responsibility.
> Phoebe
>  
> From: CCP4 bulletin board  > on behalf of Mark J van Raaij 
> mailto:mjvanra...@cnb.csic.es>>
> Reply-To: Mark J van Raaij  >
> Date: Tuesday, April 9, 2019 at 9:32 AM
> To: "CCP4BB@JISCMAIL.AC.UK " 
> mailto:CCP4BB@JISCMAIL.AC.UK>>
> Subject: Re: [ccp4bb] ORCID being mandatory for PDB depositions
>  
> 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 with it (which I might not 
> necessarily be able to judge).
> Similarly, as a structural biologist I might prefer not to be on the 
> knock-out mice database entry in case there was something wrong or unethical 
> in the way the mice were made...
>  
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij 
> 
> Section Editor of Acta Crystallographica F, Structural Biology Communications
> http://journals.iucr.org/f/ 
>  
>> On 9 Apr 2019, at 14:49, Robbie Joosten > > wrote:
>>  
>> 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 that 
>> collaborator cannot be a depositor. Let the record show that this is not 
>> your fault as your hands are tied here.
>>  
>> HTH,
>> Robbie
>>  
>> On Apr 9, 2019 14:33, V F > > wrote:
>>> 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 came to my mind, not everyone has to be an author of 
>>> > the 
>>> > PDB structure. Often all the authors of the corresponding paper are also 
>>> > on 
>>> > the PDB entry, and there is nothing wrong with that, but if a 
>>> > (non-crystallographer?) collaborator really doesn't want an ORCID, he or 
>>> > she 
>>> > doesn't have to be an author of the PDB entry. 
>>> > 
>>> > 
>>> > Mark J van Raaij 
>>> > Dpto de Estructura de Macromoleculas 
>>> > Centro Nacional de Biotecnologia - CSIC 
>>> > calle Darwin 3 
>>> > E-28049 Madrid, Spain 
>>> > tel. (+34) 91 585 4616 
>>> > http://wwwuser.cnb.csic.es/~mjvanraaij 
>>> >  
>>> > Section Editor of Acta Crystallographica F, Structural Biology 
>>> > Communications 
>>> > http://journals.iucr.org/f/  
>>> > 
>>> > 
>>> >> On 9 Apr 2019, at 14:20, Anastassis Perrakis >> >> > wrote: 
>>> >> 
>>> >> 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 

Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Phoebe A. Rice]

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 accepting authorship 
implies accepting responsibility.

  *   Phoebe

From: CCP4 bulletin board  on behalf of Mark J van Raaij 

Reply-To: Mark J van Raaij 
Date: Tuesday, April 9, 2019 at 9:32 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] ORCID being mandatory for PDB depositions

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 with it (which I might not 
necessarily be able to judge).
Similarly, as a structural biologist I might prefer not to be on the knock-out 
mice database entry in case there was something wrong or unethical in the way 
the mice were made...

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Section Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/

On 9 Apr 2019, at 14:49, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:

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 that 
collaborator cannot be a depositor. Let the record show that this is not your 
fault as your hands are tied here.

HTH,
Robbie

On Apr 9, 2019 14:33, V F 
mailto:veronicapfiorent...@gmail.com>> wrote:
On 09/04/2019, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> 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 came to my mind, not everyone has to be an author of the
> PDB structure. Often all the authors of the corresponding paper are also on
> the PDB entry, and there is nothing wrong with that, but if a
> (non-crystallographer?) collaborator really doesn't want an ORCID, he or she
> doesn't have to be an author of the PDB entry.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
>> On 9 Apr 2019, at 14:20, Anastassis Perrakis 
>> mailto:a.perra...@nki.nl>> wrote:
>>
>> 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 
>>> mailto:veronicapfiorent...@gmail.com>> wrote:
>>>
>>> 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?
>>>
>>> Many thanks,
>>> VF
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Mark J van Raaij]

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 with it (which I might not 
necessarily be able to judge).
Similarly, as a structural biologist I might prefer not to be on the knock-out 
mice database entry in case there was something wrong or unethical in the way 
the mice were made...

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Section Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/


> On 9 Apr 2019, at 14:49, Robbie Joosten  wrote:
> 
> 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 that 
> collaborator cannot be a depositor. Let the record show that this is not your 
> fault as your hands are tied here.
> 
> HTH,
> Robbie
> 
> On Apr 9, 2019 14:33, V F  wrote:
> 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 came to my mind, not everyone has to be an author of the 
> > PDB structure. Often all the authors of the corresponding paper are also on 
> > the PDB entry, and there is nothing wrong with that, but if a 
> > (non-crystallographer?) collaborator really doesn't want an ORCID, he or 
> > she 
> > doesn't have to be an author of the PDB entry. 
> > 
> > 
> > Mark J van Raaij 
> > Dpto de Estructura de Macromoleculas 
> > Centro Nacional de Biotecnologia - CSIC 
> > calle Darwin 3 
> > E-28049 Madrid, Spain 
> > tel. (+34) 91 585 4616 
> > http://wwwuser.cnb.csic.es/~mjvanraaij 
> > Section Editor of Acta Crystallographica F, Structural Biology 
> > Communications 
> > http://journals.iucr.org/f/ 
> > 
> > 
> >> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote: 
> >> 
> >> 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 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? 
> >>> 
> >>> Many thanks, 
> >>> VF 
> >>> 
> >>>  
> >>> 
> >>> To unsubscribe from the CCP4BB list, click the following link: 
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> >> 
> >>  
> >> 
> >> To unsubscribe from the CCP4BB list, click the following link: 
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> > 
> > 
> >  
> > 
> > To unsubscribe from the CCP4BB list, click the following link: 
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> > 
> 
>  
> 
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> 
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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Robbie Joosten]

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 that 
collaborator cannot be a depositor. Let the record show that this is not your 
fault as your hands are tied here.

HTH,
Robbie

On Apr 9, 2019 14:33, V F  wrote:

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 came to my mind, not everyone has to be an author of the
> PDB structure. Often all the authors of the corresponding paper are also on
> the PDB entry, and there is nothing wrong with that, but if a
> (non-crystallographer?) collaborator really doesn't want an ORCID, he or she
> doesn't have to be an author of the PDB entry.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
>> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>>
>> 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 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?
>>>
>>> Many thanks,
>>> VF
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[V F]

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 came to my mind, not everyone has to be an author of the
> PDB structure. Often all the authors of the corresponding paper are also on
> the PDB entry, and there is nothing wrong with that, but if a
> (non-crystallographer?) collaborator really doesn't want an ORCID, he or she
> doesn't have to be an author of the PDB entry.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
>> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>>
>> 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 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?
>>>
>>> Many thanks,
>>> VF
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Mark J van Raaij]

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 corresponding paper are also on the PDB 
entry, and there is nothing wrong with that, but if a (non-crystallographer?) 
collaborator really doesn't want an ORCID, he or she doesn't have to be an 
author of the PDB entry.


Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Section Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/


> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
> 
> 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 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?
>> 
>> Many thanks,
>> VF
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Anastassis Perrakis]

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 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?
> 
> Many thanks,
> VF
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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[ccp4bb] ORCID being mandatory for PDB depositions

[V F]

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?

Many thanks,
VF



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Sam Tang]

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
Ave_Completeness
 3.88   yes39933.043690.30 1398.21   28.56  10.440.48
nan
 3.67   yes44809.764257.56  778.04   57.59  10.340.58
nan
 3.43   yes 7270.25 885.61  532.75   13.65   7.610.54
nan
 2.66   yes 2070.19 488.66  156.09   13.26   3.920.46
nan


A total of >2200 reflections were already omited.

The range of poor R seems to correlate to the range 3.8-3.6A. I am thus
also thinking there may be other issues (not visibly identified on images)
other than ice rings.

We actually first merged the two datasets (high and low resolutions) in
pointless before presenting to aimless.

We are trying over other different strategies to see if we can get a better
tackle. Will report again soon.

Sam


On Tue, 9 Apr 2019 at 18:47, Johan Turkenburg <
2a539df422fe-dmarc-requ...@jiscmail.ac.uk> wrote:

>
> 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 2019 at 10:07, Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi Sam
>>
>> Did 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 should
>> not be any need to process the data twice, once for the low resolution data
>> and once for the high.
>>
>> Harry
>> --
>> Dr Harry Powell
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>> On 8 Apr 2019, at 19:50, Sam Tang wrote:
>>
>> Hello everyone
>>
>> Thanks a lot for your input and advices. To report on how we tackled the
>> issue -
>>
>> (1) We used imosflm to integrate the data.
>> (2) We eventually integrated the data in two resolution ranges, say
>> 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add that indeed
>> from the log file for our initial round the program had already identified
>> some ice ring regions.
>>
>> Aimless statistics looked fine and we were able to get a MR solution
>> which was refined to much better Rf/Rw.
>>
>> This is definitely not a smart solution because we effectively 'throw
>> away' useful data between 3.5A-3.3A, but for the purpose of MR and
>> refinement, it seems we have solved (or simply bypassed?) the problem.
>>
>> Suggestions on XDS/DIALS are appreciated. We are actually using this
>> dataset as a test set for XDS/DIALS to deal with ice rings. Will further
>> report if we've got anything interesting.
>>
>> Thanks again!
>>
>> Sam
>>
>>
>>
>>
>> On Thu, 4 Apr 2019 at 20:54, Clemens Vonrhein 
>> wrote:
>>
>>> Dear all,
>>>
>>> And if you want to process with XDS: autoPROC [1] will try to detect
>>> and exclude ice-rings automatically - if present [2].
>>>
>>> If you know that you have ice-rings you can force it [3] to exclude
>>> all known ice-rings ranges - but this might not be the best solution
>>> if you have "just" diffuse ice-rings (where the special treatment of
>>> background within DIALS might be better). Something to test and
>>> compare maybe?
>>>
>>> Cheers
>>>
>>> Clemens
>>>
>>> [1] https://www.globalphasing.com/autoproc/
>>>
>>> https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
>>> [2]
>>> https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
>>>
>>> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
>>> [3]
>>> https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically
>>>
>>> On Thu, Apr 04, 2019 at 10:51:19AM +, melanie.voll...@diamond.ac.uk
>>> wrote:
>>> > Dear Sam,
>>> >
>>> >
>>> > to continue from James Parkhurst's email...
>>> >
>>> >
>>> > You can do more analysis regarding ice rings using Auspex (
>>> https://www.auspex.de/) if you already have some integrated file.
>>> >
>>> > Regarding re-integrating images, what did you use the first time
>>> round? I think if you use DIALS it got some clever implementation in it
>>> that is better in estimating the errors of reflections in proximity to ice
>>> rings. Hence you should get better Rfactors without having to remove the
>>> effected resolution range and the data it covers (
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>>> >
>>> >
>>> > 

[ccp4bb]

[Eleanor Dodson]

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  2.0900.020
HAS.cif: HAS  FE NDsingle  2.0900.020

HCO.cif: HCO  NA FEsingle  2.0900.020
HCO.cif: HCO  NB FEsingle  2.0900.020
HCO.cif: HCO  NC FEsingle  2.0900.020
HCO.cif: HCO  FE NDsingle  2.0900.020

HDD.cif: HDD  NA FEsingle  2.0900.020
HDD.cif: HDD  NB FEsingle  2.0900.020
HDD.cif: HDD  NC FEsingle  2.0900.020
HDD.cif: HDD  FE NDsingle  1.8550.020

HDM.cif: HDM  FE NAsingle  2.0900.020
HDM.cif: HDM  FE NBsingle  2.0900.020
HDM.cif: HDM  FE NCsingle  2.0900.020
HDM.cif: HDM  FE NDsingle  2.0900.020

HE6.cif: HE6  FE NAsingle  2.0900.020
HE6.cif: HE6  NB FEsingle  2.0900.020
HE6.cif: HE6  FE NCsingle  1.9450.020
HE6.cif: HE6  FE NDsingle  2.0900.020

HEA.cif: HEA  NA FEsingle  1.9450.020
HEA.cif: HEA  NB FEsingle  2.0900.020
HEA.cif: HEA  NC FEsingle  2.0900.020
HEA.cif: HEA  FE NDsingle  2.0900.020

HEB.cif: HEB  NA FEsingle  2.0900.020
HEB.cif: HEB  NB FEsingle  2.0900.020
HEB.cif: HEB  NC FEsingle  2.0900.020
HEB.cif: HEB  FE NDsingle  2.0900.020

HEC.cif: HEC  NA FEsingle  2.0900.020
HEC.cif: HEC  NB FEsingle  2.0900.020
HEC.cif: HEC  NC FEsingle  2.0900.020
HEC.cif: HEC  FE NDsingle  2.0900.020

HEM.cif: HEM  NA FEsingle  1.9770.020
HEM.cif: HEM  NB FEsingle  2.0930.020
HEM.cif: HEM  NC FEsingle  2.0880.020
HEM.cif: HEM  FE NDsingle  1.8450.020

HEO.cif: HEO  NA FEsingle  1.9450.020
HEO.cif: HEO  NB FEsingle  1.9450.020
HEO.cif: HEO  NC FEsingle  1.9450.020
HEO.cif: HEO  FE NDsingle  1.9450.020

HEV.cif: HEV  NA FEsingle  2.0900.020
HEV.cif: HEV  NB FEsingle  2.0900.020
HEV.cif: HEV  NC FEsingle  1.9450.020
HEV.cif: HEV  FE NDsingle  2.0900.020

HFM.cif: HFM  NA FEsingle  2.0900.020
HFM.cif: HFM  NB FEsingle  2.0900.020
HFM.cif: HFM  NC FEsingle  1.9450.020
HFM.cif: HFM  FE NDsingle  2.0900.020

HIF.cif: HIF  FE NAsingle  2.0900.020
HIF.cif: HIF  FE NBsingle  2.0900.020
HIF.cif: HIF  FE NCsingle  2.0900.020
HIF.cif: HIF  FE NDsingle  2.0900.020

HKL.cif: HKL  N1 FEsingle  2.0900.020
HKL.cif: HKL  N2 FEsingle  2.0900.020
HKL.cif: HKL  N3 FEsingle  2.0900.020
HKL.cif: HKL  FE N4single  1.8550.020

HME.cif: HME  FE NCsingle  2.0900.020
HME.cif: HME  FE NBsingle  2.0900.020
HME.cif: HME  FE NAsingle  2.0900.020
HME.cif: HME  FE NDsingle  2.0900.020


On Tue, 9 Apr 2019 at 12:07, Sanaz Asadollahpour <
sanaz.asadollahp...@ocbc.uni-freiburg.de> wrote:

> 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...
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] mar2mtz command

[raj kumar]

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



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[ccp4bb]

[Sanaz Asadollahpour]

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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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Johan Turkenburg]

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 2019 at 10:07, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Sam
>
> Did 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 should
> not be any need to process the data twice, once for the low resolution data
> and once for the high.
>
> Harry
> --
> Dr Harry Powell
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> On 8 Apr 2019, at 19:50, Sam Tang wrote:
>
> Hello everyone
>
> Thanks a lot for your input and advices. To report on how we tackled the
> issue -
>
> (1) We used imosflm to integrate the data.
> (2) We eventually integrated the data in two resolution ranges, say
> 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add that indeed
> from the log file for our initial round the program had already identified
> some ice ring regions.
>
> Aimless statistics looked fine and we were able to get a MR solution which
> was refined to much better Rf/Rw.
>
> This is definitely not a smart solution because we effectively 'throw
> away' useful data between 3.5A-3.3A, but for the purpose of MR and
> refinement, it seems we have solved (or simply bypassed?) the problem.
>
> Suggestions on XDS/DIALS are appreciated. We are actually using this
> dataset as a test set for XDS/DIALS to deal with ice rings. Will further
> report if we've got anything interesting.
>
> Thanks again!
>
> Sam
>
>
>
>
> On Thu, 4 Apr 2019 at 20:54, Clemens Vonrhein 
> wrote:
>
>> Dear all,
>>
>> And if you want to process with XDS: autoPROC [1] will try to detect
>> and exclude ice-rings automatically - if present [2].
>>
>> If you know that you have ice-rings you can force it [3] to exclude
>> all known ice-rings ranges - but this might not be the best solution
>> if you have "just" diffuse ice-rings (where the special treatment of
>> background within DIALS might be better). Something to test and
>> compare maybe?
>>
>> Cheers
>>
>> Clemens
>>
>> [1] https://www.globalphasing.com/autoproc/
>> https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
>> [2]
>> https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
>> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
>> [3]
>> https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically
>>
>> On Thu, Apr 04, 2019 at 10:51:19AM +, melanie.voll...@diamond.ac.uk
>> wrote:
>> > Dear Sam,
>> >
>> >
>> > to continue from James Parkhurst's email...
>> >
>> >
>> > You can do more analysis regarding ice rings using Auspex (
>> https://www.auspex.de/) if you already have some integrated file.
>> >
>> > Regarding re-integrating images, what did you use the first time round?
>> I think if you use DIALS it got some clever implementation in it that is
>> better in estimating the errors of reflections in proximity to ice rings.
>> Hence you should get better Rfactors without having to remove the effected
>> resolution range and the data it covers (
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>> >
>> >
>> > HTH
>> >
>> >
>> > M
>> >
>> >
>> > 
>> > From: CCP4 bulletin board  on behalf of
>> herman.schreu...@sanofi.com 
>> > Sent: 04 April 2019 10:26:09
>> > To: ccp4bb
>> > Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>> >
>> >
>> > Dear Sam,
>> >
>> >
>> >
>> > I would remove the ice ring and reprocess the data. Ice rings may wreak
>> havoc with scaling so at minimum you have to redo the scaling.
>> >
>> >
>> >
>> > Best,
>> >
>> > Herman
>> >
>> >
>> >
>> > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>> Sam Tang
>> > Gesendet: Donnerstag, 4. April 2019 11:01
>> > An: CCP4BB@JISCMAIL.AC.UK
>> > Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>> >
>> >
>> >
>> >
>> > Dear Eleanor and Eric
>> >
>> >
>> >
>> > Thanks for your replies.
>> >
>> >
>> >
>> > Yes indeed when we looked at the plots e.g. R factor vs resln there was
>> a sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
>> the image. Thus our first thought was to remove the ic ring. (either
>> reprocess or can we bypass this resolution range during refinement?)
>> >
>> >
>> >
>> > The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
>> density was unassigned. We got ~3 total observations, ~15000 unique
>> 

[ccp4bb] mar2mtz command

[raj kumar]

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



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[Christian Roth]

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 <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Sam
>
> Did 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 should
> not be any need to process the data twice, once for the low resolution data
> and once for the high.
>
> Harry
> --
> Dr Harry Powell
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> On 8 Apr 2019, at 19:50, Sam Tang wrote:
>
> Hello everyone
>
> Thanks a lot for your input and advices. To report on how we tackled the
> issue -
>
> (1) We used imosflm to integrate the data.
> (2) We eventually integrated the data in two resolution ranges, say
> 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add that indeed
> from the log file for our initial round the program had already identified
> some ice ring regions.
>
> Aimless statistics looked fine and we were able to get a MR solution which
> was refined to much better Rf/Rw.
>
> This is definitely not a smart solution because we effectively 'throw
> away' useful data between 3.5A-3.3A, but for the purpose of MR and
> refinement, it seems we have solved (or simply bypassed?) the problem.
>
> Suggestions on XDS/DIALS are appreciated. We are actually using this
> dataset as a test set for XDS/DIALS to deal with ice rings. Will further
> report if we've got anything interesting.
>
> Thanks again!
>
> Sam
>
>
>
>
> On Thu, 4 Apr 2019 at 20:54, Clemens Vonrhein 
> wrote:
>
>> Dear all,
>>
>> And if you want to process with XDS: autoPROC [1] will try to detect
>> and exclude ice-rings automatically - if present [2].
>>
>> If you know that you have ice-rings you can force it [3] to exclude
>> all known ice-rings ranges - but this might not be the best solution
>> if you have "just" diffuse ice-rings (where the special treatment of
>> background within DIALS might be better). Something to test and
>> compare maybe?
>>
>> Cheers
>>
>> Clemens
>>
>> [1] https://www.globalphasing.com/autoproc/
>> https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling
>> [2]
>> https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl
>> https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings
>> [3]
>> https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically
>>
>> On Thu, Apr 04, 2019 at 10:51:19AM +, melanie.voll...@diamond.ac.uk
>> wrote:
>> > Dear Sam,
>> >
>> >
>> > to continue from James Parkhurst's email...
>> >
>> >
>> > You can do more analysis regarding ice rings using Auspex (
>> https://www.auspex.de/) if you already have some integrated file.
>> >
>> > Regarding re-integrating images, what did you use the first time round?
>> I think if you use DIALS it got some clever implementation in it that is
>> better in estimating the errors of reflections in proximity to ice rings.
>> Hence you should get better Rfactors without having to remove the effected
>> resolution range and the data it covers (
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/).
>> >
>> >
>> > HTH
>> >
>> >
>> > M
>> >
>> >
>> > 
>> > From: CCP4 bulletin board  on behalf of
>> herman.schreu...@sanofi.com 
>> > Sent: 04 April 2019 10:26:09
>> > To: ccp4bb
>> > Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>> >
>> >
>> > Dear Sam,
>> >
>> >
>> >
>> > I would remove the ice ring and reprocess the data. Ice rings may wreak
>> havoc with scaling so at minimum you have to redo the scaling.
>> >
>> >
>> >
>> > Best,
>> >
>> > Herman
>> >
>> >
>> >
>> > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>> Sam Tang
>> > Gesendet: Donnerstag, 4. April 2019 11:01
>> > An: CCP4BB@JISCMAIL.AC.UK
>> > Betreff: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
>> >
>> >
>> >
>> >
>> > Dear Eleanor and Eric
>> >
>> >
>> >
>> > Thanks for your replies.
>> >
>> >
>> >
>> > Yes indeed when we looked at the plots e.g. R factor vs resln there was
>> a sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on
>> the image. Thus our first thought was to remove the ic ring. (either
>> reprocess or can we bypass this resolution range during refinement?)
>> >
>> >
>> >
>> > The protein is 50 kDa, two molecule in the ASU, seemingly no obvious
>> density was unassigned. We got ~3 total observations, ~15000 unique
>> observations. NCS restraints was applied.
>> >
>> >
>> >
>> > Best 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

[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 should not be any need to process the data twice, once for the low resolution data and once for the high.
Harry--Dr Harry Powell

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

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