Re: [ccp4bb] AW: [ccp4bb] Pandda problems

2018-05-25 Thread Pearce, N.M. (Nick) 
I agree completely for error messages regarding errors that the user can fix.

However that is not the case with this error, which was an “unexpected” error — 
perhaps I will add a “contact developer” message to those errors to make this 
clear.

Thanks,
Nick

On 25 May 2018, at 16:22, 
"herman.schreu...@sanofi.com" 
> wrote:

Dear Nick,

Thank you for your reply. I am looking forward to test a new Pandda version 
that is hopefully compatible with the latest CCP4 version.

Concerning the error messages: I think they are very useful for developers, to 
trace back in the code what had happened, but not for users, who need 
information how to change the input files and/or parameters to fix the problem. 
However, Charles Ballard send me an email that the problem could also have been 
caused by old .pyc files and gave instructions how to remove these.

If the alignment is to get a superposition, you could consider aligning on 
sequence numbers, which is trivial and which should be identical for all data 
sets.

Best regards and have a nice weekend!
Herman




Von: Pearce, N.M. (Nick) [mailto:n.m.pea...@uu.nl]
Gesendet: Freitag, 25. Mai 2018 15:59
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Pandda problems

Hi,

Yes, that’s not a very useful error message — sorry. I am still in the process 
of intermittently rewriting the pandda code to be …better.

I don’t think you’ve necessarily done anything wrong — pandda has not been 
extensively tested on running on series of structures that are not identical 
(we normally refine one reference structure against all datasets).

However, your timing is pretty good, because I will (today) release a new 
version of pandda that should work with the latest version of ccp4. I think it 
should fix the particular problem that you have.

I’m just running tests now, but on Monday you should be able to update your 
ccp4 to the newest update and then update your version of pandda using pip, 
following the instructions on the website 
(https://pandda.bitbucket.io).

If that doesn’t work on Monday, let me know if you have any more problems.

Thanks,
Nick


On 25 May 2018, at 14:36, 
herman.schreu...@sanofi.com wrote:

Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following – for me not very helpful – error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)

[ccp4bb] AW: [ccp4bb] Pandda problems

2018-05-25 Thread Herman . Schreuder 
Dear Nick,

Thank you for your reply. I am looking forward to test a new Pandda version 
that is hopefully compatible with the latest CCP4 version.

Concerning the error messages: I think they are very useful for developers, to 
trace back in the code what had happened, but not for users, who need 
information how to change the input files and/or parameters to fix the problem. 
However, Charles Ballard send me an email that the problem could also have been 
caused by old .pyc files and gave instructions how to remove these.

If the alignment is to get a superposition, you could consider aligning on 
sequence numbers, which is trivial and which should be identical for all data 
sets.

Best regards and have a nice weekend!
Herman




Von: Pearce, N.M. (Nick) [mailto:n.m.pea...@uu.nl]
Gesendet: Freitag, 25. Mai 2018 15:59
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Pandda problems

Hi,

Yes, that’s not a very useful error message — sorry. I am still in the process 
of intermittently rewriting the pandda code to be …better.

I don’t think you’ve necessarily done anything wrong — pandda has not been 
extensively tested on running on series of structures that are not identical 
(we normally refine one reference structure against all datasets).

However, your timing is pretty good, because I will (today) release a new 
version of pandda that should work with the latest version of ccp4. I think it 
should fix the particular problem that you have.

I’m just running tests now, but on Monday you should be able to update your 
ccp4 to the newest update and then update your version of pandda using pip, 
following the instructions on the website 
(https://pandda.bitbucket.io).

If that doesn’t work on Monday, let me know if you have any more problems.

Thanks,
Nick


On 25 May 2018, at 14:36, 
herman.schreu...@sanofi.com wrote:

Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following – for me not very helpful – error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)

Re: [ccp4bb] Pandda problems

2018-05-25 Thread Pearce, N.M. (Nick) 
Hi,

Yes, that’s not a very useful error message — sorry. I am still in the process 
of intermittently rewriting the pandda code to be …better.

I don’t think you’ve necessarily done anything wrong — pandda has not been 
extensively tested on running on series of structures that are not identical 
(we normally refine one reference structure against all datasets).

However, your timing is pretty good, because I will (today) release a new 
version of pandda that should work with the latest version of ccp4. I think it 
should fix the particular problem that you have.

I’m just running tests now, but on Monday you should be able to update your 
ccp4 to the newest update and then update your version of pandda using pip, 
following the instructions on the website (https://pandda.bitbucket.io).

If that doesn’t work on Monday, let me know if you have any more problems.

Thanks,
Nick

On 25 May 2018, at 14:36, 
herman.schreu...@sanofi.com wrote:

Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following – for me not very helpful – error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)

[ccp4bb] Pandda problems

2018-05-25 Thread Herman . Schreuder 
Dear bulletin board,

I am trying to run Pandda on a set of about 50 data sets. I asked our system 
manager to roll back to CCP4 update 047 and by using unique and refmac, I could 
fix the problem of a few missing low resolution reflections.

However, then Pandda crashes apparently during alignment of the structures with 
the following - for me not very helpful - error messages:

Failed to align dataset x10
Traceback (most recent call last):
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/pandda/analyse/functions.py",
 line 68, in run
alignment = model.align_to(other_hierarchy=other.hierarchy, method=method, 
require_hierarchies_identical=False)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/dataset.py",
 line 96, in align_to
self.alignment = align_structures_flexible(mov_hierarchy=self.hierarchy, 
ref_hierarchy=other_hierarchy, **kwargs)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 254, in align_structures_flexible
l_ali = align_chains_flexible(chn_mov=chn_mov, chn_ref=chn_ref, 
altlocs=altlocs, cutoff_radius=cutoff_radius)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/align.py",
 line 285, in align_chains_flexible
chn_ref_cr, chn_mov_cr = common_residues(chn_ref_cb, chn_mov_cb)
  File 
"/DD/Applications/sb/ccp4/ccp4-7.0/lib/python2.7/site-packages/giant/structure/select.py",
 line 79, in common_residues
assert (max(m_seq_1)

[ccp4bb] Improvements to onedep deposition system

2018-05-25 Thread John Berrisford 
For depositors who subunit replacements after curation of their entries, 
the new version of wwPDB OneDep system improves this process.


This updated process ensures that all new data are checked and validated 
before the new files are merged into the deposition session.


A new validation report is produced and it should be carefully reviewed, 
and any highlighted issues inspected. The report must be accepted by the 
depositor prior to re-submission of the data.


Any major data errors or data inconsistencies between the original and new 
files are displayed for review by the depositor so that these can be 
rectified prior to resubmission.


Overall, these changes should improve the quality of the data and the 
transparency of the file replacement process. If you have any questions or 
feedback regarding the new file replacement process then please log into 
your deposition session and contact us via the communication tab.




In addition, we are also making sure that we are open and clear about how 
we handle personal data in OneDep. We have updated the wwPDB privacy policy 
(http://www.wwpdb.org/about/privacy) to comply with the changes brought by 
the European Union data protection law (GDPR). If you have any questions 
about this privacy policy, please send them to deposit-h...@mail.wwpdb.org.



John

[ccp4bb] Exciting new updates at PDBe

2018-05-25 Thread John Berrisford 
You might have noticed some changes on the PDBe website today as we’ve 
introduced some great improvements to the search options and new features 
on our entry pages. All these changes should help you to find what you’re 
looking for in the PDB archive and give you better biological context for 
the molecules in your search results.


See our news announcement for further details
https://www.ebi.ac.uk/pdbe/about/news/exciting-new-updates-pdbe

John

[ccp4bb] Vacancy@the SPC Facility, EMBL Hamburg Unit

2018-05-25 Thread Margret Fischer 

Dear colleagues,

I would like to inform you that EMBL Hamburg is currently advertising 
for a Scientific Officer for the Sample Preparation & Characterization 
(SPC).
The facility supports external researchers carrying out experiments on 3 
EMBL beamlines ( 2x MX and 1 SAXS). An extension of the SPC activities
is hosted in the new Centre for Structural Systems Biology (CSSB).The 
Scientific Officer – Biophysical Characterization will support users 
with the design,

execution and data analysis of biophysical experiments.

The facility currently covers a broad range of biophysical techniques, 
including calorimetry, mass spectroscopy, circular dichroism, 
fluorescence, microscale
thermophoresis, dynamic/static light scattering, infrared spectroscopy, 
surface plasmon resonance and biolayer Interferometry. The postholder 
will be responsible for
the maintenance and operation of biophysical instruments as well as for 
training users to operate the equipment independently. He/She will have an
opportunity to develop own relevant research activities within the 
framework of the group by Maria Garcia Alai related to the development 
of new methods at the SPC.


Deadline for application is the 1st July 2018

More detailed information can be found here: http://s.embl.org/HH00140

best wishes,

Margret
--

Margret Fischer
European Molecular Biology Laboratory
Senior Administrative Officer
Notkestrasse 85
22607 Hamburg
Germany
Tel: +49 40 89902110
Mob: +49 1754105760