Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Engin Özkan]

Dear Jasmine,

Thank you for contributing to this thread.

This has been asked in a different way, but can we simply assume at this 
point that the mmCIF/PDB records will no longer contain any or separate 
chain ID-like item that reflects chains including proteins and their 
glycans, as has been the universal practice in glycoprotein structural 
biology for decades before.


In other words, as one usually needs to select chain A and all its 
glycans in visualization software (e.g., using select chain A in PyMOL, 
which will no longer work), will we need distance-cutoff based 
selections to define new selections to work with or use scripts to 
interpret connectivity records?


Not a big deal; still a single-liner in PyMOL. But I'd rather not do it 
every time, if PyMOL or other software can be convinced to read a 
separate chain-ID like item from mmCIF files that allows us to select 
those actual chains easily using those identifiers.


Thank you,

Engin


On 12/10/20 1:47 PM, Jasmine Young wrote:

Dear Marcin,

The cif item, _pdbx_branch_scheme.pdb_asym_id, in the 
pdbx_branch_scheme category is a pointer to _atom_site.auth_asym_id in 
the atom_site category (I know this is confusing). The labels are 
consistently defined as the ones in _pdbx_poly_seq_scheme and 
_pdbx_nonpoly_scheme.


To use the wwPDB-assigned chain ID in publications, 
_atom_site.auth_seq_id _atom_site.auth_comp_id, and 
_atom_site.auth_asym_id can be used for the residue number, residue 
ID, and chain ID, respectively.



Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/9/20 4:31 PM, Marcin Wojdyr wrote:

Dear Jasmine,

thank you for this explanation. It's the best explanation of this
remediation I've read.

The use of IDs may confuse people, so I'd like to reiterate it and ask
for clarification.
Every residue in the mmCIF format has three (3) independent chain IDs
assigned to it (and three sequence numbers, and three residue names).

In your example:
J 4 NAG 1 I NAG 1 A NAG 1310 n

J - asym_id = _atom_site.label_asym_id
I - pdb_asym_id = _atom_site.auth_asym_id (?!)
A - auth_asym_id = n/a

(correct me if I got it wrong, but I see that _atom_site.auth_asym_id
corresponds to _pdbx_branch_scheme.pdb_asym_id and not to auth_asym_id
as one could expect).

How to call these chain IDs? When I write software documentation, I
need to refer to chain IDs (and sequence numbers), but I can't find
proper words to clearly tell which ID I'm referring to. I was using
hard to read names such as auth_asym_id, but now I see that even this
is ambiguous.

BTW, when you write that wwPDB encourages depositors to use the
wwPDB-assigned chain ID in publications, which of the two
wwPDB-assigned chain IDs do you mean?

Thank you,
Marcin




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--
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://voices.uchicago.edu/ozkanlab



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[ccp4bb] Postdoc position

[Alexandra Deaconescu]

Dear ccp4bb enthusiasts,

I have a postdoc position available in my lab. We are a small and collaborative 
lab and are looking for someone enthusiastic to join our efforts. Multiple 
projects in different stages of development are available.
Previous experience with structural biology would be a plus, but we would be 
equally excited by someone who is familiar with assay development and bacterial 
genetics. Full ad below.

Thanks so much!

Alexandra



POSTDOCTORAL POSITION

at Brown University, USA

 

The Deaconescu Lab at Brown University has one opening for a postdoctoral 
researcher. The laboratory's interests lie primarily in stress responses, with 
particular emphasis on responses to stress, DNA damage and the mechanochemistry 
of DNA-based motors. We utilize a combination of biochemical, biophysical and 
structural techniques. (e.g. X-ray crystallography, transmission electron 
microscopy). Examples of work are: Brugger et al, Nature Communications (2020), 
Dorich et al, Genes & Development (2019), Vemu et al. Science (2018), Le TT et 
al. Cell (2018), Deaconescu et al. Photochemistry and Photobiology (2017), 
Kutter et al. JMB (2016), Szyk et al, Cell (2014), Deaconescu et al., PNAS 
(2012), Szyk et al., NSMB (2012) and Deaconescu et al., TIBS (2013) and 
Deaconescu et al., Cell (2006).

 A successful candidate should have an established track-record of publications 
in peer-reviewed journals; solid experience with protein biochemistry 
(including their purification from E.coli/yeast,  functional characterization 
and assay development).  Prior knowledge of crystallography and/or 
single-particle electron microscopy is highly desirable, but not required. Must 
be highly motivated and work well independently as well as in a team. Excellent 
spoken and written English are required. New Ph.D. graduates are encouraged to 
apply. We have a variety of projects available at different stages of 
development.

   Interested candidates should send a CV, a one page research experience 
summary and contact information for three references to 
alexandra_deaconescu[at]brown.edu. Please use “postdoctoral candidate” as a 
subject.

 

Salary and starting date are negotiable.   Please write Postdoctoral Candidate 
in the e-mail subject header.   Brown University, an Ivy League school, is 
located in Providence, Rhode Island less than one hour away by train from 
Boston.   Rhode Island provides plenty of opportunities for outdoor recreation 
with beautiful beaches and sailing.

 

Lab webpage: https://deaconesculab.com 
 

 







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Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

[Jasmine Young]

Dear Marcin,

The cif item, _pdbx_branch_scheme.pdb_asym_id, in the pdbx_branch_scheme 
category is a pointer to _atom_site.auth_asym_id in the atom_site 
category (I know this is confusing). The labels are consistently defined 
as the ones in _pdbx_poly_seq_scheme and _pdbx_nonpoly_scheme.


To use the wwPDB-assigned chain ID in publications, 
_atom_site.auth_seq_id _atom_site.auth_comp_id, and 
_atom_site.auth_asym_id can be used for the residue number, residue ID, 
and chain ID, respectively.



Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 12/9/20 4:31 PM, Marcin Wojdyr wrote:

Dear Jasmine,

thank you for this explanation. It's the best explanation of this
remediation I've read.

The use of IDs may confuse people, so I'd like to reiterate it and ask
for clarification.
Every residue in the mmCIF format has three (3) independent chain IDs
assigned to it (and three sequence numbers, and three residue names).

In your example:
J 4 NAG 1 I NAG 1 A NAG 1310 n

J - asym_id = _atom_site.label_asym_id
I - pdb_asym_id = _atom_site.auth_asym_id (?!)
A - auth_asym_id = n/a

(correct me if I got it wrong, but I see that _atom_site.auth_asym_id
corresponds to _pdbx_branch_scheme.pdb_asym_id and not to auth_asym_id
as one could expect).

How to call these chain IDs? When I write software documentation, I
need to refer to chain IDs (and sequence numbers), but I can't find
proper words to clearly tell which ID I'm referring to. I was using
hard to read names such as auth_asym_id, but now I see that even this
is ambiguous.

BTW, when you write that wwPDB encourages depositors to use the
wwPDB-assigned chain ID in publications, which of the two
wwPDB-assigned chain IDs do you mean?

Thank you,
Marcin




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[ccp4bb] Job posting: Scientific Software Engineer at NSLS-II

[Jun Aishima]

The National Synchrotron Light Source II (NSLS-II) is seeking a scientific 
software developer to join the Scientific Computing & Data Acquisition, Data 
Management, Data Analysis Group. This position is needed to support the 
development and maintenance of a software infrastructure for data acquisition, 
management and analysis to support the scientific mission of NSLS-II.

You will work on the development and application of user software for big 
scientific data acquisition, management, reduction, analysis, and visualization 
to serve the requirements of the Structural Biology Program.  The development 
work will also need to be coordinated and compatible with larger developments 
at the facility.

For a full list of duties, requirements, and a link to apply, please see:

https://jobs.bnl.gov/job/upton/scientific-software-engineer/3437/2861985264 

For any questions, please feel free to contact me at jaish...@bnl.gov

Jun Aishima
Computational Scientist
Data Acquisition Management and Analysis (DAMA) group
NSLS-II
Long Island, NY, USA



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Re: [ccp4bb] AW: [ccp4bb] Finding partial occupancy monomer by MR ?

[Dale Tronrud]

On 12/10/2020 6:46 AM, Schreuder, Herman /DE wrote:

Dear Phil,
0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my 
mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied 
monomers... It may also be related to a (trigonal??) space group...

You probably have already tried it, but phaser has the option to give it 
already solved molecules and ask it to search for additional molecules. Here I 
would indeed lower the expected % homology significantly, to crudely compensate 
for the low occupancy. In contrast to the advice of Dale, I would play around 
with the % homology to find the value which works best.


   It was not my intention to imply that one should not "explore" your 
problem with multiple interpretations -- Only that you have to adjust 
your assessment of the significance of the results of those tests.


   For example, following MR, where you have varied some small multiple 
of 6 parameters, you trust the working R factor.  After you have 
"explored" an great number of models by varying thousands of parameters 
the working R now has to be judged by different criteria.  If this 
change is not made one will be misled to have more confidence in the 
model than is truly justified.  We all agree on this.


   This problem, however, is not specific to the working R.  If you 
calculate five kinds of maps and pick the one with the tallest peak at 
your favorite site, the "sigma" of that peak has to be considered less 
significant than a peak of equal "sigma" in a map that you decided to 
calculate before you collected data.  (I'll leave my objections to the 
idea of measuring peaks in "sigma"s for another day.)


   When we go hunting in situations like Prof. Jeffrey's our criteria 
are more squishy.  Usually one varies a parameter or chooses a 
alternative map type based on "interpretivity".  All I'm saying is, if 
you calculate twenty different maps and pick the one that is easiest to 
interpret, you have to consider the significance of that increase in 
ease of interpretation to be less than if you defined ahead of time the 
map you planed to look at.


   Yes, when your defined protocol fails, look around for alternatives. 
 Just ensure that your personal skepticism setting is cranked up when 
doing so.


Dale Tronrud



My 2 cents,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Phil Jeffrey
Gesendet: Donnerstag, 10. Dezember 2020 14:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Finding partial occupancy monomer by MR ?

Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and 
apparently one at much reduced occupancy.  It was built recently from Se-SAD and was in 
moderately good condition: Rfree=32% for trimer, 2.6 Å.  In recent refinement cycles it 
became obvious that there was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc 
density that corresponded to a "confusing" set of low-occupancy SeMet sites 
found by SHELXD and Phaser-EP.  The experimental map was bad in that region and was 
probably flattened during density modification anyway, in retrospect.

Question:
Phaser failed to find the 4th monomer after trivially finding the other
3 with a recent version of the monomer.  I'm wondering if there's a way to indicate 
"this one is partial occupancy" to Phaser, or if there's a way to improve the 
odds of success beyond just lowering the expected % homology.  Or if anyone has had 
success with other programs.  This is perhaps a rare edge case but I naively expected 
Phaser to work.

In the end I used the weak SeMet sites to locate the monomer and the occupancy 
appears to be around 0.32 in refinement.

Cheers,
Phil Jeffrey
Princeton



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Re: [ccp4bb] Finding partial occupancy monomer by MR ?

[Randy John Read]

Hi Phil,

It’s always a difficult balance between looking hard in a difficult case and 
possibly finding an answer with a weak signal, and stopping when the search is 
really unlikely to succeed.  Phaser perhaps errs too much toward trying really 
hard.

There’s one really blunt tool in Phaser, the KILL TIME command that tells it to 
stop after a certain number of minutes have passed.  I don’t particularly like 
or recommend that option.

A more nuanced approach is to use the PURGE commands to control the amount of 
branching that takes place in the searches — this is where the CPU time can 
really build up.  What I like is to set something like PURGE RNP NUM 20, in 
which case only 20 possible partial solutions after refinement are preserved as 
starting points to look for the next copy.  You can choose the number depending 
on your case and how long each rotation search and each translation search 
takes.  There are PURGE commands to control things at the rotation and 
translation stages as well, but I usually find that the RNP one gives enough 
control.

Best wishes,

Randy

> On 10 Dec 2020, at 16:00, Phil Jeffrey  wrote:
> 
> Thanks for the suggestions.
> 
> The idea that it's related to a trigonal space group and twinning or pseudo 
> space group is an interesting one, but this is C2221 and the intensity stats 
> don't show twinning.  Twinned P21 -> C2221 doesn't solve the non-unit 
> occupancy in this case.  Since the other monomers are full-occupancy it can't 
> be 3 overlapping dimers so the phenomenon is rather unusual in my finite 
> experience.  (Also only one set of Se peaks for this 4th monomer).
> 
> I used Herman's suggestion of finding 3 monomers first (with very large 
> RFZ/TFZ/LLG since the monomers had been refined against the data) since 
> that's very fast.  And then Phaser took a long while to not find the 4th 
> monomer.  Once I figure out how to make modern versions of phaser to "fail 
> quickly" like the older versions I'll scan a range of homology% and see if 
> that changes anything.
> 
> Phil
> 
> 
> On 12/10/20 9:46 AM, Schreuder, Herman /DE wrote:
>> Dear Phil,
>> 0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my 
>> mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied 
>> monomers... It may also be related to a (trigonal??) space group...
>> You probably have already tried it, but phaser has the option to give it 
>> already solved molecules and ask it to search for additional molecules. Here 
>> I would indeed lower the expected % homology significantly, to crudely 
>> compensate for the low occupancy. In contrast to the advice of Dale, I would 
>> play around with the % homology to find the value which works best.
>> My 2 cents,
>> Herman
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board  Im Auftrag von Phil Jeffrey
>> Gesendet: Donnerstag, 10. Dezember 2020 14:49
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: [ccp4bb] Finding partial occupancy monomer by MR ?
>> Preamble:
>> I have an interesting crystal form with 3 monomers (~400aa) at full 
>> occupancy and apparently one at much reduced occupancy.  It was built 
>> recently from Se-SAD and was in moderately good condition: Rfree=32% for 
>> trimer, 2.6 Å.  In recent refinement cycles it became obvious that there was 
>> a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc density that 
>> corresponded to a "confusing" set of low-occupancy SeMet sites found by 
>> SHELXD and Phaser-EP.  The experimental map was bad in that region and was 
>> probably flattened during density modification anyway, in retrospect.
>> Question:
>> Phaser failed to find the 4th monomer after trivially finding the other
>> 3 with a recent version of the monomer.  I'm wondering if there's a way to 
>> indicate "this one is partial occupancy" to Phaser, or if there's a way to 
>> improve the odds of success beyond just lowering the expected % homology.  
>> Or if anyone has had success with other programs.  This is perhaps a rare 
>> edge case but I naively expected Phaser to work.
>> In the end I used the weak SeMet sites to locate the monomer and the 
>> occupancy appears to be around 0.32 in refinement.
>> Cheers,
>> Phil Jeffrey
>> Princeton
>> 
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Re: [ccp4bb] Finding partial occupancy monomer by MR ?

[Phil Jeffrey]

Thanks for the suggestions.

The idea that it's related to a trigonal space group and twinning or 
pseudo space group is an interesting one, but this is C2221 and the 
intensity stats don't show twinning.  Twinned P21 -> C2221 doesn't solve 
the non-unit occupancy in this case.  Since the other monomers are 
full-occupancy it can't be 3 overlapping dimers so the phenomenon is 
rather unusual in my finite experience.  (Also only one set of Se peaks 
for this 4th monomer).


I used Herman's suggestion of finding 3 monomers first (with very large 
RFZ/TFZ/LLG since the monomers had been refined against the data) since 
that's very fast.  And then Phaser took a long while to not find the 4th 
monomer.  Once I figure out how to make modern versions of phaser to 
"fail quickly" like the older versions I'll scan a range of homology% 
and see if that changes anything.


Phil


On 12/10/20 9:46 AM, Schreuder, Herman /DE wrote:

Dear Phil,
0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my 
mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied 
monomers... It may also be related to a (trigonal??) space group...

You probably have already tried it, but phaser has the option to give it 
already solved molecules and ask it to search for additional molecules. Here I 
would indeed lower the expected % homology significantly, to crudely compensate 
for the low occupancy. In contrast to the advice of Dale, I would play around 
with the % homology to find the value which works best.

My 2 cents,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Phil Jeffrey
Gesendet: Donnerstag, 10. Dezember 2020 14:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Finding partial occupancy monomer by MR ?

Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and 
apparently one at much reduced occupancy.  It was built recently from Se-SAD and was in 
moderately good condition: Rfree=32% for trimer, 2.6 Å.  In recent refinement cycles it 
became obvious that there was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc 
density that corresponded to a "confusing" set of low-occupancy SeMet sites 
found by SHELXD and Phaser-EP.  The experimental map was bad in that region and was 
probably flattened during density modification anyway, in retrospect.

Question:
Phaser failed to find the 4th monomer after trivially finding the other
3 with a recent version of the monomer.  I'm wondering if there's a way to indicate 
"this one is partial occupancy" to Phaser, or if there's a way to improve the 
odds of success beyond just lowering the expected % homology.  Or if anyone has had 
success with other programs.  This is perhaps a rare edge case but I naively expected 
Phaser to work.

In the end I used the weak SeMet sites to locate the monomer and the occupancy 
appears to be around 0.32 in refinement.

Cheers,
Phil Jeffrey
Princeton



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[ccp4bb] AW: [ccp4bb] Finding partial occupancy monomer by MR ?

[Schreuder, Herman /DE]

Dear Phil,
0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my 
mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied 
monomers... It may also be related to a (trigonal??) space group...

You probably have already tried it, but phaser has the option to give it 
already solved molecules and ask it to search for additional molecules. Here I 
would indeed lower the expected % homology significantly, to crudely compensate 
for the low occupancy. In contrast to the advice of Dale, I would play around 
with the % homology to find the value which works best.

My 2 cents,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Phil Jeffrey
Gesendet: Donnerstag, 10. Dezember 2020 14:49
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Finding partial occupancy monomer by MR ?

Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full occupancy 
and apparently one at much reduced occupancy.  It was built recently from 
Se-SAD and was in moderately good condition: Rfree=32% for trimer, 2.6 Å.  In 
recent refinement cycles it became obvious that there was a 4th monomer in a 
region of weaker/choppy 2Fo-Fc and Fo-Fc density that corresponded to a 
"confusing" set of low-occupancy SeMet sites found by SHELXD and Phaser-EP.  
The experimental map was bad in that region and was probably flattened during 
density modification anyway, in retrospect.

Question:
Phaser failed to find the 4th monomer after trivially finding the other
3 with a recent version of the monomer.  I'm wondering if there's a way to 
indicate "this one is partial occupancy" to Phaser, or if there's a way to 
improve the odds of success beyond just lowering the expected % homology.  Or 
if anyone has had success with other programs.  This is perhaps a rare edge 
case but I naively expected Phaser to work.

In the end I used the weak SeMet sites to locate the monomer and the occupancy 
appears to be around 0.32 in refinement.

Cheers,
Phil Jeffrey
Princeton



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Re: [ccp4bb] Finding partial occupancy monomer by MR ?

[Anastassis Perrakis]

Dear Phil,

What is the space group? Could it be that the 4th monomer makes also a trimer 
by symmetry, in an alternative SG?

A.


> On 10 Dec 2020, at 14:49, Phil Jeffrey  wrote:
> 
> Preamble:
> I have an interesting crystal form with 3 monomers (~400aa) at full occupancy 
> and apparently one at much reduced occupancy.  It was built recently from 
> Se-SAD and was in moderately good condition: Rfree=32% for trimer, 2.6 Å.  In 
> recent refinement cycles it became obvious that there was a 4th monomer in a 
> region of weaker/choppy 2Fo-Fc and Fo-Fc density that corresponded to a 
> "confusing" set of low-occupancy SeMet sites found by SHELXD and Phaser-EP.  
> The experimental map was bad in that region and was probably flattened during 
> density modification anyway, in retrospect.
> 
> Question:
> Phaser failed to find the 4th monomer after trivially finding the other 3 
> with a recent version of the monomer.  I'm wondering if there's a way to 
> indicate "this one is partial occupancy" to Phaser, or if there's a way to 
> improve the odds of success beyond just lowering the expected % homology.  Or 
> if anyone has had success with other programs.  This is perhaps a rare edge 
> case but I naively expected Phaser to work.
> 
> In the end I used the weak SeMet sites to locate the monomer and the 
> occupancy appears to be around 0.32 in refinement.
> 
> Cheers,
> Phil Jeffrey
> Princeton
> 
> 
> 
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[ccp4bb] Finding partial occupancy monomer by MR ?

[Phil Jeffrey]

Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full 
occupancy and apparently one at much reduced occupancy.  It was built 
recently from Se-SAD and was in moderately good condition: Rfree=32% for 
trimer, 2.6 Å.  In recent refinement cycles it became obvious that there 
was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc density 
that corresponded to a "confusing" set of low-occupancy SeMet sites 
found by SHELXD and Phaser-EP.  The experimental map was bad in that 
region and was probably flattened during density modification anyway, in 
retrospect.


Question:
Phaser failed to find the 4th monomer after trivially finding the other 
3 with a recent version of the monomer.  I'm wondering if there's a way 
to indicate "this one is partial occupancy" to Phaser, or if there's a 
way to improve the odds of success beyond just lowering the expected % 
homology.  Or if anyone has had success with other programs.  This is 
perhaps a rare edge case but I naively expected Phaser to work.


In the end I used the weak SeMet sites to locate the monomer and the 
occupancy appears to be around 0.32 in refinement.


Cheers,
Phil Jeffrey
Princeton



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Re: [ccp4bb] version for old AMD processors

[Palm, Gottfried]

Thanks Tim and Oleg for suggestions. 

The legacy version works and should be sufficient for my purpose.
Maybe there could be a link or hint in the chapter "Old AMD
processors" to avoid unnecessary questions.

Greetings
  Gottfried




On Thursday, 10-12-2020 at 12:46 Kovalevskiy, Oleg (STFC,RAL,SC)
wrote:


  

 



Dear Gottfried,



 



If this is 64-bit AMD, there is legacy build of CCP4 for Linux
available for download at the bottom of this page (under ‘Legacy
systems’):



http://www.ccp4.ac.uk/download/#os=linux



 



Hope this helps.



 



All the best,



Oleg



 



-- 



Dr Oleg Kovalevskiy



CCP4 Core team



UKRI Science and Technology Facilities Council



Rutherford Appleton Laboratory



Harwell Campus



Didcot, Oxfordshire



OX11 0QX



UK



 



From: CCP4 bulletin board 



Date: Thursday, 10 December 2020 at 15:08



To: ccp4bb 



Subject: [ccp4bb] version for old AMD processors



Dear all, 



  I am running into a "known issue" upon installing ccp4-7.1 on a
pre2010 AMD machine. The download page says



 



CCP4 7.1: Known issues



...



Old AMD processors



...



We are in the process of preparing an alternative release package for
those processors. 



 



Is there a solution in the meanwhile?



Greetings



  Gottfried 



 



 



 



 



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This email and any attachments are intended solely for the use of the
named recipients. If you are not the intended recipient you must not
use, disclose, copy or distribute this email or any of its attachments
and should notify the sender immediately and delete this email from
your system. UK Research and Innovation (UKRI) has taken every
reasonable precaution to minimise risk of this email or any
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Re: [ccp4bb] version for old AMD processors

[Kovalevskiy, Oleg (STFC,RAL,SC)]

Dear Gottfried,



If this is 64-bit AMD, there is legacy build of CCP4 for Linux available for 
download at the bottom of this page (under ‘Legacy systems’):

http://www.ccp4.ac.uk/download/#os=linux



Hope this helps.



All the best,

Oleg



--

Dr Oleg Kovalevskiy

CCP4 Core team

UKRI Science and Technology Facilities Council

Rutherford Appleton Laboratory

Harwell Campus

Didcot, Oxfordshire

OX11 0QX

UK



From: CCP4 bulletin board 

Date: Thursday, 10 December 2020 at 15:08

To: ccp4bb 

Subject: [ccp4bb] version for old AMD processors

Dear all,

  I am running into a "known issue" upon installing ccp4-7.1 on a pre2010 AMD 
machine. The download page says



CCP4 7.1: Known issues

...

Old AMD processors

...

We are in the process of preparing an alternative release package for those 
processors.



Is there a solution in the meanwhile?

Greetings

  Gottfried









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This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
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attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses. Opinions, conclusions 
or other information in this message and attachments that are not related 
directly to UKRI business are solely those of the author and do not represent 
the views of UKRI.




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Re: [ccp4bb] version for old AMD processors

[Tim Gruene]

Dear Gottfried,

you can compile from source, http://www.ccp4.ac.uk/download/#os=src 

and/or spend 150-200Euro for a new computer.

Best,
Tim

On Thu, 10 Dec 2020 12:07:17 +0100
"Palm, Gottfried"  wrote:

> Dear all, 
> 
>   I am running into a "known issue" upon installing ccp4-7.1 on a
> pre2010 AMD machine. The download page says
> 
> 
> 
> CCP4 7.1: Known issues
> ...
> Old AMD processors
> ...
> We are in the process of preparing an alternative release package for
> those processors. 
> 
> 
> 
> Is there a solution in the meanwhile?
> Greetings
>   Gottfried
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgptqsB3JlD_L.pgp
Description: OpenPGP digital signature

[ccp4bb] version for old AMD processors

[Palm, Gottfried]

Dear all, 

  I am running into a "known issue" upon installing ccp4-7.1 on a
pre2010 AMD machine. The download page says



CCP4 7.1: Known issues
...
Old AMD processors
...
We are in the process of preparing an alternative release package for
those processors. 



Is there a solution in the meanwhile?
Greetings
  Gottfried



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[ccp4bb] Call for papers "Web Tools for Modeling and Analysis of Biomolecular Interactions"

[ANDREANI Jessica]

Dear all,

together with Brian Jiménez-García (Utrecht University) and Masahito Ohue 
(Tokyo Institute of Technology), we are editing a Research Topic entitled "Web 
Tools for Modeling and Analysis of Biomolecular Interactions" for the journal 
"Frontiers in Molecular Biosciences".



Full details and links to participate and submit contributions can be found at

https://www.frontiersin.org/research-topics/17397



Our goal is to gather a collection of user-friendly tools (web servers and 
databases) useful for non-specialists. The collection is focused on 
biomolecular interactions and may therefore include resources for computational 
modeling, visualization, prediction, analysis of experimental (structural, 
proteomics, other -omics) data, analysis of interaction networks…



The abstract submission deadline is 15 January 2021 and the submission deadline 
for manuscripts is 28 May 2021. Please note that manuscripts will be peer 
reviewed, and if accepted for publication, are subject to publishing fees 
(https://www.frontiersin.org/about/publishing-fees). It is possible to apply 
for fees support.

If you are interested in participating or if you need any further information, 
please do not hesitate to contact me.

Best regards,



Jessica Andreani



---

Jessica Andreani

I2BC (Institute for Integrative Biology of the Cell)

Institut des Sciences du Vivant Frédéric Joliot

Bâtiment 144 - Point courrier 22

CEA

91191 Gif sur Yvette cedex

France

jessica.andre...@cea.fr





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Re: [ccp4bb] [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Randy John Read]

Several people have mentioned lack of peer review as a reason to doubt the 
significance of the AlphaFold2 results.  There are different routes to peer 
review and, while the results have not been published in a peer review journal, 
I would have to say (as someone who has been an assessor for two CASPs, as well 
as having editorial responsibilities for a peer-reviewed journal), the peer 
review at CASP is much more rigorous than the peer review that most papers 
undergo.  The targets are selected from structures that have recently been 
solved but not published or disseminated, and even just tweeting a C-alpha 
trace is probably enough to get a target cancelled.  In some cases (as we’ve 
heard here) the people determining the structure are overly optimistic about 
when their structure solution will be finished, so even they may not know the 
structure at the time it is predicted.  The assessors are blinded to the 
identities of the predictors, and they carry out months of calculations and 
inspections of the models, computing ranking scores before they find out who 
made the predictions.  Most assessors try to bring something new to the 
assessment, because the criteria should get more stringent as the predictions 
get better, and they have new ideas of what to look for, but there’s always 
some overlap with “traditional” measures such as GDT-TS, GDT-HA (more stringent 
high-accuracy version of GDT) and lDDT.

Of course we’d all like to know the details of how AlphaFold2 works, and the 
DeepMind people could have been (and should be) much more forthcoming, but 
their results are real.  They didn’t have any way of cheating, being selective 
about what they reported, or gaming the system in any other way that the other 
groups couldn’t do.  (And yes, when we learned that DeepMind was behind the 
exceptionally good results two years ago at CASP13, we made the same half-jokes 
about whether Gmail had been in the database they were mining!)

Best wishes,

Randy Read

> On 9 Dec 2020, at 10:36, Hughes, Jonathan 
>  wrote:
> 
> i think the answer to all these doubts and questions is quite simple: the 
> AlphaFold2 people must make all details of their methods public (source code) 
> and, as would probably be necessary, open their system for inspection and use 
> by independent experts. isn't that what peer review and reproducibility are 
> all about? those rules date from the time before every tom, dick and 
> henriette could publicize anything they like inside their own zuckerberg 
> bubble. my opinion is that this is a virtual infectious disease that will 
> cause humanity far bigger problems than corona ever will – i just hope i'm 
> wrong!
> best
> jon
>  
> Von: CCP4 bulletin board  Im Auftrag von Mark J van 
> Raaij
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and 
> less pipetting (?)
>  
> on the day the news came out, I did wonder if the AlphaFold2 team somehow had 
> access to all the preliminary PDB files sent around via Gmail (which belongs 
> to the same company), but more as a joke/conspirational thought.
> "our" target T1052, was also predicted very well by domains and as a monomer. 
> It will be interesting to see how well future iterations of the method can 
> assemble the complete protein chain and the complete protein chains into the 
> correct heteromer.
>  
> 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
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> 
>  
> On 9 Dec 2020, at 10:37, Cedric Govaerts  wrote:
>  
> Dear All
>  
> After about 10 (!) years of (very) hard work we solved the structures of our 
> dearest membrane transporter.  Dataset at 2.9 And resolution, fairly 
> anisotropic, experimental phasing, and many long nights with Coot and 
> Buster to achieve model refinement. 
>  
> The experimental structure had a well defined ligand nicely coordinated but 
> also a lipid embedded inside the binding cavity (a complete surprise but 
> biologically relevant) and two detergent molecules well defined 
> (experimental/crystallisation artefact).
>  
> As our paper was accepted basically when CASP organisers were calling for 
> targets I offered my baby to the computing Gods. However we only provided the 
> sequence to CASP, no info regarding any ligand or lipid.
>  
> Less than a month after, the CASP team contacted us and send us the best 
> model.  In fact it was 2 half models as the transporter is a pseudo dimer, 
> with the N-lobe and C-lobe moving relative to each other during transport 
> cycle, thus divided as two domains in CASP.
>  
> The results were breathtaking. 0.7 And RSMD on one half, 0.6 on the other. 
> And yes, group 427 was the superpower (did not know at the time that it was 
> AlphaFold).
>  
> We had long discussions with