[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] molecular replacement_protein-glycan complex

[Herman . Schreuder]

Hi Shen,

I agree with Eleanor that the split spots will cause worse statistics, but 
should not be a reason for molrep to fail.
What I would do:
Molecular replacement with a resolution cut of 3 or 3.5 Å.
Process and run molecular replacement in P1. You may have some tricky 
pseudo-symmetry. With 8 molecules, molrep may take somewhat longer, but I think 
it is worth a try.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Xu, Shenyuan
Gesendet: Montag, 11. November 2019 16:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] molecular replacement_protein-glycan complex


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Hello Eleanor,

I used the solved one as the input model. The space group of the solved 
crystals are: P1 21 1, and P 21.

I will turn the anomalous processing off.

Thanks,

Shen

On Mon, Nov 11, 2019 at 10:40 AM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Why dont you use one of your solved structures as a model?
What space group are the solved ones in?
The split spots are not good, but they are well separated and integration 
programs are not bad at such spacings? And your R merges etc look OK.
Just a Q - why turn off the anomalous processing. You dont need to use it, but 
at some point it may help you find Ss or Ca or whatever..
Eleanor


On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan 
mailto:x...@miamioh.edu>> wrote:
Dear All,

Thanks for all of your nice suggestions! (Sorry I did not respond to individual 
email to say Thanks.) I have used phaser to go through all possible space 
groups in the same point group(choose "all possible in same pointgroup" in the 
space group menu). I also try P43212 alone. The best result I get from phaser 
is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41 2 2), and refinement ends in 
the R-work: ~0.54, R-free:~0.57.

I go back to see the diffraction data, and it seems that spots in the high 
resolution bin are severely split (pictures are attached). I feel like the fail 
of replacement is caused by this. Is this caused by twinning?

I am looking forward suggestions!

Thanks,

Shenyuan Xu

On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:
Dear  Shenyuan,

it seems you assumed P41 21 2 is correct but it isn't - did you try P43 21 2 in 
molecular replacement?

The pointless log file mentions this alternative a few lines above the ones 
you've quoted.

If that does not work, try the other P4x 2y 2 space groups. All of this can be 
done in a single phaser run (choose "all possible in same pointgroup" in the 
space group menu).

Why did you cut the data at 2.29A? They are very strong in the high resolution 
shell!

HTH,
Kay

On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan 
mailto:x...@miamioh.edu>> wrote:

>Dear all,
>
>I am working on a protein-glycan complex trying to use molecular
>replacement.This protein is a VP8* domain from rotavirus, adopting a
>classical galectin-like fold. I already used MR to solve some other strains
>(apo-form and complex form). However, When I want to use the same model to
>solve this particular strain (sequence identity > 95%), MR seems to be
>failed with R=0.54, Free R = 0.57, and the model does not agree with the
>electron density map once viewed on coot. One difference of this
>protein-glycan complex between others is that the glycan is longer, which
>has six carbohydrate unit.
>
>I used imosflm trying to reindex and use pointless to check the space
>group, it usually ends up with the current choice:
>25_pointless.log
>
>WARNING! one or more zones have data systematically missing from the input
>file
>thus we cannot determine if reflections are truly systematically absent
>
>Best Solution: space group P 41 21 2
>Reindex operator: [h,k,l]
>Laue group probability: 1.000
>Systematic absence probability: 0.995
>Total probability: 0.995
>Space group confidence: 0.993
>Laue group confidence 1.000
>
>WARNING: You will have to resolve the enantiomorphic ambiguity later
>
>Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00
>
>84.58 to 2.43 - Resolution range used for Laue group search
>
>84.58 to 2.29 - Resolution range in file, used for systematic absence check
>
>Number of batches in file: 1
>
>The data do not appear to be twinned, from the L-test
>I also use Zanuda to validate the space group, it ends with the same choice:
>
>Step 3.
>   Refinement of the best model.
>   Candidate symmetry elements are added one by one.
>
>   current time:Nov 06 16:17 GMT
>   expected end of job: Nov 06 17:06 GMT
>
>   ^
>   | >>   3   | C 1 2 1|  0.3736  |  0.5334  |  0.5044  |  0.5586  |
>   -
>   |  1   | P 1|  0.4058  |  0.5318  |  0.5020  |  0.5624  |
>   |  5   | P 1 21 1   |  0.4928  |--|  0.4973  |  0

[ccp4bb] Submissions to the Computational Crystallography Newsletter – 30 NOV 19

[Nigel Moriarty]

Folks

Calling for articles and short communications of interest to
structural biologists. The deadline for submission for the January
2020 issue is 30 November 2019.

The Computational Crystallography Newsletter (CCN) is an electronic
newsletter for structural biologists, and is published online every 6
months. Feature articles, meeting announcements and reports can be
submitted to me at any time for consideration. Submission of text by
email or word-processing files using the CCN templates is requested.
Past newsletters and a Microsoft Word template are available at
www.phenix-online.org/newsletter
.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov



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[ccp4bb] Announcement of 11th International Workshop on Radiation Damage to Biological Samples. Swiss Light Source, 25-27th March 2020: registration and Abstract submission now open

[Elspeth Garman]

Registration and Abstract submission is now open for the 11th International 
Workshop on Radiation Damage to Biological Samples will be held at the Swiss 
Light Source, 25th-27th March 2020.
Further details can be found at:
https://indico.psi.ch/event/7811/overview

The Workshop will address essential questions and challenges of radiation 
damage to biological samples during their examination with ionizing radiation. 
The workshop will cover various X-ray and electron scattering techniques, from 
crystallography to imaging, and offers ample opportunities for information 
exchange and discussion among researchers from around the globe.
Sessions will cover:

1) Basic Understanding of Radiation Damage Mechanisms

2) Biological Studies Affected by Radiation Damage

3) Practical Aspects of Reducing Radiation Damage at Synchrotrons

4) Damage at New Sources - XFEL and 4th generation synchrotrons

5) Radiation Damage in Complementary Fields (incl. CryoEM, ED, imaging)

Best wishes
Elspeth Garman
On behalf of the Organising Committee

Elspeth F. Garman,
Professor of Molecular Biophysics,
Senior Kurti Fellow, Brasenose College, University of Oxford
Postal address:
Laboratory of Molecular Biophysics,
Department of Biochemistry,
University of Oxford, Tel: (44)-1865-613297
South Parks Road, FAX: (44)-1865-613201
OXFORD, OX1 3QU, U.K. E-mail: 
elspeth.gar...@bioch.ox.ac.uk
http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=garman
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Re: [ccp4bb] molecular replacement_protein-glycan complex

[Xu, Shenyuan]

Here are some solved models information (no P 21):

1: 56.69, 75.87, 74.927; 90, 91.857, 90; P1 21 1;4 copies
in asynmm unit.
2: 46.732, 32.276, 51.065;90, 94.372, 90; P 1 21 1;   1
copy in ASU.
3. 115.631, 115.631, 101.828;90, 90, 90;I 41;2 copies in
ASU.

The estimated molecules in my new form is 4 copies in ASU.

Thanks,

Shen


On Mon, Nov 11, 2019 at 11:06 AM Eleanor Dodson 
wrote:

> Hmm -
> cell dimension of your solved model? Number of molecules in the P21
> crystal?
>
> Likely number of molecules in asymm unit for your new form?
>
> Eleanor
>
>
>
> On Mon, 11 Nov 2019 at 15:51, Xu, Shenyuan  wrote:
>
>> Hello Eleanor,
>>
>> I used the solved one as the input model. The space group of the solved
>> crystals are: P1 21 1, and P 21.
>>
>> I will turn the anomalous processing off.
>>
>> Thanks,
>>
>> Shen
>>
>> On Mon, Nov 11, 2019 at 10:40 AM Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> wrote:
>>
>>> Why dont you use one of your solved structures as a model?
>>> What space group are the solved ones in?
>>> The split spots are not good, but they are well separated and
>>> integration programs are not bad at such spacings? And your R merges etc
>>> look OK.
>>> Just a Q - why turn off the anomalous processing. You dont need to use
>>> it, but at some point it may help you find Ss or Ca or whatever..
>>> Eleanor
>>>
>>>
>>> On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan  wrote:
>>>
 Dear All,

 Thanks for all of your nice suggestions! (Sorry I did not respond to
 individual email to say Thanks.) I have used phaser to go through all
 possible space groups in the same point group(choose "all possible in same
 pointgroup" in the space group menu). I also try P43212 alone. The best
 result I get from phaser is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41
 2 2), and refinement ends in the R-work: ~0.54, R-free:~0.57.

 I go back to see the diffraction data, and it seems that spots in the
 high resolution bin are severely split (pictures are attached). I feel like
 the fail of replacement is caused by this. Is this caused by twinning?

 I am looking forward suggestions!

 Thanks,

 Shenyuan Xu

 On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs <
 kay.diederi...@uni-konstanz.de> wrote:

> Dear  Shenyuan,
>
> it seems you assumed P41 21 2 is correct but it isn't - did you try
> P43 21 2 in molecular replacement?
>
> The pointless log file mentions this alternative a few lines above the
> ones you've quoted.
>
> If that does not work, try the other P4x 2y 2 space groups. All of
> this can be done in a single phaser run (choose "all possible in same
> pointgroup" in the space group menu).
>
> Why did you cut the data at 2.29A? They are very strong in the high
> resolution shell!
>
> HTH,
> Kay
>
> On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan 
> wrote:
>
> >Dear all,
> >
> >I am working on a protein-glycan complex trying to use molecular
> >replacement.This protein is a VP8* domain from rotavirus, adopting a
> >classical galectin-like fold. I already used MR to solve some other
> strains
> >(apo-form and complex form). However, When I want to use the same
> model to
> >solve this particular strain (sequence identity > 95%), MR seems to be
> >failed with R=0.54, Free R = 0.57, and the model does not agree with
> the
> >electron density map once viewed on coot. One difference of this
> >protein-glycan complex between others is that the glycan is longer,
> which
> >has six carbohydrate unit.
> >
> >I used imosflm trying to reindex and use pointless to check the space
> >group, it usually ends up with the current choice:
> >25_pointless.log
> >
> >WARNING! one or more zones have data systematically missing from the
> input
> >file
> >thus we cannot determine if reflections are truly systematically
> absent
> >
> >Best Solution: space group P 41 21 2
> >Reindex operator: [h,k,l]
> >Laue group probability: 1.000
> >Systematic absence probability: 0.995
> >Total probability: 0.995
> >Space group confidence: 0.993
> >Laue group confidence 1.000
> >
> >WARNING: You will have to resolve the enantiomorphic ambiguity later
> >
> >Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00
> >
> >84.58 to 2.43 - Resolution range used for Laue group search
> >
> >84.58 to 2.29 - Resolution range in file, used for systematic absence
> check
> >
> >Number of batches in file: 1
> >
> >The data do not appear to be twinned, from the L-test
> >I also use Zanuda to validate the space group, it ends with the same
> choice:
> >
> >Step 3.
> >   Refinement of the best model.
> >   Candidate symmetry elements are added one by o

Re: [ccp4bb] molecular replacement_protein-glycan complex

[Eleanor Dodson]

Hmm -
cell dimension of your solved model? Number of molecules in the P21 crystal?

Likely number of molecules in asymm unit for your new form?

Eleanor



On Mon, 11 Nov 2019 at 15:51, Xu, Shenyuan  wrote:

> Hello Eleanor,
>
> I used the solved one as the input model. The space group of the solved
> crystals are: P1 21 1, and P 21.
>
> I will turn the anomalous processing off.
>
> Thanks,
>
> Shen
>
> On Mon, Nov 11, 2019 at 10:40 AM Eleanor Dodson 
> wrote:
>
>> Why dont you use one of your solved structures as a model?
>> What space group are the solved ones in?
>> The split spots are not good, but they are well separated and integration
>> programs are not bad at such spacings? And your R merges etc look OK.
>> Just a Q - why turn off the anomalous processing. You dont need to use
>> it, but at some point it may help you find Ss or Ca or whatever..
>> Eleanor
>>
>>
>> On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan  wrote:
>>
>>> Dear All,
>>>
>>> Thanks for all of your nice suggestions! (Sorry I did not respond to
>>> individual email to say Thanks.) I have used phaser to go through all
>>> possible space groups in the same point group(choose "all possible in same
>>> pointgroup" in the space group menu). I also try P43212 alone. The best
>>> result I get from phaser is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41
>>> 2 2), and refinement ends in the R-work: ~0.54, R-free:~0.57.
>>>
>>> I go back to see the diffraction data, and it seems that spots in the
>>> high resolution bin are severely split (pictures are attached). I feel like
>>> the fail of replacement is caused by this. Is this caused by twinning?
>>>
>>> I am looking forward suggestions!
>>>
>>> Thanks,
>>>
>>> Shenyuan Xu
>>>
>>> On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs <
>>> kay.diederi...@uni-konstanz.de> wrote:
>>>
 Dear  Shenyuan,

 it seems you assumed P41 21 2 is correct but it isn't - did you try P43
 21 2 in molecular replacement?

 The pointless log file mentions this alternative a few lines above the
 ones you've quoted.

 If that does not work, try the other P4x 2y 2 space groups. All of this
 can be done in a single phaser run (choose "all possible in same
 pointgroup" in the space group menu).

 Why did you cut the data at 2.29A? They are very strong in the high
 resolution shell!

 HTH,
 Kay

 On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan 
 wrote:

 >Dear all,
 >
 >I am working on a protein-glycan complex trying to use molecular
 >replacement.This protein is a VP8* domain from rotavirus, adopting a
 >classical galectin-like fold. I already used MR to solve some other
 strains
 >(apo-form and complex form). However, When I want to use the same
 model to
 >solve this particular strain (sequence identity > 95%), MR seems to be
 >failed with R=0.54, Free R = 0.57, and the model does not agree with
 the
 >electron density map once viewed on coot. One difference of this
 >protein-glycan complex between others is that the glycan is longer,
 which
 >has six carbohydrate unit.
 >
 >I used imosflm trying to reindex and use pointless to check the space
 >group, it usually ends up with the current choice:
 >25_pointless.log
 >
 >WARNING! one or more zones have data systematically missing from the
 input
 >file
 >thus we cannot determine if reflections are truly systematically absent
 >
 >Best Solution: space group P 41 21 2
 >Reindex operator: [h,k,l]
 >Laue group probability: 1.000
 >Systematic absence probability: 0.995
 >Total probability: 0.995
 >Space group confidence: 0.993
 >Laue group confidence 1.000
 >
 >WARNING: You will have to resolve the enantiomorphic ambiguity later
 >
 >Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00
 >
 >84.58 to 2.43 - Resolution range used for Laue group search
 >
 >84.58 to 2.29 - Resolution range in file, used for systematic absence
 check
 >
 >Number of batches in file: 1
 >
 >The data do not appear to be twinned, from the L-test
 >I also use Zanuda to validate the space group, it ends with the same
 choice:
 >
 >Step 3.
 >   Refinement of the best model.
 >   Candidate symmetry elements are added one by one.
 >
 >   current time:Nov 06 16:17
 GMT
 >   expected end of job: Nov 06 17:06
 GMT
 >
 >
  ^
 >   | >>   3   | C 1 2 1|  0.3736  |  0.5334  |  0.5044  |  0.5586
 |
 >
  -
 >   |  1   | P 1|  0.4058  |  0.5318  |  0.5020  |  0.5624
 |
 >   |  5   | P 1 21 1   |  0.4928  |--|  0.4973  |  0.5701
 |
 >   |   

Re: [ccp4bb] molecular replacement_protein-glycan complex

[Xu, Shenyuan]

Hello Eleanor,

I used the solved one as the input model. The space group of the solved
crystals are: P1 21 1, and P 21.

I will turn the anomalous processing off.

Thanks,

Shen

On Mon, Nov 11, 2019 at 10:40 AM Eleanor Dodson 
wrote:

> Why dont you use one of your solved structures as a model?
> What space group are the solved ones in?
> The split spots are not good, but they are well separated and integration
> programs are not bad at such spacings? And your R merges etc look OK.
> Just a Q - why turn off the anomalous processing. You dont need to use it,
> but at some point it may help you find Ss or Ca or whatever..
> Eleanor
>
>
> On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan  wrote:
>
>> Dear All,
>>
>> Thanks for all of your nice suggestions! (Sorry I did not respond to
>> individual email to say Thanks.) I have used phaser to go through all
>> possible space groups in the same point group(choose "all possible in same
>> pointgroup" in the space group menu). I also try P43212 alone. The best
>> result I get from phaser is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41
>> 2 2), and refinement ends in the R-work: ~0.54, R-free:~0.57.
>>
>> I go back to see the diffraction data, and it seems that spots in the
>> high resolution bin are severely split (pictures are attached). I feel like
>> the fail of replacement is caused by this. Is this caused by twinning?
>>
>> I am looking forward suggestions!
>>
>> Thanks,
>>
>> Shenyuan Xu
>>
>> On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs <
>> kay.diederi...@uni-konstanz.de> wrote:
>>
>>> Dear  Shenyuan,
>>>
>>> it seems you assumed P41 21 2 is correct but it isn't - did you try P43
>>> 21 2 in molecular replacement?
>>>
>>> The pointless log file mentions this alternative a few lines above the
>>> ones you've quoted.
>>>
>>> If that does not work, try the other P4x 2y 2 space groups. All of this
>>> can be done in a single phaser run (choose "all possible in same
>>> pointgroup" in the space group menu).
>>>
>>> Why did you cut the data at 2.29A? They are very strong in the high
>>> resolution shell!
>>>
>>> HTH,
>>> Kay
>>>
>>> On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan 
>>> wrote:
>>>
>>> >Dear all,
>>> >
>>> >I am working on a protein-glycan complex trying to use molecular
>>> >replacement.This protein is a VP8* domain from rotavirus, adopting a
>>> >classical galectin-like fold. I already used MR to solve some other
>>> strains
>>> >(apo-form and complex form). However, When I want to use the same model
>>> to
>>> >solve this particular strain (sequence identity > 95%), MR seems to be
>>> >failed with R=0.54, Free R = 0.57, and the model does not agree with the
>>> >electron density map once viewed on coot. One difference of this
>>> >protein-glycan complex between others is that the glycan is longer,
>>> which
>>> >has six carbohydrate unit.
>>> >
>>> >I used imosflm trying to reindex and use pointless to check the space
>>> >group, it usually ends up with the current choice:
>>> >25_pointless.log
>>> >
>>> >WARNING! one or more zones have data systematically missing from the
>>> input
>>> >file
>>> >thus we cannot determine if reflections are truly systematically absent
>>> >
>>> >Best Solution: space group P 41 21 2
>>> >Reindex operator: [h,k,l]
>>> >Laue group probability: 1.000
>>> >Systematic absence probability: 0.995
>>> >Total probability: 0.995
>>> >Space group confidence: 0.993
>>> >Laue group confidence 1.000
>>> >
>>> >WARNING: You will have to resolve the enantiomorphic ambiguity later
>>> >
>>> >Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00
>>> >
>>> >84.58 to 2.43 - Resolution range used for Laue group search
>>> >
>>> >84.58 to 2.29 - Resolution range in file, used for systematic absence
>>> check
>>> >
>>> >Number of batches in file: 1
>>> >
>>> >The data do not appear to be twinned, from the L-test
>>> >I also use Zanuda to validate the space group, it ends with the same
>>> choice:
>>> >
>>> >Step 3.
>>> >   Refinement of the best model.
>>> >   Candidate symmetry elements are added one by one.
>>> >
>>> >   current time:Nov 06 16:17 GMT
>>> >   expected end of job: Nov 06 17:06 GMT
>>> >
>>> >   ^
>>> >   | >>   3   | C 1 2 1|  0.3736  |  0.5334  |  0.5044  |  0.5586  |
>>> >   -
>>> >   |  1   | P 1|  0.4058  |  0.5318  |  0.5020  |  0.5624  |
>>> >   |  5   | P 1 21 1   |  0.4928  |--|  0.4973  |  0.5701  |
>>> >   |  9   | P 21 21 21 |  0.5470  |--|  0.5011  |  0.5736  |
>>> >   | 10   | P 41 21 2  |  0.5749  |--|  0.5018  |  0.5778  |
>>> >   -
>>> >   | <<  10   | P 41 21 2  |  0.5749  |--|  0.5018  |  0.5778  |
>>> >   -
>

Re: [ccp4bb] molecular replacement_protein-glycan complex

[Eleanor Dodson]

Why dont you use one of your solved structures as a model?
What space group are the solved ones in?
The split spots are not good, but they are well separated and integration
programs are not bad at such spacings? And your R merges etc look OK.
Just a Q - why turn off the anomalous processing. You dont need to use it,
but at some point it may help you find Ss or Ca or whatever..
Eleanor


On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan  wrote:

> Dear All,
>
> Thanks for all of your nice suggestions! (Sorry I did not respond to
> individual email to say Thanks.) I have used phaser to go through all
> possible space groups in the same point group(choose "all possible in same
> pointgroup" in the space group menu). I also try P43212 alone. The best
> result I get from phaser is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41
> 2 2), and refinement ends in the R-work: ~0.54, R-free:~0.57.
>
> I go back to see the diffraction data, and it seems that spots in the high
> resolution bin are severely split (pictures are attached). I feel like the
> fail of replacement is caused by this. Is this caused by twinning?
>
> I am looking forward suggestions!
>
> Thanks,
>
> Shenyuan Xu
>
> On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Dear  Shenyuan,
>>
>> it seems you assumed P41 21 2 is correct but it isn't - did you try P43
>> 21 2 in molecular replacement?
>>
>> The pointless log file mentions this alternative a few lines above the
>> ones you've quoted.
>>
>> If that does not work, try the other P4x 2y 2 space groups. All of this
>> can be done in a single phaser run (choose "all possible in same
>> pointgroup" in the space group menu).
>>
>> Why did you cut the data at 2.29A? They are very strong in the high
>> resolution shell!
>>
>> HTH,
>> Kay
>>
>> On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan  wrote:
>>
>> >Dear all,
>> >
>> >I am working on a protein-glycan complex trying to use molecular
>> >replacement.This protein is a VP8* domain from rotavirus, adopting a
>> >classical galectin-like fold. I already used MR to solve some other
>> strains
>> >(apo-form and complex form). However, When I want to use the same model
>> to
>> >solve this particular strain (sequence identity > 95%), MR seems to be
>> >failed with R=0.54, Free R = 0.57, and the model does not agree with the
>> >electron density map once viewed on coot. One difference of this
>> >protein-glycan complex between others is that the glycan is longer, which
>> >has six carbohydrate unit.
>> >
>> >I used imosflm trying to reindex and use pointless to check the space
>> >group, it usually ends up with the current choice:
>> >25_pointless.log
>> >
>> >WARNING! one or more zones have data systematically missing from the
>> input
>> >file
>> >thus we cannot determine if reflections are truly systematically absent
>> >
>> >Best Solution: space group P 41 21 2
>> >Reindex operator: [h,k,l]
>> >Laue group probability: 1.000
>> >Systematic absence probability: 0.995
>> >Total probability: 0.995
>> >Space group confidence: 0.993
>> >Laue group confidence 1.000
>> >
>> >WARNING: You will have to resolve the enantiomorphic ambiguity later
>> >
>> >Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00
>> >
>> >84.58 to 2.43 - Resolution range used for Laue group search
>> >
>> >84.58 to 2.29 - Resolution range in file, used for systematic absence
>> check
>> >
>> >Number of batches in file: 1
>> >
>> >The data do not appear to be twinned, from the L-test
>> >I also use Zanuda to validate the space group, it ends with the same
>> choice:
>> >
>> >Step 3.
>> >   Refinement of the best model.
>> >   Candidate symmetry elements are added one by one.
>> >
>> >   current time:Nov 06 16:17 GMT
>> >   expected end of job: Nov 06 17:06 GMT
>> >
>> >   ^
>> >   | >>   3   | C 1 2 1|  0.3736  |  0.5334  |  0.5044  |  0.5586  |
>> >   -
>> >   |  1   | P 1|  0.4058  |  0.5318  |  0.5020  |  0.5624  |
>> >   |  5   | P 1 21 1   |  0.4928  |--|  0.4973  |  0.5701  |
>> >   |  9   | P 21 21 21 |  0.5470  |--|  0.5011  |  0.5736  |
>> >   | 10   | P 41 21 2  |  0.5749  |--|  0.5018  |  0.5778  |
>> >   -
>> >   | <<  10   | P 41 21 2  |  0.5749  |--|  0.5018  |  0.5778  |
>> >   -
>> >
>> >   R-factor in the original subgroup is (almost) the best.
>> >   The original spacegroup assignment seems to be correct.
>> >
>> >  The statistics of the dataset seems good:
>> >Summary data forProject: Test Crystal: A Dataset: 1
>> >
>> >   Overall  InnerShell
>> OuterShell
>> >Low resolution limit

[ccp4bb] Field Applications Scientist opening at TTP Labtech

[Michele Darrow]

We have an opening for a Field Applications Scientist, specializing in cryoEM, 
based in the US. You can apply here: 
https://apply.workable.com/ttp-labtech/j/9BDDA5AF01/

Applications will be assessed on an ongoing basis. Feel free to get in touch 
with any questions.

Best,
Michele
|  Michele Darrow  |  development scientist  |  TTP Labtech Ltd.  |  +44 1223 
627555  |  +44 01223 627320  (direct dial)
Description
TTP Labtech is looking for an experienced Field Applications Scientist, 
specialising in CryoEM, to help deliver and support new sample preparation 
technologies that will enable emerging methods of determining biomolecular 
structures. This is a fantastic opportunity to work on cutting-edge sample 
preparation technology and aid in its introduction to the market.
You will be part of the global FAS team which serves as the key interface 
between the Sales team, Marketing and end-users and will help shape the 
development and delivery of a range of new products as a key member of the 
structural biology team.
The role will require significant travel across North America, and occasional 
travel to the UK headquarters.
About us
We are a global supplier of innovative products for advancing life sciences and 
accelerating drug development, combining the best science with first-rate 
engineering. We design and manufacture a wide range of low volume liquid 
handling equipment and sample management systems addressing high growth markets 
in genomics, structural biology and drug discovery.
About the role
You will be:

  *   Supporting the development and roll-out of early systems and the 
progression to full commercial products;
  *   Engaging with early customers to provide applications advice;
  *   Supporting the sales team with product demonstrations;
  *   Understanding product requirements through collaboration with customers;
  *   Liaising between customers and development teams to identify and enable 
product improvements;
  *   Managing placements with customer development partners, including 
training, analysis and interpretation of customer data and providing feedback 
on the customer experience;
  *   Advising on the possible direction of further development as a product 
expert;
  *   Preparing and presenting written material for marketing, such as posters 
and applications notes.
Requirements
You should have:

  *   Good understanding and hands-on experience of CryoEM sample preparation 
and structure determination;
  *   Significant CryoEM and structural biology domain knowledge and a keen 
awareness of current trends in the field;
  *   A good grounding in commercial and business principles. Specific 
experience in this area would be a distinct advantage.
  *   Undergraduate degree or equivalent qualification in Structural Biology. A 
PhD qualification in a relevant field is strongly preferred, although 
equivalent experience will be considered;
  *   Ability and willingness to travel extensively (up to 75%)
  *   Creative thinking and logical problem solving;
  *   Ability to analyse complex technical data/equipment;
  *   First class verbal and written communication skills, fully proficient in 
Word, Excel and PowerPoint;
  *   Good interpersonal and organisational skills, great team-working skills.

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[ccp4bb] CCP4i2 London Road Show

[Nicholas Keep]

Reminder CCP4i2 London Road show  TOMORROW.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Job position at Evotec in the Structural Biology group

[Stephanie Duclos]

Dear CCP4 community,


Evotec (UK) Ltd is currently seeking to add to our Structural Biology 
Department.  The group works closely with our Discovery Chemistry Department 
and with clients to develop novel small molecule drugs.  The group is at the 
forefront of new science and technology, and is seeking to expand as business 
needs grow.

If you are interested, please apply using this link:

https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Abingdon-Evotec/Scientist---Senior-Purification-Scientist--Structural-Biology_REQ-01246



Best wishes,



Stephanie on behalf of Sandrine Thieffine



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Evotec (UK) Ltd is a limited company registered in England and Wales. 
Registration number:2674265. Registered office: 114 Innovation Drive, Milton 
Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom.



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Re: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters

[Eleanor Dodson]

To answer some queries - crystallisation lost in time - post doc has left
and I am left to do the deposition!. There are lots of PEG fragments built
but that is floating in the solvent..

Distances for N  - O1  1.8
O1 - O2 1.7
O2-O3   1.8

A smigeon of difference densities within bonding distance of the N and O1

But like a lot of high res maps there are diff peaks galore; maybe
alternate solvent regiona??  R 10% /13% so it is pretty OK
E


On Mon, 11 Nov 2019 at 10:56, Clemens Vonrhein 
wrote:

> Dear Eleanor,
>
> Considering some (potential) very strong model bias here: is the
> difference mFo-DFc map totally flat or just not shown in your picture?
> Does the density come back as such if the three waters are removed?
>
> Cheers
>
> Clemens
>
> On Thu, Nov 07, 2019 at 01:12:14PM +, Eleanor Dodson wrote:
> > seen in a high resolution map?
> >
> > There is at least one other similar feature???
> >
> > Eleanor
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>



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Re: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters

[Clemens Vonrhein]

Dear Eleanor,

Considering some (potential) very strong model bias here: is the
difference mFo-DFc map totally flat or just not shown in your picture?
Does the density come back as such if the three waters are removed?

Cheers

Clemens

On Thu, Nov 07, 2019 at 01:12:14PM +, Eleanor Dodson wrote:
> seen in a high resolution map?
> 
> There is at least one other similar feature???
> 
> Eleanor

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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