Re: [ccp4bb] muti-crystal averaging

[Eleanor Dodson]

As you say - HKL200 has a nomerge output.
Pointless/Aimless can read such outputs and sort out any indexing
alternatives, etc
You can specify that the spacegroup should not change.
(I presume this is not a major change? If your original SG is set to P1 and
the program detects 222 symmetry the I would reconsider my SG assognment!)

Cheers Eleanor

On Tue, 16 Jul 2019 at 04:29, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Thanks all, I can merge them together with HKL2000 now, and I found it
> also can do "No merge original index" and merge different data sets with
> same unit cell by new version of HKL2000, which is better than old version
>
>
>
>
> -Original Messages-
> *From:*"Eleanor Dodson" 
> *Sent Time:*2019-07-15 22:08:01 (Monday)
> *To:* "张士军" <21620150150...@stu.xmu.edu.cn>
> *Cc:* "CCP4BB@JISCMAIL.AC.UK" 
> *Subject:* Re: [ccp4bb] muti-crystal averaging
>
> Do you mean these crystals have different unit cells? If so then DMMULTI
> is a useful technique..
>
> Or do you mean you have collected isomorphous data from several crystals
> and want to merge that data?
>
> In that case BLEND will help you decide how isomorhous the data sets are..
> Eleanor
>
> On Mon, 15 Jul 2019 at 13:12, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:
>
>> Dear all
>>
>> I want to average several sets of crystal data together, and I saw some
>> paper used DMMULTI program in CCP4, but I didn't find this program in
>> ccp4, but only find Blend in ccp4 which only used for unmerged reflection
>> files. I wondering is there any programs could use HKL2000 processed *.sca
>> file to do this. Thanks a lot!!!
>>
>> Best Regards
>>
>> Shijun
>>
>> --
>>
>> 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] challenges in structural biology

[Frank Von Delft]

1.1  Getting many diverse conformations routinely into well-diffracting 
crystals;  and knowing how to interpret them biologically.

On 15/07/2019 20:44, Holton, James M wrote:
> Hello folks,
>
> I have the distinct honor of chairing the next Gordon Research
> Conference on Diffraction Methods in Structural Biology (July 26-31
> 2020).  This meeting will focus on the biggest challenges currently
> faced by structural biologists, and I mean actual real-world
> challenges.  As much as possible, these challenges will take the form of
> friendly competitions with defined parameters, data, a scoring system,
> and "winners", to be established along with other unpublished results
> only at the meeting, as is tradition at GRCs.
>
> But what are the principle challenges in biological structure
> determination today?  I of course have my own ideas, but I feel like I'm
> forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
>
> What am I missing?  Is industry facing different problems than
> academics?  Are there specific challenges facing electron-based
> techniques?  If so, could the combined strength of all the world's
> methods developers solve them?  I'm interested in hearing the voice of
> this community.  On or off-list is fine.
>
> -James Holton
> MAD Scientist
>
>
> 
>
> 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] challenges in structural biology

[Keller, Jacob]

I like both of these points! I would comment/add the following:

1) What are the tools we can use for metals in structural biology? Note, I am 
biased here.

-Including validation of solute ions like Na/K/Cl etc
-Some metric of identity confidence?

2) Micro electron diffraction methods - ability to use on small crystals (which 
speaks to Tom's point) and a potential bridge between cryo-EM and X-ray 
diffraction techniques?

-What about an XFEL equivalent for electrons with their greater scattering? I 
looked into this a while back, and there seemed to be some pretty tough things 
about it, but is there hope? Maybe any purifiable protein could be solved in 
this way? Would it have to be done by diffraction, or could focusing work 
somehow?

JPK




Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute 
Director, High-Throughput Crystallization Screening Center

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.getacrystal.org=DwIF-g=LU6cRtx0xgB8s29tIz9Olw=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI=HLRpGMGxTyZSjqW-aeakIElqVXKo3CvO_O36dUmNgKY=7uXULBobMzHYWnHc-YO4fFjHH7PbGQXufIRarsr4dQE=
 

sbow...@hwi.buffalo.edu


From: CCP4 bulletin board  on behalf of Peat, Tom 
(Manufacturing, Parkville) 
Sent: Monday, July 15, 2019 8:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: challenges in structural biology

Hello Tim,

I'm not sure this question is specific to crystallography- I believe the same 
can be asked of any experiment in any field?
And if one wants to get into true costs- was it worth it to build the Large 
Hadron Collider to statistically prove that the Higgs boson exists?
I'm guessing it was worth it to the folks that got their name on the paper...
Cheers, tom

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology

Dear James,

10) are the biological questions that you can answer with a (crystal) structure 
sufficiently relevant to justify the resources?

Best,
Tim



Am 15.07.2019 21:44, schrieb Holton, James M:
> Hello folks,
>
> I have the distinct honor of chairing the next Gordon Research 
> Conference on Diffraction Methods in Structural Biology (July 26-31 
> 2020).  This meeting will focus on the biggest challenges currently 
> faced by structural biologists, and I mean actual real-world 
> challenges.  As much as possible, these challenges will take the form 
> of friendly competitions with defined parameters, data, a scoring 
> system, and "winners", to be established along with other unpublished 
> results only at the meeting, as is tradition at GRCs.
>
> But what are the principle challenges in biological structure 
> determination today?  I of course have my own ideas, but I feel like 
> I'm forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule 
> ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
>
> What am I missing?  Is industry facing different problems than 
> academics?  Are there specific challenges facing electron-based 
> techniques?  If so, could the combined strength of all the world's 
> methods developers solve them?  I'm interested in hearing the voice of 
> this community.  On or off-list is fine.
>
> -James Holton
> MAD Scientist
>
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.u
> k_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIF-g=LU6cRtx0xgB8
> s29tIz9Olw=eLCg9eJ4Rs_LnxfUWsp7FSxhIEcZYmTSU4Uyq1bRYPI=HLRpGMGxTyZ
> SjqW-aeakIElqVXKo3CvO_O36dUmNgKY=Q23TMeWBhuH2_xEAYk3-wjMz65NwxYH-I3E
> fSr0dcAs=

--
--
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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Re: [ccp4bb] muti-crystal averaging

[张士军]

Thanks all, I can merge them together with HKL2000 now, and I found it also can 
do "No merge original index" and merge different data sets with same unit cell 
by new version of HKL2000, which is better than old version






-Original Messages-
From:"Eleanor Dodson" 
Sent Time:2019-07-15 22:08:01 (Monday)
To: "张士军" <21620150150...@stu.xmu.edu.cn>
Cc: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] muti-crystal averaging


Do you mean these crystals have different unit cells? If so then DMMULTI is a 
useful technique..


Or do you mean you have collected isomorphous data from several crystals and 
want to merge that data?


In that case BLEND will help you decide how isomorhous the data sets are..
Eleanor



On Mon, 15 Jul 2019 at 13:12, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:


Dear all

I want to average several sets of crystal data together, and I saw some paper 
used DMMULTI program in CCP4, but I didn't find this program in ccp4, but only 
find Blend in ccp4 which only used for unmerged reflection files. I wondering 
is there any programs could use HKL2000 processed *.sca file to do this. Thanks 
a lot!!!

Best Regards

Shijun




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Re: [ccp4bb] challenges in structural biology

[Sarah Bowman]

Hi James,

2 things come to mind.

1) What are the tools we can use for metals in structural biology? Note, I am 
biased here…

2) Micro electron diffraction methods - ability to use on small crystals (which 
speaks to Tom’s point) and a potential bridge between cryo-EM and X-ray 
diffraction techniques?

Awesome that you are asking for community engagement on this!
Cheers,
Sarah


Sarah EJ Bowman, PhD

Associate Research Scientist, Hauptman-Woodward Medical Research Institute
Director, High-Throughput Crystallization Screening Center

www.getacrystal.org

sbow...@hwi.buffalo.edu


From: CCP4 bulletin board  on behalf of Peat, Tom 
(Manufacturing, Parkville) 
Sent: Monday, July 15, 2019 8:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: challenges in structural biology

Hello Tim,

I'm not sure this question is specific to crystallography- I believe the same 
can be asked of any experiment in any field?
And if one wants to get into true costs- was it worth it to build the Large 
Hadron Collider to statistically prove that the Higgs boson exists?
I'm guessing it was worth it to the folks that got their name on the paper...
Cheers, tom

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology

Dear James,

10) are the biological questions that you can answer with a (crystal) structure 
sufficiently relevant to justify the resources?

Best,
Tim



Am 15.07.2019 21:44, schrieb Holton, James M:
> Hello folks,
>
> I have the distinct honor of chairing the next Gordon Research
> Conference on Diffraction Methods in Structural Biology (July 26-31
> 2020).  This meeting will focus on the biggest challenges currently
> faced by structural biologists, and I mean actual real-world
> challenges.  As much as possible, these challenges will take the form
> of friendly competitions with defined parameters, data, a scoring
> system, and "winners", to be established along with other unpublished
> results only at the meeting, as is tradition at GRCs.
>
> But what are the principle challenges in biological structure
> determination today?  I of course have my own ideas, but I feel like
> I'm forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule
> ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
>
> What am I missing?  Is industry facing different problems than
> academics?  Are there specific challenges facing electron-based
> techniques?  If so, could the combined strength of all the world's
> methods developers solve them?  I'm interested in hearing the voice of
> this community.  On or off-list is fine.
>
> -James Holton
> MAD Scientist
>
>
> ##
> ##
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--
--
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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Re: [ccp4bb] Coot 0.9 curlew has no entry

[Chen Zhao]

Dear Paul,

Thank you for your response and your time! In this case I will just try it
again sometime later.

Best,
Chen

On Mon, Jul 15, 2019 at 7:05 PM Paul Emsley 
wrote:

> On 15/07/2019 12:37, Chen Zhao wrote:
> >
> > I am sorry to bother you, but I was trying to install the long range
> refine, sphere refine, tandem refine,
> > etc. utilities in coot 0.9 for cryo EM map. I was following the
> instructions on the youtube video, however,
> > when I typed in curlew() in python scripting interface, I got a
> completely empty list. Does anyone know why
> > this is happening?
>
> The Curlew function connects to the Coot web site to find the latest list
> of extensions. However, I have
> been unable to rebuild the web site since it was restored from backup
> several days ago. I will try to get it
> done this week.
>
> Regards,
>
> Paul.
>
>



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Re: [ccp4bb] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

Hello Tim, 

I'm not sure this question is specific to crystallography- I believe the same 
can be asked of any experiment in any field? 
And if one wants to get into true costs- was it worth it to build the Large 
Hadron Collider to statistically prove that the Higgs boson exists? 
I'm guessing it was worth it to the folks that got their name on the paper... 
Cheers, tom 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Grüne
Sent: Tuesday, 16 July 2019 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] challenges in structural biology

Dear James,

10) are the biological questions that you can answer with a (crystal) structure 
sufficiently relevant to justify the resources?

Best,
Tim



Am 15.07.2019 21:44, schrieb Holton, James M:
> Hello folks,
> 
> I have the distinct honor of chairing the next Gordon Research 
> Conference on Diffraction Methods in Structural Biology (July 26-31 
> 2020).  This meeting will focus on the biggest challenges currently 
> faced by structural biologists, and I mean actual real-world 
> challenges.  As much as possible, these challenges will take the form 
> of friendly competitions with defined parameters, data, a scoring 
> system, and "winners", to be established along with other unpublished 
> results only at the meeting, as is tradition at GRCs.
> 
> But what are the principle challenges in biological structure 
> determination today?  I of course have my own ideas, but I feel like 
> I'm forgetting something.  Obvious choices are:
> 1) getting crystals to diffract better
> 2) building models into low-resolution maps (after failing at #1)
> 3) telling if a ligand is really there or not
> 4) the phase problem (dealing with weak signal, twinning and
> pseudotranslation)
> 5) what does "resolution" really mean?
> 6) why are macromolecular R factors so much higher than small-molecule 
> ones?
> 7) what is the best way to process serial crystallography data?
> 8) how should one deal with non-isomorphism in multi-crystal methods?
> 9) what is the "structure" of something that won't sit still?
> 
> What am I missing?  Is industry facing different problems than 
> academics?  Are there specific challenges facing electron-based 
> techniques?  If so, could the combined strength of all the world's 
> methods developers solve them?  I'm interested in hearing the voice of 
> this community.  On or off-list is fine.
> 
> -James Holton
> MAD Scientist
> 
> 
> ##
> ##
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--
--
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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Re: [ccp4bb] SA_flag vs PDB

[Bernhard Rupp]

Hmm….this is all a mess. 

 

If the objective is that the users can generate the EXACT map the depositor 
saw, I agree, the output of the Refmac mtz file with the map coefficients would 
be good.

 

Alas, no can do, because the Fs are not the same as in the input file, if I am 
understanding this correctly – reportedly Refmac does something (which is?) to 
them before it dumps them into the output mtz.

 

So I deposit the SA file xyz-staraniso-merged-aniso _free.mtz to get closer to 
the data I used to input into refmac. Bad boy:

 

(a) no can do, PDB no eat SA_flag. Maybe because the FreeR_flag is added as a 
second data set to the xyz-staraniso-merged-aniso.mtz. Ok, fixable.

 

(b) no should do, because we actually want unmerged untruncated and unalterted 
I(obs) – which I agree - and with the XDS_whatever.HKL as close as I can get 
it. 

 

Seems we need a file description that includes all the desired items, and a 
little program the can harvest all that in a single cif file. As I put the 
ASCII XDS*.HKL

file into StarAniso, there seems to be the perfect pre-processing site for all 
our desires. This SuperStar.mtz file then would additionally need only the map 
coefficients for the reflections

actually used by Refmac to generate the map. Might well be that such does 
already exist as some sort of intermediate file. PDB_REPROCESS could take the 
unmerged HKL, process, and F-convert if desired, PDB_REDO could use these data 
then (or the I’s/F’s from SuperStar.mtz). I am sure this does not cover every 
conceivable combination, but it’s worth a discussion. Not that it could ever 
move through glacial committees….

 

In any case, I provide a link to the images for REDO_THE_DARN_JOB_YOURSELF. 

 

Cheers, BR

 

PS: About the deposition read errors on mmcif files later.

 

From: Ian Tickle  
Sent: Monday, July 15, 2019 3:00 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] SA_flag vs PDB

 

 

Hi Bernhard

 

Oh dear, yes that's quite possible.

 

But in any case we recommend _not_ to deposit the output from STARANISO:

 

http://staraniso.globalphasing.org/deposition_about.html

 

Cheers

 

-- Ian

 

 

Cheers

 

-- Ian

 

 

On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Hi Fellows – 

 

wondering if there is a particular reason the PDB cannot process a mtz file 
that in addition to FreeR_flag includes a SA_Flag column from StarAniso?

Can there be no more than one I column type because that is automatically 
interpreted as the free flag??

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

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 =1 




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Re: [ccp4bb] Coot 0.9 curlew has no entry

[Paul Emsley]

On 15/07/2019 12:37, Chen Zhao wrote:


I am sorry to bother you, but I was trying to install the long range refine, sphere refine, tandem refine, 
etc. utilities in coot 0.9 for cryo EM map. I was following the instructions on the youtube video, however, 
when I typed in curlew() in python scripting interface, I got a completely empty list. Does anyone know why 
this is happening?


The Curlew function connects to the Coot web site to find the latest list of extensions. However, I have 
been unable to rebuild the web site since it was restored from backup several days ago. I will try to get it 
done this week.


Regards,

Paul.



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

Re: [ccp4bb] SA_flag vs PDB

[Ian Tickle]

Hi Bernhard

Oh dear, yes that's quite possible.

But in any case we recommend _not_ to deposit the output from STARANISO:

http://staraniso.globalphasing.org/deposition_about.html

Cheers

-- Ian


Cheers

-- Ian


On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp 
wrote:

> Hi Fellows –
>
>
>
> wondering if there is a particular reason the PDB cannot process a mtz
> file that in addition to FreeR_flag includes a SA_Flag column from
> StarAniso?
>
> Can there be no more than one I column type because that is automatically
> interpreted as the free flag??
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> Crystallographiae Vindicis Militum Ordo
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> 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] challenges in structural biology

[Peat, Tom (Manufacturing, Parkville)]

If one were able to crystallise almost all proteins (and complexes) reliably 
and with good diffraction, that would make most people's lives much easier. So 
I would go with 1) as a grand challenge.

Many of the rest follow on from not having 'good' crystals to start with.

cheers, tom


Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au



From: CCP4 bulletin board  on behalf of Holton, James M 
<270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 16, 2019 5:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] challenges in structural biology

Hello folks,

I have the distinct honor of chairing the next Gordon Research
Conference on Diffraction Methods in Structural Biology (July 26-31
2020).  This meeting will focus on the biggest challenges currently
faced by structural biologists, and I mean actual real-world
challenges.  As much as possible, these challenges will take the form of
friendly competitions with defined parameters, data, a scoring system,
and "winners", to be established along with other unpublished results
only at the meeting, as is tradition at GRCs.

But what are the principle challenges in biological structure
determination today?  I of course have my own ideas, but I feel like I'm
forgetting something.  Obvious choices are:
1) getting crystals to diffract better
2) building models into low-resolution maps (after failing at #1)
3) telling if a ligand is really there or not
4) the phase problem (dealing with weak signal, twinning and
pseudotranslation)
5) what does "resolution" really mean?
6) why are macromolecular R factors so much higher than small-molecule ones?
7) what is the best way to process serial crystallography data?
8) how should one deal with non-isomorphism in multi-crystal methods?
9) what is the "structure" of something that won't sit still?

What am I missing?  Is industry facing different problems than
academics?  Are there specific challenges facing electron-based
techniques?  If so, could the combined strength of all the world's
methods developers solve them?  I'm interested in hearing the voice of
this community.  On or off-list is fine.

-James Holton
MAD Scientist




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[ccp4bb] SA_flag vs PDB

[Bernhard Rupp]

Hi Fellows - 

 

wondering if there is a particular reason the PDB cannot process a mtz file
that in addition to FreeR_flag includes a SA_Flag column from StarAniso?

Can there be no more than one I column type because that is automatically
interpreted as the free flag??

 

Best, BR

 

--

Bernhard Rupp

Crystallographiae Vindicis Militum Ordo

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




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Re: [ccp4bb] challenges in structural biology

[Minmin Yu]

Hi James, 
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage  ---
RT serial crystallography
            Temperature vs multiple
conformers 
 
Thanks,
Minmin
 
> Dear James,

>

> 10) are the biological questions that you can answer with a
(crystal)

> structure sufficiently relevant to justify the resources?

>

> Best,

> Tim

>

>

>

> Am 15.07.2019 21:44, schrieb Holton, James M:

>> Hello folks,

>>

>> I have the distinct honor of chairing the next Gordon Research

>> Conference on Diffraction Methods in Structural Biology (July
26-31

>> 2020).  This meeting will focus on the biggest
challenges currently

>> faced by structural biologists, and I mean actual real-world

>> challenges.  As much as possible, these challenges
will take the form

>> of

>> friendly competitions with defined parameters, data, a scoring
system,

>> and "winners", to be established along with other
unpublished results

>> only at the meeting, as is tradition at GRCs.

>>

>> But what are the principle challenges in biological structure

>> determination today?  I of course have my own ideas,
but I feel like

>> I'm

>> forgetting something.  Obvious choices are:

>> 1) getting crystals to diffract better

>> 2) building models into low-resolution maps (after failing at
#1)

>> 3) telling if a ligand is really there or not

>> 4) the phase problem (dealing with weak signal, twinning and

>> pseudotranslation)

>> 5) what does "resolution" really mean?

>> 6) why are macromolecular R factors so much higher than
small-molecule

>> ones?

>> 7) what is the best way to process serial crystallography
data?

>> 8) how should one deal with non-isomorphism in multi-crystal
methods?

>> 9) what is the "structure" of something that won't sit
still?

>>

>> What am I missing?  Is industry facing different
problems than

>> academics?  Are there specific challenges facing
electron-based

>> techniques?  If so, could the combined strength of
all the world's

>> methods developers solve them?  I'm interested in
hearing the voice of

>> this community.  On or off-list is fine.

>>

>> -James Holton

>> MAD Scientist

>>

>>

>>


>>

>> To unsubscribe from the CCP4BB list, click the following link:

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

>

> --

> --

> 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

>

>


>

> 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] challenges in structural biology

[Minmin Yu]

Hi James, 
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage  ---
RT serial crystallography
            Temperature vs multiple
conformers 
 
Thanks,
Minmin
 
> Dear James,

>

> 10) are the biological questions that you can answer with a
(crystal)

> structure sufficiently relevant to justify the resources?

>

> Best,

> Tim

>

>

>

> Am 15.07.2019 21:44, schrieb Holton, James M:

>> Hello folks,

>>

>> I have the distinct honor of chairing the next Gordon Research

>> Conference on Diffraction Methods in Structural Biology (July
26-31

>> 2020).  This meeting will focus on the biggest
challenges currently

>> faced by structural biologists, and I mean actual real-world

>> challenges.  As much as possible, these challenges
will take the form

>> of

>> friendly competitions with defined parameters, data, a scoring
system,

>> and "winners", to be established along with other
unpublished results

>> only at the meeting, as is tradition at GRCs.

>>

>> But what are the principle challenges in biological structure

>> determination today?  I of course have my own ideas,
but I feel like

>> I'm

>> forgetting something.  Obvious choices are:

>> 1) getting crystals to diffract better

>> 2) building models into low-resolution maps (after failing at
#1)

>> 3) telling if a ligand is really there or not

>> 4) the phase problem (dealing with weak signal, twinning and

>> pseudotranslation)

>> 5) what does "resolution" really mean?

>> 6) why are macromolecular R factors so much higher than
small-molecule

>> ones?

>> 7) what is the best way to process serial crystallography
data?

>> 8) how should one deal with non-isomorphism in multi-crystal
methods?

>> 9) what is the "structure" of something that won't sit
still?

>>

>> What am I missing?  Is industry facing different
problems than

>> academics?  Are there specific challenges facing
electron-based

>> techniques?  If so, could the combined strength of
all the world's

>> methods developers solve them?  I'm interested in
hearing the voice of

>> this community.  On or off-list is fine.

>>

>> -James Holton

>> MAD Scientist

>>

>>

>>


>>

>> To unsubscribe from the CCP4BB list, click the following link:

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

>

> --

> --

> 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

>

>


>

> 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] challenges in structural biology

[Minmin Yu]

Hi James, 
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage  ---
RT serial crystallography
            Temperature vs multiple
conformers 
 
Thanks,
Minmin
 
> Dear James,

>

> 10) are the biological questions that you can answer with a
(crystal)

> structure sufficiently relevant to justify the resources?

>

> Best,

> Tim

>

>

>

> Am 15.07.2019 21:44, schrieb Holton, James M:

>> Hello folks,

>>

>> I have the distinct honor of chairing the next Gordon Research

>> Conference on Diffraction Methods in Structural Biology (July
26-31

>> 2020).  This meeting will focus on the biggest
challenges currently

>> faced by structural biologists, and I mean actual real-world

>> challenges.  As much as possible, these challenges
will take the form

>> of

>> friendly competitions with defined parameters, data, a scoring
system,

>> and "winners", to be established along with other
unpublished results

>> only at the meeting, as is tradition at GRCs.

>>

>> But what are the principle challenges in biological structure

>> determination today?  I of course have my own ideas,
but I feel like

>> I'm

>> forgetting something.  Obvious choices are:

>> 1) getting crystals to diffract better

>> 2) building models into low-resolution maps (after failing at
#1)

>> 3) telling if a ligand is really there or not

>> 4) the phase problem (dealing with weak signal, twinning and

>> pseudotranslation)

>> 5) what does "resolution" really mean?

>> 6) why are macromolecular R factors so much higher than
small-molecule

>> ones?

>> 7) what is the best way to process serial crystallography
data?

>> 8) how should one deal with non-isomorphism in multi-crystal
methods?

>> 9) what is the "structure" of something that won't sit
still?

>>

>> What am I missing?  Is industry facing different
problems than

>> academics?  Are there specific challenges facing
electron-based

>> techniques?  If so, could the combined strength of
all the world's

>> methods developers solve them?  I'm interested in
hearing the voice of

>> this community.  On or off-list is fine.

>>

>> -James Holton

>> MAD Scientist

>>

>>

>>


>>

>> To unsubscribe from the CCP4BB list, click the following link:

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

>

> --

> --

> 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

>

>


>

> 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] challenges in structural biology

[Minmin Yu]

Hi James, 
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage  ---
RT serial crystallography
            Temperature vs multiple
conformers 
 
Thanks,
Minmin
 
> Dear James,

>

> 10) are the biological questions that you can answer with a
(crystal)

> structure sufficiently relevant to justify the resources?

>

> Best,

> Tim

>

>

>

> Am 15.07.2019 21:44, schrieb Holton, James M:

>> Hello folks,

>>

>> I have the distinct honor of chairing the next Gordon Research

>> Conference on Diffraction Methods in Structural Biology (July
26-31

>> 2020).  This meeting will focus on the biggest
challenges currently

>> faced by structural biologists, and I mean actual real-world

>> challenges.  As much as possible, these challenges
will take the form

>> of

>> friendly competitions with defined parameters, data, a scoring
system,

>> and "winners", to be established along with other
unpublished results

>> only at the meeting, as is tradition at GRCs.

>>

>> But what are the principle challenges in biological structure

>> determination today?  I of course have my own ideas,
but I feel like

>> I'm

>> forgetting something.  Obvious choices are:

>> 1) getting crystals to diffract better

>> 2) building models into low-resolution maps (after failing at
#1)

>> 3) telling if a ligand is really there or not

>> 4) the phase problem (dealing with weak signal, twinning and

>> pseudotranslation)

>> 5) what does "resolution" really mean?

>> 6) why are macromolecular R factors so much higher than
small-molecule

>> ones?

>> 7) what is the best way to process serial crystallography
data?

>> 8) how should one deal with non-isomorphism in multi-crystal
methods?

>> 9) what is the "structure" of something that won't sit
still?

>>

>> What am I missing?  Is industry facing different
problems than

>> academics?  Are there specific challenges facing
electron-based

>> techniques?  If so, could the combined strength of
all the world's

>> methods developers solve them?  I'm interested in
hearing the voice of

>> this community.  On or off-list is fine.

>>

>> -James Holton

>> MAD Scientist

>>

>>

>>


>>

>> To unsubscribe from the CCP4BB list, click the following link:

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

>

> --

> --

> 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

>

>


>

> 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] challenges in structural biology

[Minmin Yu]

Hi James, 
7) or 8) What are a few different collection methods
including at RT for serial crystallography data?
Temperature vs global and site-specific radiation damage  ---
RT serial crystallography
            Temperature vs multiple
conformers 
 
Thanks,
Minmin
 
> Dear James,

>

> 10) are the biological questions that you can answer with a
(crystal)

> structure sufficiently relevant to justify the resources?

>

> Best,

> Tim

>

>

>

> Am 15.07.2019 21:44, schrieb Holton, James M:

>> Hello folks,

>>

>> I have the distinct honor of chairing the next Gordon Research

>> Conference on Diffraction Methods in Structural Biology (July
26-31

>> 2020).  This meeting will focus on the biggest
challenges currently

>> faced by structural biologists, and I mean actual real-world

>> challenges.  As much as possible, these challenges
will take the form

>> of

>> friendly competitions with defined parameters, data, a scoring
system,

>> and "winners", to be established along with other
unpublished results

>> only at the meeting, as is tradition at GRCs.

>>

>> But what are the principle challenges in biological structure

>> determination today?  I of course have my own ideas,
but I feel like

>> I'm

>> forgetting something.  Obvious choices are:

>> 1) getting crystals to diffract better

>> 2) building models into low-resolution maps (after failing at
#1)

>> 3) telling if a ligand is really there or not

>> 4) the phase problem (dealing with weak signal, twinning and

>> pseudotranslation)

>> 5) what does "resolution" really mean?

>> 6) why are macromolecular R factors so much higher than
small-molecule

>> ones?

>> 7) what is the best way to process serial crystallography
data?

>> 8) how should one deal with non-isomorphism in multi-crystal
methods?

>> 9) what is the "structure" of something that won't sit
still?

>>

>> What am I missing?  Is industry facing different
problems than

>> academics?  Are there specific challenges facing
electron-based

>> techniques?  If so, could the combined strength of
all the world's

>> methods developers solve them?  I'm interested in
hearing the voice of

>> this community.  On or off-list is fine.

>>

>> -James Holton

>> MAD Scientist

>>

>>

>>


>>

>> To unsubscribe from the CCP4BB list, click the following link:

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

>

> --

> --

> 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

>

>


>

> 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] challenges in structural biology

[Nukri Sanishvili]

I know it is going to hijack the original topic but I could not help...

“The reports of death of (macromolecular) crystallography are greatly
exaggerated.
If we believed the prognosticators, it has been dead since the 80s when
some folks made the claim that the only relevant structures were those
solved by NMR.
I think we've done quite well since then...
Best,
Nukri

On Mon, Jul 15, 2019 at 3:45 PM  wrote:

> Hi Tassos, Tim,
>
> I wonder why would you or anyone on this list worry whether biological
> questions that can be asked and answered with structures are relevant to
> justify the resources? I think there is abundant evidence that this is the
> case. Unless your point is that crystallography is now dead for all
> practical
> purposes... then yes, I fully agree :-) It would however be wrong to erase
> its
> historical contribution to understanding biology.
>
> Best wishes,
>
> Radu
>
>
> > I would wonder more if the biological questions you can *ask* with a
> (crystal)
> > structure are sufficiently relevant to justify the resources.
> >
> > Sent from my iPhone
> >
> >> On 15 Jul 2019, at 22:08, Tim Grüne  wrote:
> >>
> >> Dear James,
> >>
> >> 10) are the biological questions that you can answer with a (crystal)
> >> structure sufficiently relevant to justify the resources?
> >>
> >> Best,
> >> Tim
> >>
> >>
> >>
> >> Am 15.07.2019 21:44, schrieb Holton, James M:
> >>> Hello folks,
> >>> I have the distinct honor of chairing the next Gordon Research
> >>> Conference on Diffraction Methods in Structural Biology (July 26-31
> >>> 2020).  This meeting will focus on the biggest challenges currently
> >>> faced by structural biologists, and I mean actual real-world
> >>> challenges.  As much as possible, these challenges will take the form
> of
> >>> friendly competitions with defined parameters, data, a scoring system,
> >>> and "winners", to be established along with other unpublished results
> >>> only at the meeting, as is tradition at GRCs.
> >>> But what are the principle challenges in biological structure
> >>> determination today?  I of course have my own ideas, but I feel like
> I'm
> >>> forgetting something.  Obvious choices are:
> >>> 1) getting crystals to diffract better
> >>> 2) building models into low-resolution maps (after failing at #1)
> >>> 3) telling if a ligand is really there or not
> >>> 4) the phase problem (dealing with weak signal, twinning and
> >>> pseudotranslation)
> >>> 5) what does "resolution" really mean?
> >>> 6) why are macromolecular R factors so much higher than small-molecule
> >>> ones?
> >>> 7) what is the best way to process serial crystallography data?
> >>> 8) how should one deal with non-isomorphism in multi-crystal methods?
> >>> 9) what is the "structure" of something that won't sit still?
> >>> What am I missing?  Is industry facing different problems than
> >>> academics?  Are there specific challenges facing electron-based
> >>> techniques?  If so, could the combined strength of all the world's
> >>> methods developers solve them?  I'm interested in hearing the voice of
> >>> this community.  On or off-list is fine.
> >>> -James Holton
> >>> MAD Scientist
> >>>
> 
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >>
> >> --
> >> --
> >> 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
> >>
> >> 
> >>
> >> 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
> >
>
>
> --
> Radu Aricescu
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue
> Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44-(0)1223-267049
> fax: +44-(0)1223-268305
> www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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Re: [ccp4bb] challenges in structural biology

[Anastassis Perrakis]

I would wonder more if the biological questions you can *ask* with a (crystal) 
structure are sufficiently relevant to justify the resources. 

Sent from my iPhone

> On 15 Jul 2019, at 22:08, Tim Grüne  wrote:
> 
> Dear James,
> 
> 10) are the biological questions that you can answer with a (crystal) 
> structure sufficiently relevant to justify the resources?
> 
> Best,
> Tim
> 
> 
> 
> Am 15.07.2019 21:44, schrieb Holton, James M:
>> Hello folks,
>> I have the distinct honor of chairing the next Gordon Research
>> Conference on Diffraction Methods in Structural Biology (July 26-31
>> 2020).  This meeting will focus on the biggest challenges currently
>> faced by structural biologists, and I mean actual real-world
>> challenges.  As much as possible, these challenges will take the form of
>> friendly competitions with defined parameters, data, a scoring system,
>> and "winners", to be established along with other unpublished results
>> only at the meeting, as is tradition at GRCs.
>> But what are the principle challenges in biological structure
>> determination today?  I of course have my own ideas, but I feel like I'm
>> forgetting something.  Obvious choices are:
>> 1) getting crystals to diffract better
>> 2) building models into low-resolution maps (after failing at #1)
>> 3) telling if a ligand is really there or not
>> 4) the phase problem (dealing with weak signal, twinning and
>> pseudotranslation)
>> 5) what does "resolution" really mean?
>> 6) why are macromolecular R factors so much higher than small-molecule ones?
>> 7) what is the best way to process serial crystallography data?
>> 8) how should one deal with non-isomorphism in multi-crystal methods?
>> 9) what is the "structure" of something that won't sit still?
>> What am I missing?  Is industry facing different problems than
>> academics?  Are there specific challenges facing electron-based
>> techniques?  If so, could the combined strength of all the world's
>> methods developers solve them?  I'm interested in hearing the voice of
>> this community.  On or off-list is fine.
>> -James Holton
>> MAD Scientist
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> -- 
> --
> 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
> 
> 
> 
> 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] challenges in structural biology

[Holton, James M]

Hello folks,

I have the distinct honor of chairing the next Gordon Research 
Conference on Diffraction Methods in Structural Biology (July 26-31 
2020).  This meeting will focus on the biggest challenges currently 
faced by structural biologists, and I mean actual real-world 
challenges.  As much as possible, these challenges will take the form of 
friendly competitions with defined parameters, data, a scoring system, 
and "winners", to be established along with other unpublished results 
only at the meeting, as is tradition at GRCs.

But what are the principle challenges in biological structure 
determination today?  I of course have my own ideas, but I feel like I'm 
forgetting something.  Obvious choices are:
1) getting crystals to diffract better
2) building models into low-resolution maps (after failing at #1)
3) telling if a ligand is really there or not
4) the phase problem (dealing with weak signal, twinning and 
pseudotranslation)
5) what does "resolution" really mean?
6) why are macromolecular R factors so much higher than small-molecule ones?
7) what is the best way to process serial crystallography data?
8) how should one deal with non-isomorphism in multi-crystal methods?
9) what is the "structure" of something that won't sit still?

What am I missing?  Is industry facing different problems than 
academics?  Are there specific challenges facing electron-based 
techniques?  If so, could the combined strength of all the world's 
methods developers solve them?  I'm interested in hearing the voice of 
this community.  On or off-list is fine.

-James Holton
MAD Scientist




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[ccp4bb] Coot 0.9 curlew has no entry

[Chen Zhao]

Dear all,

I am sorry to bother you, but I was trying to install the long range
refine, sphere refine, tandem refine, etc. utilities in coot 0.9 for cryo
EM map. I was following the instructions on the youtube video, however,
when I typed in curlew() in python scripting interface, I got a completely
empty list. Does anyone know why this is happening? I appreciate all the
inputs!

Best,
Chen



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Re: [ccp4bb] muti-crystal averaging

[Eleanor Dodson]

Do you mean these crystals have different unit cells? If so then DMMULTI is
a useful technique..

Or do you mean you have collected isomorphous data from several crystals
and want to merge that data?

In that case BLEND will help you decide how isomorhous the data sets are..
Eleanor

On Mon, 15 Jul 2019 at 13:12, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
> I want to average several sets of crystal data together, and I saw some
> paper used DMMULTI program in CCP4, but I didn't find this program in
> ccp4, but only find Blend in ccp4 which only used for unmerged reflection
> files. I wondering is there any programs could use HKL2000 processed *.sca
> file to do this. Thanks a lot!!!
>
> Best Regards
>
> Shijun
>
> --
>
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> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] coot crashing

[Paul Emsley]

On 11/07/2019 01:51, Tom Peat wrote:


Just wondering if anyone else is having issues with Coot crashing (regularly, 
not just once in a while).


Are you doing anything in particular before the crash?



platform:
/bin/uname
core: #f
No core file found.  No debugging


This is a message for *you*. If you turn on core dumps, then coot will (if it can find them) give you a much 
more useful termination message.





I'm currently using Ubuntu 18.04.2 LTS and I think I'm reasonably up to date 
wrt updates...


OK.  When I've restored the web site (scheduled for this week) you should try 
out the 0.8.9.3-pre binary.

If your computer is locked-up after coot crashes, that sounds more like a hardware/driver/OS problem to me 
(i.e. not a coot problem).


Paul.



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[ccp4bb] muti-crystal averaging

[张士军]

Dear all

I want to average several sets of crystal data together, and I saw some paper 
used DMMULTI program in CCP4, but I didn't find this program in ccp4, but only 
find Blend in ccp4 which only used for unmerged reflection files. I wondering 
is there any programs could use HKL2000 processed *.sca file to do this. Thanks 
a lot!!!

Best Regards

Shijun



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[ccp4bb] Postdoc in Pearl/Oliver lab at Genome Damage and Stability Centre, Sussex

[Laurence Pearl]

Post-Doctoral Research Fellow : Structural Biology of DNA Single-strand Break 
Repair
(Ref 1739)


A Post-doctoral position funded by Cancer Research UK is available from 1st 
October 2019 in the laboratory of Prof. Laurence Pearl FRS and Dr. Antony 
Oliver in the Genome Damage and Stability Centre at the University of Sussex, 
to study the structure and mechanism of multi-protein complexes involved in the 
recognition and repair of DNA single-strand breaks and gaps, primarily using 
single particle reconstruction by cryo-electron microscopy.

Based in the School of Life Sciences, the Genome Damage and Stability Centre, 
is an internationally renowned Institute carrying out research on the response 
of cells to DNA damage, genome instability and its relationship to disease.

Recent work from the Pearl and Oliver groups and an overview of research in the 
Genome Damage and Stability Centre can be found at 
http://www.sussex.ac.uk/gdsc/researchgroups

The School of Life Sciences is committed to equality and valuing diversity, and 
currently holds an Athena SWAN Silver Award. Applications are particularly 
welcomed from women and black and minority ethnic candidates, who are 
under-represented in academic posts in Science, Technology, Engineering, 
Medicine and Mathematics (STEMM) at Sussex. The School of Life Sciences 
welcomes applications to academic posts from candidates who wish to work 
part-time or as job-sharers.

The University offers various schemes to provide real benefits to parents, 
these can be found at Family Friendly 
Policies

Potential candidates are strongly encouraged to make informal contact with 
Prof. Pearl laurence.pe...@sussex.ac.uk or 
Dr. Oliver antony.oli...@sussex.ac.uk before 
applying.

   The University of Sussex values the diversity of its staff and students and 
we welcome applicants from all backgrounds

Download job description and person specification Ref 1739 [PDF 
81.79KB]


How to apply

Download our academic post application form [DOC 
301.50KB] and 
personal details and equal opportunities form [DOC 
162.50KB]
 and fill in all sections.

Applications should be accompanied by a full CV, a statement of research 
interests and aspirations (not more than 4 pages), and the names of three 
academic referees.

Email your completed application,CV, statement of research interests and 
aspirations, and personal details and equal opportunities form, to 
lifescirecruitm...@sussex.ac.uk

You should attach your application form and all documents to the email (don't 
use a web-based upload/weblink service) and use the format job reference number 
/ job title / your name in the subject line.

You can also send your application by post to Human Resources Division, Sussex 
House, University of Sussex, Falmer, Brighton, BN1 9RH.

Download our terms and conditions summary for Research Faculty Terms and 
Conditions [DOC 
36.00KB]


Laurence H. Pearl PhD FRS FMedSci

Professor of Structural Biology
Genome Damage and Stability Centre
University of Sussex, Brighton, BN1 9RQ, UK

Phone +44-(0)1273 678 349

"Live Modestly and do Serious Things .. "
- Dorothy Crowfoot Hodgkin








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[ccp4bb] Head of Cryo-Electron Microscopy Core Facility

[oliver.dau...@mdc-berlin.de]

Dear structural biologists,

Based on a successful application for large infrastructure, the Charité will 
establish a cryo-EM facility on its Campus in Berlin-Buch, with a particular 
focus on cryo-electron tomography applications. We seek a head for this 
facility at the earliest convenience.

We offer:
A three-year fixed-term position according to German public pay grade E14 to 
establish the facility, with the possibility to convert it into a permanent 
position afterwards. Starting date from September 1, 2019.
An international scientific environment with exciting projects and partners.
A dedicated cryo-EM building with state-of-the-art instrumentation including a 
Titan Krios with a Gatan K3 Direct Electron Detector and energy filter, an 
Aquilos Focused Ion Beam Scanning Electron Microscope (FIB-SEM) and a Cryo 
Correlative Light Electron Microscope (CLEM).

Your tasks:
- Establishment of a cryo-EM facility in tight cooperation with the involved 
institutions and companies
- Technical supervision of high-end cryo-electron microscopes and equipment
- Development and application of new cryo-EM methods related to sample 
preparation, data acquisition, data processing, generation of samples for 
FIB-SEM, application of CLEM methods
- Project coordination, including third-party funding acquisition. Preparation 
of applications and publications
- User acquisition and consultation, maintenance of national and international 
co-operations
- Budget and staff responsibility for the core facility
- Education of staff and users
- Establishment of a web page and booking system for the core facility 
(https://iris.charite.de)
- Preparation of legal documents related to the operation of the facility

Your profile:
- Scientific university degree, including PhD
- Several years of working experience in the field of cryo-electron microscopy 
and structural biology
- Experience in the preparation of cryo-EM samples and in the operation of 
cryo-electron microscopes, in data collection and processing of cryo-EM data 
and model building
- Experience in the acquisition and processing of cryo-electron tomography data 
and application of CLEM approaches would be highly desired
- Experience in Linux-based server systems and scripting
- Very good communication skills in English
- Coordination and organization skills, ability to work independently, team 
player

Please send your applications until August 2, 2019, to Claudia Flügel 
(claudia.flue...@charite.de). For questions and more details, please contact 
Oliver Daumke (oliver.dau...@mdc-berlin.de).



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[ccp4bb] Bidentate GLU vs two monodentate GLU in metalloproteins

[Chandra Prakash Tiwari]

Dear all,
What is more preferable or conserved by evolution point of view between
glutamate acting as bidentate ligand by its carboxylate group or two
monodentate GLU at metal binding site in natural metalloprotein.
I was thinking 2 GLU are better than one bidentate GLU because if one GLU
gets mutated other GLU will still be able to form a coordination bond to a
metal.
Please comment and help if i am right or wrong.



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Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

[Peat, Tom (Manufacturing, Parkville)]

Hello Kay, 

Yes, locks the whole machine means it is dead in the water- no mouse, no other 
windows can be activated, no sequence of buttons (e.g. Ctrl-Alt-Del, Ctrl-C, 
etc) to stop or bring anything back to life. What I would call a classic case 
of the machine crashing- the window with the molecule is there, I just can't do 
anything. 
I can look into the magic SysRq system and see if that can help at all. 

Cheers, tom 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay 
Diederichs
Sent: Monday, 15 July 2019 4:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

Hi Tom,

does "locks my whole machine" mean that you cannot open another terminal 
window? If you still can, use the "ps -ef | grep coot" command to find out if 
the coot process still exists, and note its process id ("pid"). If it does, 
remove it with "kill -9 ". 
Or does the window system crash? This would be a bug of the latter.
Or does (the crashed) coot still take input focus, with the effect that you 
cannot use your mouse to activate another window? In that case, try "Alt-tab" 
to switch window focus.
Or can you not even type in another window? For such cases, it pays off to set 
up the machine for the "Alt-SysRq"commands; see 
https://en.wikipedia.org/wiki/Magic_SysRq_key . These can be used to trigger a 
reboot. On Linux I see rarely a need to reset a machine with the power button. 

HTH,
Kay

On Mon, 15 Jul 2019 05:24:38 +, Peat, Tom (Manufacturing, Parkville) 
 wrote:

>Hello again, 
>
>To be more specific- sometimes when Coot crashes, I can just restart Coot. 
>Sometimes it locks my whole machine (maybe 30% of the time) and I need to 
>reboot. 
>The former is just a small pain, the latter is a true pain and I prefer 
>software not to crash the machine in such an untidy way. 
>
...
>
>I'm currently using Ubuntu 18.04.2 LTS and I think I'm reasonably up to date 
>wrt updates... 
>



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Re: [ccp4bb] [ExternalEmail] [ccp4bb] coot crashing

[Kay Diederichs]

Hi Tom,

does "locks my whole machine" mean that you cannot open another terminal 
window? If you still can, use the "ps -ef | grep coot" command to find out if 
the coot process still exists, and note its process id ("pid"). If it does, 
remove it with "kill -9 ". 
Or does the window system crash? This would be a bug of the latter.
Or does (the crashed) coot still take input focus, with the effect that you 
cannot use your mouse to activate another window? In that case, try "Alt-tab" 
to switch window focus.
Or can you not even type in another window? For such cases, it pays off to set 
up the machine for the "Alt-SysRq"commands; see 
https://en.wikipedia.org/wiki/Magic_SysRq_key . These can be used to trigger a 
reboot. On Linux I see rarely a need to reset a machine with the power button. 

HTH,
Kay

On Mon, 15 Jul 2019 05:24:38 +, Peat, Tom (Manufacturing, Parkville) 
 wrote:

>Hello again, 
>
>To be more specific- sometimes when Coot crashes, I can just restart Coot. 
>Sometimes it locks my whole machine (maybe 30% of the time) and I need to 
>reboot. 
>The former is just a small pain, the latter is a true pain and I prefer 
>software not to crash the machine in such an untidy way. 
>
...
>
>I'm currently using Ubuntu 18.04.2 LTS and I think I'm reasonably up to date 
>wrt updates... 
>



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