Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Rezaul Karim]

Hi Devbrat,Have you tried indexing using XDS multi-lattice processing? It is a very useful indexing process for multi-lattice and/or 2nd lattice interference with the major one. Best,Rezaul Karim, Ph.D.Structural Biology ScientistNurix Therapeutics Inc.Sent from my iPhoneOn Nov 15, 2023, at 6:22 PM, Devbrat Kumar  wrote:Dear Prof JohnThank you for your valuable time and insight. I will do as you have suggested.Warm Regards-Devbrat Kumar On Wed, Nov 15, 2023 at 11:28 PM John Bacik  wrote:
Hi Devbrat, here are a couple of other things to try:- When screening crystals use rastering to find regions of the sample where multiple lattices may be less problematic. If multiple lattices are observed, often regions on the crystal(s) close to the edge will not be as affected by twinning/multiple lattices. Also try using fine slicing if you are not already.- Try using AlphaFold to generate a model for the MR template.All the best,John





On Wednesday, November 15, 2023 at 06:10:06 AM CST, Phil Evans  wrote:



Is the space group really P2? P21 is MUCH more commonPhil> On 14 Nov 2023, at 15:55, Devbrat Kumar  wrote:> > sed data were integrated with the data reduction tool AIMLESS in the CCP4i2 suite.To unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/




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



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



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

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Devbrat Kumar]

Dear Prof John

Thank you for your valuable time and insight. I will do as you have
suggested.

*Warm Regards-*
*Devbrat Kumar*





On Wed, Nov 15, 2023 at 11:28 PM John Bacik <
b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> wrote:

>
> Hi Devbrat, here are a couple of other things to try:
>
> - When screening crystals use rastering to find regions of the sample
> where multiple lattices may be less problematic. If multiple lattices are
> observed, often regions on the crystal(s) close to the edge will not be as
> affected by twinning/multiple lattices. Also try using fine slicing if you
> are not already.
>
> - Try using AlphaFold to generate a model for the MR template.
>
> All the best,
> John
>
> On Wednesday, November 15, 2023 at 06:10:06 AM CST, Phil Evans <
> p...@mrc-lmb.cam.ac.uk> wrote:
>
>
> Is the space group really P2? P21 is MUCH more common
> Phil
>
> > On 14 Nov 2023, at 15:55, Devbrat Kumar  wrote:
> >
> > sed data were integrated with the data reduction tool AIMLESS in the
> CCP4i2 suite.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Devbrat Kumar]

Dear Prof Gerard

Thank you for your in-depth analysis of the possibilities I am facing. The
image slicing was at 0.1 degrees.

*Warm Regards-*
*Devbrat Kumar*





On Wed, Nov 15, 2023 at 5:21 PM Gerard Bricogne 
wrote:

> Dear Devbrat,
>
>  With the unit-cell geometry you have, namely a very long axis and two
> much shorter ones, you have to be exceedingly careful about how the data
> are
> collected, and in particular about the crystal orientation and image width.
>
>  If the long axis can be brought close to being parallel to the
> rotation
> axis - either because the crystal morphology tends to make this happen or
> (better) because you can use a multi-axis goniometer to orient it that way
> -
> the images will have rows of closely-spaced spots that should be resolvable
> if the detector is placed far enough. If on the other hand the long axis is
> at a large angle to the rotation axis, there will be image ranges where
> that
> axis gets close to being parallel to the beam, so that the separation of
> reflections along that long axis (in fact, along the short reciprocal axis)
> will depends on their angular distance. Unless the image width is small
> enough, there will be overlap of the spots for consecutive reflections
> along
> that short reciprocal axis. Indexing diagnostics may then give an
> impression
> that there is more than one lattice, but most of all, because two distinct
> reflexions may overlap into a single spot, many integrated intensities will
> be corrupted.
>
>  Perhaps this is not the case, but out of curiosity: what is the
> angular
> width of your images?
>
>
>  With best wishes,
>
>   Gerard.
>
> --
> On Tue, Nov 14, 2023 at 09:25:30PM +0530, Devbrat Kumar wrote:
> > Hello everyone,
> >
> > The issue with the crystal is its multi-lattice nature; even the
> truncated
> > protein, which has been crystallized, exhibits multi-lattice
> > characteristics (detectable only after XRD).
> >
> > I have multiple native and selenium datasets with similar unit cell
> > parameters. (One axis is excessively long.) The XRD images were processed
> > using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> > 27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data
> were
> > integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> > CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> > suggested the presence of monomer NCS with a solvent content of 63.6%.
> The
> > FA estimation and substructure detection were performed by SHELXC, which
> > detected a very weak signal below 3.4 Å. Substructure determination was
> > carried out using SHELXD, yielding a maximum figure of merit of 27.8
> after
> > 640 trials and suggesting 11 atoms in the substructure with an occupancy
> of
> > at least 25%. Phasing and substructure refinement were conducted using
> the
> > BP3 program, resulting in an FOM of 0.2. During hand determination, the
> > programs suggested combined DM (density modification) FOM and phasing CLD
> > score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> > choose the hand because the value is less than the threshold. Density
> > modification with Fourier recycling suggests that the final FOM for hand
> > one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives
> the
> > R factor and Rfree factor as 0.4262 and 0.4912.
> >
> > One of the MR templates (model with balbes) works(For MR, Identity with
> the
> > PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> > Angstrom cut-off (the total resolution in the dataset is 2 Angstrom).
> The R
> > & Rfree is not decreasing for the dataset. I have played with detector
> > distances for spot resolution, but at one pHi the spots have merged as a
> > single spot, while at 90 degrees will give us the streak of spots.
> >
> > Looking forward to hearing from you regarding dataset processing ideas
> for
> > multi-lattice crystals(Native & Se dataset) and structure solution
> strategy.
> >
> > Thank you.
> > Regards
> > Devbrat
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Devbrat Kumar]

Dear Professor,

Thank you for your valuable suggestions.

I have attempted to investigate the NCS operator, but it seems to be a
monomer. Nevertheless, I will reconsider your suggestion regarding this
matter.

I employed the concept of using high-resolution data (2 Angstroms) without
cutoff for model building and refinement cycling, along with phases from MR
(2.7 Angstroms). I will revisit this process.

I will follow your advice for the peak search. If I cannot find any leads,
I hope to seek your guidance.

Thank you again for your support.
*Warm Regards-*
*Devbrat Kumar*





On Wed, Nov 15, 2023 at 4:38 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> You seem pretty near to having solved your structure!
> Ignoring the data problems..
>
> Extra steps I might have used.
> 1) Self rotation function. (in CCP4I2 the task is under data analysis ..)
> Does it suggest a NCS operator?
> If so is this a two fold? which might mean you have a dimer..
>
>
> 2) Now you have a reasonable R factor try extending the resolution. the
> refinement program will weight down the high resolution less reliable data
> but the extra information might marginally improve the maps.
>
> 3) Use the calculated phases to run an anomalous map - REFMAC will produce
> the appropriate coefficients and you can display the map in COOT.
> Do a peaksearch and you should of course see the sites SHELX found..
> But sometimes you get peaks over S atoms and that makes you pretty
> confident that the sequence there is correct.
>
>
>
> On Wed, 15 Nov 2023 at 10:42, Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> Hello Devbrat,
>>
>> your project is difficult and there is no magic bullet to solve its
>> problems. Your approach is good because it always pays off to process
>> the data carefully.
>> In this respect, let me make a few comments.
>> 1) you don't say why you call the diffraction patterns "multi-lattice".
>> What exactly do you mean by that? Non-merohedral
>> twinning? How many lattices superimposed and visible on all frames? Can
>> they be separately indexed by XDS
>> (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)?
>> 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling.
>> 3) what do you mean by "monomer NCS"? NCS implies two or more copies of
>> the same molecule in the asymmetric unit.
>> These copies often form dimers, trimers, tetramers, ... by making
>> more-or-less strong and specific interactions.
>> 4) you've advanced amazingly far and it sounds to me that with a
>> combination of your refined MR model with the SAD data you
>> should be able to improve your solution. Look up the MR-SAD pipeline (for
>> SAD after MR and for model rebuilding using anomalous
>> data) of Crank2.
>>
>> If you want me to take a look at your raw data, upload the best datasets
>> (native and SeMet) to a cloud service and send me the link.
>>
>> Good luck,
>> Kay
>>
>> On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar 
>> wrote:
>>
>> >Hello everyone,
>> >
>> >The issue with the crystal is its multi-lattice nature; even the
>> truncated
>> >protein, which has been crystallized, exhibits multi-lattice
>> >characteristics (detectable only after XRD).
>> >
>> >I have multiple native and selenium datasets with similar unit cell
>> >parameters. (One axis is excessively long.) The XRD images were processed
>> >using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
>> >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data
>> were
>> >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
>> >CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
>> >suggested the presence of monomer NCS with a solvent content of 63.6%.
>> The
>> >FA estimation and substructure detection were performed by SHELXC, which
>> >detected a very weak signal below 3.4 Å. Substructure determination was
>> >carried out using SHELXD, yielding a maximum figure of merit of 27.8
>> after
>> >640 trials and suggesting 11 atoms in the substructure with an occupancy
>> of
>> >at least 25%. Phasing and substructure refinement were conducted using
>> the
>> >BP3 program, resulting in an FOM of 0.2. During hand determination, the
>> >programs suggested combined DM (density modification) FOM and phasing CLD
>> >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
>> >choose the hand because the value is less than the threshold. Density
>> >modification with Fourier recycling suggests that the final FOM for hand
>> >one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives
>> the
>> >R factor and Rfree factor as 0.4262 and 0.4912.
>> >
>> >One of the MR templates (model with balbes) works(For MR, Identity with
>> the
>> >PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
>> >Angstrom cut-off (the total resolution in the dataset is 2 Angstrom).
>> The R
>> >& Rfree is not decreasing for the dataset. I have played 

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Devbrat Kumar]

Hello Professor Kay

Thank you for your in-depth and valuable suggestions.

1. I used to observe multiple spots at one Phi, and at 90 degrees, I would
find a streak of spots. The crystal used to be spade-shaped. The spots are
visible in a count of 8 (matching the total number of crystal lattices).
2. I tried MR-SAD, but couldn't find the selenium substructure at
the Sulpher position of the sequence.
3. I will follow your suggestion to read about XDS  and conduct the
integration using XDS.
4. If I do not find any leads, I will email you the dataset.

*Warm Regards-*
*Devbrat *



On Wed, Nov 15, 2023 at 4:12 PM Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> Hello Devbrat,
>
> your project is difficult and there is no magic bullet to solve its
> problems. Your approach is good because it always pays off to process
> the data carefully.
> In this respect, let me make a few comments.
> 1) you don't say why you call the diffraction patterns "multi-lattice".
> What exactly do you mean by that? Non-merohedral
> twinning? How many lattices superimposed and visible on all frames? Can
> they be separately indexed by XDS
> (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)?
> 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling.
> 3) what do you mean by "monomer NCS"? NCS implies two or more copies of
> the same molecule in the asymmetric unit.
> These copies often form dimers, trimers, tetramers, ... by making
> more-or-less strong and specific interactions.
> 4) you've advanced amazingly far and it sounds to me that with a
> combination of your refined MR model with the SAD data you
> should be able to improve your solution. Look up the MR-SAD pipeline (for
> SAD after MR and for model rebuilding using anomalous
> data) of Crank2.
>
> If you want me to take a look at your raw data, upload the best datasets
> (native and SeMet) to a cloud service and send me the link.
>
> Good luck,
> Kay
>
> On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar 
> wrote:
>
> >Hello everyone,
> >
> >The issue with the crystal is its multi-lattice nature; even the truncated
> >protein, which has been crystallized, exhibits multi-lattice
> >characteristics (detectable only after XRD).
> >
> >I have multiple native and selenium datasets with similar unit cell
> >parameters. (One axis is excessively long.) The XRD images were processed
> >using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data
> were
> >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> >CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> >suggested the presence of monomer NCS with a solvent content of 63.6%. The
> >FA estimation and substructure detection were performed by SHELXC, which
> >detected a very weak signal below 3.4 Å. Substructure determination was
> >carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
> >640 trials and suggesting 11 atoms in the substructure with an occupancy
> of
> >at least 25%. Phasing and substructure refinement were conducted using the
> >BP3 program, resulting in an FOM of 0.2. During hand determination, the
> >programs suggested combined DM (density modification) FOM and phasing CLD
> >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> >choose the hand because the value is less than the threshold. Density
> >modification with Fourier recycling suggests that the final FOM for hand
> >one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
> >R factor and Rfree factor as 0.4262 and 0.4912.
> >
> >One of the MR templates (model with balbes) works(For MR, Identity with
> the
> >PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> >Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The
> R
> >& Rfree is not decreasing for the dataset. I have played with detector
> >distances for spot resolution, but at one pHi the spots have merged as a
> >single spot, while at 90 degrees will give us the streak of spots.
> >
> >Looking forward to hearing from you regarding dataset processing ideas for
> >multi-lattice crystals(Native & Se dataset) and structure solution
> strategy.
> >
> >Thank you.
> >Regards
> >Devbrat
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of 

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Devbrat Kumar]

Dear Professor Phil

Thank you for highlighting and providing input. Yes, The space group is P21.

*Warm Regards-*
*Devbrat Kumar*





On Wed, Nov 15, 2023 at 5:39 PM Phil Evans  wrote:

> Is the space group really P2? P21 is MUCH more common
> Phil
>
> > On 14 Nov 2023, at 15:55, Devbrat Kumar  wrote:
> >
> > sed data were integrated with the data reduction tool AIMLESS in the
> CCP4i2 suite.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Fwd: Post-Doctoral Position in Integrative structural biology of sarcomeric cytoskeleton in @EMBL Grenoble

[Kristina Djinovic Carugo]

Dear All,


We are recruiting a highly motivated a highly motivated*Post-Doctoral 
Scientist *to join**our teamat EMBL Grenoble, interested in the 
molecular mechanisms underlying the architecture and assembly of muscle 
sarcomeres, particular Z-discs. We use a multidisciplinary approach to 
tackle complex biological problems by combining complementary structural 
biology techniques, computational modelling, and other biochemical and 
biophysical methods. The main focus of this position will be integrative 
structural studies of reconstituted assemblies.


*Your role***

•Taking up and leading a challenging structural biology project

•Designing and performing experimental procedures

•Analysing and interpreting experimental data

•Taking part in regular group meetings, unit seminars and international 
conferences


•Staying up to date with the literature and the latest methodological 
developments relevant to the project


You will embark on an exciting journey to decipher the structures of 
selected reconstituted complexes and macromolecular condensates using an 
integrative structural biology approach, which encompasses molecular 
biophysics characterisation, combined with small angles X-ray 
scattering, macromolecular crystallography, and cryo-electron 
microscopy/tomography, depending on their size and dynamics. As a team 
member, you will play a crucial role in uncovering the detailed 
biophysical and structural principles that regulate complex assembly. 
Joining collaborative efforts, you will contribute to the generation of 
a 4D multiscale integrative molecular model.


*You have*

 * PhD degree in molecular biology or a related field

·Extensive experience in molecular cloning, expression, and purification 
of protein complexes is essential.


·Prior knowledge of crystallography and/or single-particle electron 
microscopy is needed.


·Track record of writing papers as evidenced by publications or 
submitted manuscripts.


 * Independence and ability to solve problems
 * Good time management and pro-active attitude
 * Excellent communication skills and ability to work in a team

*You might also have*

·Previous experience in complementary structural biology methods (e.g. 
SAXS), molecular and cell biophysics approaches and cell culture will be 
considered an advantage.


·Experience with cryo-electron tomography.

·Experience with working in multidisciplinary research teams.

**

*Why join us*

The European Molecular Biology Laboratory (EMBL) is one of the 
highest-ranked scientific research organisations in the worldaimed to 
explore the secrets of life. The Headquarters Laboratory is located in 
Heidelberg (Germany) and further Units are situated in Grenoble 
(France), Hamburg (Germany), Hinxton (UK), Rome (Italy) and Barcelona 
(Spain).


EMBL Grenoble shares the European Photon and Neutron Science (EPN) 
Campus with the European Synchrotron Radiation Facility (ESRF), the 
/Institut Laue Langevin /(ILL) and the French national /Institut de 
Biologie Structurale /(IBS), whose complementary and integrated 
facilities provide a vibrant environment for structural biologists.



EMBL Grenoble enables access to state-of-the-art structural biology 
technologies with the local EM facility equipped with the T12 screening 
microscope and a 200kV Glacios microscope with Falcon4i/SelectrisX 
detector. Additionally, we have a regular access to five 300kV 
microscopes located locally at ESRF and at EMBL Heidelberg. Other 
facilities include high-performance computing cluster, dedicated GPU 
workstations for data processing and deep learning applications, ESRF 
synchrotron X-ray beamlines, high-field NMR at the IBS as well as 
mammalian and insect cell facilities, biophysical platform, confocal 
microscopy and high-throughput crystallization facilities.


EMBL is an inclusive, equal opportunity employer offering attractive 
conditions and benefits appropriate to an international research 
organisation with a very collegial and family friendly working 
environment. The remuneration package comprises a competitive salary, a 
comprehensive pension scheme, medical, educational and other social 
benefits, as well as financial support for relocation and installation, 
including your family.


*What else you need to know*

We are Europe’s flagship research laboratory for the life sciences – an 
intergovernmental organisation performing scientific research in 
disciplines including molecular biology, physics, chemistry and computer 
science. We are an international, innovative and interdisciplinary 
laboratory with more than 1900 employees from many nations, operating 
across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, 
Hamburg, Grenoble and Rome.


Our mission is to offer vital services in training scientists, students 
and visitors at all levels; to develop new instruments and methods in 
the life sciences and actively engage in technology transfer activities, 
and to integrate European 

[ccp4bb] PDRA positions: CAZyme structural biology/biochemistry

[Alan Cartmell]

Dear All,

I have 3 PDRA positions available in my group at York for
Biochemists/Structural biologists interested in CAZymes (sulfatases,
lyases, GHs) associated with the HGM:

https://jobs.york.ac.uk/vacancy/structural-biologist-research-associate-543041.html

https://jobs.york.ac.uk/vacancy/biochemist-research-associate-543032.html

If you know a good candidate please pass this email on to them as well as
any relevant people in your structural biology departments.

Best regards,

Alan

Dr Alan Cartmell
Department of Biology,
University of York, Wentworth Way,
York, YO10 5DD.



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[John Bacik]

 
Hi Devbrat, here are a couple of other things to try:
- When screening crystals use rastering to find regions of the sample where 
multiple lattices may be less problematic. If multiple lattices are observed, 
often regions on the crystal(s) close to the edge will not be as affected by 
twinning/multiple lattices. Also try using fine slicing if you are not already.
- Try using AlphaFold to generate a model for the MR template.
All the best,John
On Wednesday, November 15, 2023 at 06:10:06 AM CST, Phil Evans 
 wrote:  
 
 Is the space group really P2? P21 is MUCH more common
Phil

> On 14 Nov 2023, at 15:55, Devbrat Kumar  wrote:
> 
> sed data were integrated with the data reduction tool AIMLESS in the CCP4i2 
> suite.



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/
  

Re: [ccp4bb] Problem with ligand identification

[Matthew Feasey (PGR)]

Hi Rafal,

Have you tried automated ligand finding tools e.g. Checkmyblob? 
https://checkmyblob.bioreproducibility.org/server/

Cheers,
Matt


From: CCP4 bulletin board  on behalf of Rafal Dolot 

Sent: 15 November 2023 14:00
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Problem with ligand identification


⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Hello everyone,

I need help identifying the ligand I found on the electron density maps. I have 
soaked ribonuclease A crystals with the phosphorothioate dinucleotide. The 
diffraction experiment was performed on a home source (Cu). When I analysed the 
data, I found both the dinucleotide and this strange object near two 
histidines. Since I did not find anything similar on the list of possibly used 
compounds, it could be a contamination but still unknown to me. I tried 
modelling glycolic acid (GOA) here, but it looks like the electron density 
around the hydroxyl group is greater. Maybe a sulphur containing compound - 
MCR? Do you have any other idea?

Regards
Rafal

--
--
Rafal Dolot, Ph.D.
Polish Academy of Sciences
Centre of Molecular and Macromolecular Studies
Division of Bioorganic Chemistry
Macromolecular Crystallography Laboratory
Sienkiewicza 112
90-363 Lodz, Poland
Phone: +48(42)6803325
Cell:  +48 502897781
--

-
Administratorem Pani/Pana danych osobowych jest Centrum Badań Molekularnych i 
Makromolekularnych Polskiej Akademii Nauk, ul. Sienkiewicza 112, 90-363 Łódź. 
Przetwarzamy dane osobowe w celu wykonywania działalności Instytutu, w 
szczególności w zakresie prowadzenia badań naukowych w zakresie nauk 
chemicznych, fizycznych i technicznych oraz upowszechniania wyników tych badań 
czy też wykonywania umów w zakresie realizowania projektów badawczych, praktyk, 
staży, konferencji naukowych, stypendiów, przeprowadzanych przewodów 
doktorskich/habilitacyjnych. Przechowujemy dane przez okres niezbędny do 
realizacji ww. celów, dochodzenia lub obrony roszczeń oraz przez czas wymagany 
przepisami prawa. Ma Pani/Pan prawo dostępu do informacji o przetwarzaniu 
danych, prawo żądania ich sprostowania, usunięcia, prawo do sprzeciwu wobec 
przetwarzania, prawo do przenoszenia danych oraz prawo wniesienia skargi do 
Prezesa Urzędu Ochrony Danych Osobowych. Decyzji wobec Pani/Pana danych 
osobowych nie podejmujemy w sposób zautomatyzowany, w tym nie dokonujemy 
profilowania. Szczegółowe informacje o ochronie danych osobowych zgodnie z RODO 
znajdują się na stronie www.cbmm.lodz.pl. W sprawach 
ochrony danych osobowych prosimy o kontakt z naszym Inspektorem Ochrony Danych 
pod adresem: e-mail: i...@cbmm.lodz.pl.
-
NOTICE: This message and any attachment are confidential.
If you are not the intended recipient, please notify the sender and delete this 
e-mail and any copies.
Incoming e-mails are not accepted as legally binding unless legal validity is 
confirmed by us by reply-mail.
An automatically generated acknowledgement of receipt cannot be considered as 
confirmation of legal validity.
-



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



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Problem with ligand identification

[FULVIO SACCOCCIA]

DTT?

Inviato da Outlook per Android

From: CCP4 bulletin board  on behalf of Rafal Dolot 

Sent: Wednesday, November 15, 2023 3:00:50 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Problem with ligand identification

Hello everyone,

I need help identifying the ligand I found on the electron density maps. I have 
soaked ribonuclease A crystals with the phosphorothioate dinucleotide. The 
diffraction experiment was performed on a home source (Cu). When I analysed the 
data, I found both the dinucleotide and this strange object near two 
histidines. Since I did not find anything similar on the list of possibly used 
compounds, it could be a contamination but still unknown to me. I tried 
modelling glycolic acid (GOA) here, but it looks like the electron density 
around the hydroxyl group is greater. Maybe a sulphur containing compound - 
MCR? Do you have any other idea?

Regards
Rafal

--
--
Rafal Dolot, Ph.D.
Polish Academy of Sciences
Centre of Molecular and Macromolecular Studies
Division of Bioorganic Chemistry
Macromolecular Crystallography Laboratory
Sienkiewicza 112
90-363 Lodz, Poland
Phone: +48(42)6803325
Cell:  +48 502897781
--

-
Administratorem Pani/Pana danych osobowych jest Centrum Badań Molekularnych i 
Makromolekularnych Polskiej Akademii Nauk, ul. Sienkiewicza 112, 90-363 Łódź. 
Przetwarzamy dane osobowe w celu wykonywania działalności Instytutu, w 
szczególności w zakresie prowadzenia badań naukowych w zakresie nauk 
chemicznych, fizycznych i technicznych oraz upowszechniania wyników tych badań 
czy też wykonywania umów w zakresie realizowania projektów badawczych, praktyk, 
staży, konferencji naukowych, stypendiów, przeprowadzanych przewodów 
doktorskich/habilitacyjnych. Przechowujemy dane przez okres niezbędny do 
realizacji ww. celów, dochodzenia lub obrony roszczeń oraz przez czas wymagany 
przepisami prawa. Ma Pani/Pan prawo dostępu do informacji o przetwarzaniu 
danych, prawo żądania ich sprostowania, usunięcia, prawo do sprzeciwu wobec 
przetwarzania, prawo do przenoszenia danych oraz prawo wniesienia skargi do 
Prezesa Urzędu Ochrony Danych Osobowych. Decyzji wobec Pani/Pana danych 
osobowych nie podejmujemy w sposób zautomatyzowany, w tym nie dokonujemy 
profilowania. Szczegółowe informacje o ochronie danych osobowych zgodnie z RODO 
znajdują się na stronie www.cbmm.lodz.pl. W sprawach 
ochrony danych osobowych prosimy o kontakt z naszym Inspektorem Ochrony Danych 
pod adresem: e-mail: i...@cbmm.lodz.pl.
-
NOTICE: This message and any attachment are confidential.
If you are not the intended recipient, please notify the sender and delete this 
e-mail and any copies.
Incoming e-mails are not accepted as legally binding unless legal validity is 
confirmed by us by reply-mail.
An automatically generated acknowledgement of receipt cannot be considered as 
confirmation of legal validity.
-



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



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Problem with ligand identification

[Pallan, Pradeep S]

Hi Rafal,
Did you try oxalic acid? The density being close to His,
and with the shape, give it a try!

Good luck!
Pradeep Pallan



From: CCP4 bulletin board  on behalf of Rafal Dolot 

Sent: Wednesday, November 15, 2023 8:00 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Problem with ligand identification

Some people who received this message don't often get email from 
b44974de149e-dmarc-requ...@jiscmail.ac.uk. Learn why this is 
important
Hello everyone,

I need help identifying the ligand I found on the electron density maps. I have 
soaked ribonuclease A crystals with the phosphorothioate dinucleotide. The 
diffraction experiment was performed on a home source (Cu). When I analysed the 
data, I found both the dinucleotide and this strange object near two 
histidines. Since I did not find anything similar on the list of possibly used 
compounds, it could be a contamination but still unknown to me. I tried 
modelling glycolic acid (GOA) here, but it looks like the electron density 
around the hydroxyl group is greater. Maybe a sulphur containing compound - 
MCR? Do you have any other idea?

Regards
Rafal

--
--
Rafal Dolot, Ph.D.
Polish Academy of Sciences
Centre of Molecular and Macromolecular Studies
Division of Bioorganic Chemistry
Macromolecular Crystallography Laboratory
Sienkiewicza 112
90-363 Lodz, Poland
Phone: +48(42)6803325
Cell:  +48 502897781
--

-
Administratorem Pani/Pana danych osobowych jest Centrum Badań Molekularnych i 
Makromolekularnych Polskiej Akademii Nauk, ul. Sienkiewicza 112, 90-363 Łódź. 
Przetwarzamy dane osobowe w celu wykonywania działalności Instytutu, w 
szczególności w zakresie prowadzenia badań naukowych w zakresie nauk 
chemicznych, fizycznych i technicznych oraz upowszechniania wyników tych badań 
czy też wykonywania umów w zakresie realizowania projektów badawczych, praktyk, 
staży, konferencji naukowych, stypendiów, przeprowadzanych przewodów 
doktorskich/habilitacyjnych. Przechowujemy dane przez okres niezbędny do 
realizacji ww. celów, dochodzenia lub obrony roszczeń oraz przez czas wymagany 
przepisami prawa. Ma Pani/Pan prawo dostępu do informacji o przetwarzaniu 
danych, prawo żądania ich sprostowania, usunięcia, prawo do sprzeciwu wobec 
przetwarzania, prawo do przenoszenia danych oraz prawo wniesienia skargi do 
Prezesa Urzędu Ochrony Danych Osobowych. Decyzji wobec Pani/Pana danych 
osobowych nie podejmujemy w sposób zautomatyzowany, w tym nie dokonujemy 
profilowania. Szczegółowe informacje o ochronie danych osobowych zgodnie z RODO 
znajdują się na stronie www.cbmm.lodz.pl. W sprawach 
ochrony danych osobowych prosimy o kontakt z naszym Inspektorem Ochrony Danych 
pod adresem: e-mail: i...@cbmm.lodz.pl.
-
NOTICE: This message and any attachment are confidential.
If you are not the intended recipient, please notify the sender and delete this 
e-mail and any copies.
Incoming e-mails are not accepted as legally binding unless legal validity is 
confirmed by us by reply-mail.
An automatically generated acknowledgement of receipt cannot be considered as 
confirmation of legal validity.
-



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



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Problem with ligand identification

[Jon Cooper]

How does it look with gl gl... glycerol fitted ;-?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 15 Nov 2023, 14:00, Rafal Dolot wrote:

> Hello everyone,
>
> I need help identifying the ligand I found on the electron density maps. I 
> have soaked ribonuclease A crystals with the phosphorothioate dinucleotide. 
> The diffraction experiment was performed on a home source (Cu). When I 
> analysed the data, I found both the dinucleotide and this strange object near 
> two histidines. Since I did not find anything similar on the list of possibly 
> used compounds, it could be a contamination but still unknown to me. I tried 
> modelling glycolic acid (GOA) here, but it looks like the electron density 
> around the hydroxyl group is greater. Maybe a sulphur containing compound - 
> MCR? Do you have any other idea?
>
> RegardsRafal
> --
>
> --
> Rafal Dolot, Ph.D.
> Polish Academy of Sciences
> Centre of Molecular and Macromolecular Studies
> Division of Bioorganic Chemistry
> Macromolecular Crystallography Laboratory
> Sienkiewicza 112
> 90-363 Lodz, Poland
> Phone: +48(42)6803325
> Cell: +48 502897781
> --
>
> -
> Administratorem Pani/Pana danych osobowych jest Centrum Badań Molekularnych i 
> Makromolekularnych Polskiej Akademii Nauk, ul. Sienkiewicza 112, 90-363 Łódź. 
> Przetwarzamy dane osobowe w celu wykonywania działalności Instytutu, w 
> szczególności w zakresie prowadzenia badań naukowych w zakresie nauk 
> chemicznych, fizycznych i technicznych oraz upowszechniania wyników tych 
> badań czy też wykonywania umów w zakresie realizowania projektów badawczych, 
> praktyk, staży, konferencji naukowych, stypendiów, przeprowadzanych przewodów 
> doktorskich/habilitacyjnych. Przechowujemy dane przez okres niezbędny do 
> realizacji ww. celów, dochodzenia lub obrony roszczeń oraz przez czas 
> wymagany przepisami prawa. Ma Pani/Pan prawo dostępu do informacji o 
> przetwarzaniu danych, prawo żądania ich sprostowania, usunięcia, prawo do 
> sprzeciwu wobec przetwarzania, prawo do przenoszenia danych oraz prawo 
> wniesienia skargi do Prezesa Urzędu Ochrony Danych Osobowych. Decyzji wobec 
> Pani/Pana danych osobowych nie podejmujemy w sposób zautomatyzowany, w tym 
> nie dokonujemy profilowania. Szczegółowe informacje o ochronie danych 
> osobowych zgodnie z RODO znajdują się na stronie www.cbmm.lodz.pl. W sprawach 
> ochrony danych osobowych prosimy o kontakt z naszym Inspektorem Ochrony 
> Danych pod adresem: e-mail: i...@cbmm.lodz.pl.
> -
> NOTICE: This message and any attachment are confidential.
> If you are not the intended recipient, please notify the sender and delete 
> this e-mail and any copies.
> Incoming e-mails are not accepted as legally binding unless legal validity is 
> confirmed by us by reply-mail.
> An automatically generated acknowledgement of receipt cannot be considered as 
> confirmation of legal validity.
> -
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Two positions available at EMBL Grenoble

[Jose A. MARQUEZ]

Dear All,

We have two job openings at EMBL Grenoble

Full-Stack Developer

https://www.embl.org/jobs/position/GR00219

Research Technician

https://www.embl.org/jobs/position/GR00220

Best wishes

_
Jose A. Marquez, Senior Scientist
Head of the Crystallization Facility
European Molecular Biology Laboratory, Grenoble.
Delivery address: EMBL, 71, Avenue des Martyrs
38000 Grenoble, France
Postal address: EMBL, 71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99

https://www.embl.org/groups/marquez/  
https://www.embl.org/services-facilities/grenoble/high-throughput-crystallisation/  
https://htxlab.embl.org/  
_




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Phil Evans]

Is the space group really P2? P21 is MUCH more common
Phil

> On 14 Nov 2023, at 15:55, Devbrat Kumar  wrote:
> 
> sed data were integrated with the data reduction tool AIMLESS in the CCP4i2 
> suite.



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Gerard Bricogne]

Dear Devbrat,

 With the unit-cell geometry you have, namely a very long axis and two
much shorter ones, you have to be exceedingly careful about how the data are
collected, and in particular about the crystal orientation and image width.

 If the long axis can be brought close to being parallel to the rotation
axis - either because the crystal morphology tends to make this happen or
(better) because you can use a multi-axis goniometer to orient it that way -
the images will have rows of closely-spaced spots that should be resolvable
if the detector is placed far enough. If on the other hand the long axis is
at a large angle to the rotation axis, there will be image ranges where that
axis gets close to being parallel to the beam, so that the separation of
reflections along that long axis (in fact, along the short reciprocal axis)
will depends on their angular distance. Unless the image width is small
enough, there will be overlap of the spots for consecutive reflections along
that short reciprocal axis. Indexing diagnostics may then give an impression
that there is more than one lattice, but most of all, because two distinct
reflexions may overlap into a single spot, many integrated intensities will
be corrupted. 

 Perhaps this is not the case, but out of curiosity: what is the angular
width of your images?


 With best wishes,

  Gerard.

--
On Tue, Nov 14, 2023 at 09:25:30PM +0530, Devbrat Kumar wrote:
> Hello everyone,
> 
> The issue with the crystal is its multi-lattice nature; even the truncated
> protein, which has been crystallized, exhibits multi-lattice
> characteristics (detectable only after XRD).
> 
> I have multiple native and selenium datasets with similar unit cell
> parameters. (One axis is excessively long.) The XRD images were processed
> using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> 27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data were
> integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> suggested the presence of monomer NCS with a solvent content of 63.6%. The
> FA estimation and substructure detection were performed by SHELXC, which
> detected a very weak signal below 3.4 Å. Substructure determination was
> carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
> 640 trials and suggesting 11 atoms in the substructure with an occupancy of
> at least 25%. Phasing and substructure refinement were conducted using the
> BP3 program, resulting in an FOM of 0.2. During hand determination, the
> programs suggested combined DM (density modification) FOM and phasing CLD
> score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> choose the hand because the value is less than the threshold. Density
> modification with Fourier recycling suggests that the final FOM for hand
> one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
> R factor and Rfree factor as 0.4262 and 0.4912.
> 
> One of the MR templates (model with balbes) works(For MR, Identity with the
> PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The R
> & Rfree is not decreasing for the dataset. I have played with detector
> distances for spot resolution, but at one pHi the spots have merged as a
> single spot, while at 90 degrees will give us the streak of spots.
> 
> Looking forward to hearing from you regarding dataset processing ideas for
> multi-lattice crystals(Native & Se dataset) and structure solution strategy.
> 
> Thank you.
> Regards
> Devbrat
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Eleanor Dodson]

You seem pretty near to having solved your structure!
Ignoring the data problems..

Extra steps I might have used.
1) Self rotation function. (in CCP4I2 the task is under data analysis ..)
Does it suggest a NCS operator?
If so is this a two fold? which might mean you have a dimer..


2) Now you have a reasonable R factor try extending the resolution. the
refinement program will weight down the high resolution less reliable data
but the extra information might marginally improve the maps.

3) Use the calculated phases to run an anomalous map - REFMAC will produce
the appropriate coefficients and you can display the map in COOT.
Do a peaksearch and you should of course see the sites SHELX found..
But sometimes you get peaks over S atoms and that makes you pretty
confident that the sequence there is correct.



On Wed, 15 Nov 2023 at 10:42, Kay Diederichs 
wrote:

> Hello Devbrat,
>
> your project is difficult and there is no magic bullet to solve its
> problems. Your approach is good because it always pays off to process
> the data carefully.
> In this respect, let me make a few comments.
> 1) you don't say why you call the diffraction patterns "multi-lattice".
> What exactly do you mean by that? Non-merohedral
> twinning? How many lattices superimposed and visible on all frames? Can
> they be separately indexed by XDS
> (see https://wiki.uni-konstanz.de/xds/index.php/Indexing)?
> 2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling.
> 3) what do you mean by "monomer NCS"? NCS implies two or more copies of
> the same molecule in the asymmetric unit.
> These copies often form dimers, trimers, tetramers, ... by making
> more-or-less strong and specific interactions.
> 4) you've advanced amazingly far and it sounds to me that with a
> combination of your refined MR model with the SAD data you
> should be able to improve your solution. Look up the MR-SAD pipeline (for
> SAD after MR and for model rebuilding using anomalous
> data) of Crank2.
>
> If you want me to take a look at your raw data, upload the best datasets
> (native and SeMet) to a cloud service and send me the link.
>
> Good luck,
> Kay
>
> On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar 
> wrote:
>
> >Hello everyone,
> >
> >The issue with the crystal is its multi-lattice nature; even the truncated
> >protein, which has been crystallized, exhibits multi-lattice
> >characteristics (detectable only after XRD).
> >
> >I have multiple native and selenium datasets with similar unit cell
> >parameters. (One axis is excessively long.) The XRD images were processed
> >using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
> >27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data
> were
> >integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
> >CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
> >suggested the presence of monomer NCS with a solvent content of 63.6%. The
> >FA estimation and substructure detection were performed by SHELXC, which
> >detected a very weak signal below 3.4 Å. Substructure determination was
> >carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
> >640 trials and suggesting 11 atoms in the substructure with an occupancy
> of
> >at least 25%. Phasing and substructure refinement were conducted using the
> >BP3 program, resulting in an FOM of 0.2. During hand determination, the
> >programs suggested combined DM (density modification) FOM and phasing CLD
> >score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
> >choose the hand because the value is less than the threshold. Density
> >modification with Fourier recycling suggests that the final FOM for hand
> >one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
> >R factor and Rfree factor as 0.4262 and 0.4912.
> >
> >One of the MR templates (model with balbes) works(For MR, Identity with
> the
> >PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
> >Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The
> R
> >& Rfree is not decreasing for the dataset. I have played with detector
> >distances for spot resolution, but at one pHi the spots have merged as a
> >single spot, while at 90 degrees will give us the streak of spots.
> >
> >Looking forward to hearing from you regarding dataset processing ideas for
> >multi-lattice crystals(Native & Se dataset) and structure solution
> strategy.
> >
> >Thank you.
> >Regards
> >Devbrat
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
> 

Re: [ccp4bb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!

[Karen McIntyre - STFC UKRI]

Dear all,

Registration is open for the 2024 CCP4 study weekend entitled "Decision making 
in MX - how to be a productive structural biologist".

Important Key Dates:
* Early bird registration final date: 19 November 2023;
* We have assisted places available for students registering during early bird 
period i.e. now until 19 November - which cover the cost of registration plus 
one night accommodation meaning students only pay for aqdditional nights 
accommodation @ £63 per night;
* Registration for in-person delegates closes 4 December 2023 (or earlier if 
in-person places sell out although you will be able to join the in-person 
waitlist).

This year we are focusing on decision-making in macromolecular crystallography: 
when to use what automated tool, how to interpret the output and when you need 
to get your hands dirty instead. The frontiers of crystallography now involve 
massive multi-crystal and multi-dimensional experiments. This means the more 
that you can leave to the automated pipelines, the more you can focus on the 
novel elements of your experiment. Sometimes those automated tools work, and 
sometimes they fail (but have maybe not told you exactly why or how). Sometimes 
they don't even exist. In that case, how can you return to the basics and 
develop new strategies to break down the barriers to publication?

Once again, this year the CCP4 Study Weekend will be held as a hybrid event 
from the 3rd to 5th January 2024, enabling people to choose whether to attend 
in-person or virtually. The in-person event will be held at the East Midlands 
Conference Centre, Nottingham, UK.


We would like to invite you to another iteration of the ever-popular CCP4 Study 
Weekend - to start the year 2024 with a lot of fresh ideas, new insights and 
(hopefully) new friends and contacts to boost. As always it will be an eclectic 
mix of bleeding-edge science, in-depth presentations, discussion panel, 
poster-sessions, hands-on tutorials and plenty of opportunities for social 
interactions including the ceilidh. For full details, programme, logistics and 
registration, please visit the Study Weekend 
website.


Sessions will cover:
Day 1
Diamond MX User Meeting
Session 1:
Key note talk
Discussion panel - "Crystallography is dead - long live Crystallography!"
Day 2
Session 2: Preparation and data collection: Planning and execution of 
diffraction experiment
Session 3: Structure Solution & Model Building (post-AlphaFold)
Session 4: The important final touches: Modelling Subtle / Difficult Structural 
Features
Day 3
Session 5: Weak Signal / Large Datasets: Partial Data and Partial Occupancies
Session 6: Experimental Interactions: Ligands, everywhere, all at once
Session 7: Structural Analysis: Climbing the data mountain



Speakers include:


Ashwin Chari (Max Planck Institute for Multidisciplinary Sciences, GERMANY)
Tristan Croll (Altos Labs, UK)
Ed Daniel (University of Oulu, FINLAND)
Judit Debreczeni (AstraZeneca, UK)
Elke de Zitter (Institut de Biologie Structurale, FRANCE)
Kamel El Omari (Diamond Light Source, UK)
Paul Emsley (UKRI-MRC LMB, UK)
Elspeth Garman (University of Oxford, UK)
Rasmus Fogh (Global Phasing Ltd, UK)
Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA)
Garib Murshudov (UKRI-MRC LMB, UK)
Arwen Pearson (Center for Free-Electron Laser Science - CFEL, GERMANY)
Patrick Reinke (Deutsches Elektronen-Synchrotron, DESY, GERMANY)
Lucy Schofield (University of York, UK)
Oliver Smart (Global Phasing Ltd, UK)
Graeme Winter (Diamond Light Source, UK)
Briony Yorke (University of Leeds, UK)

We hope to see you there!

Scientific Organisers:
  Helen Ginn (Deutsches Elektronen-Synchrotron, DESY, Germany)
  Nick Pearce (Linköping University, Sweden)
  Clemens Vonrhein (Global Phasing Ltd, UK)

Administrative Organisers:
  Karen McIntyre (CCP4, UK)




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

[Kay Diederichs]

Hello Devbrat,

your project is difficult and there is no magic bullet to solve its problems. 
Your approach is good because it always pays off to process 
the data carefully. 
In this respect, let me make a few comments.
1) you don't say why you call the diffraction patterns "multi-lattice". What 
exactly do you mean by that? Non-merohedral 
twinning? How many lattices superimposed and visible on all frames? Can they be 
separately indexed by XDS 
(see https://wiki.uni-konstanz.de/xds/index.php/Indexing)?
2) "XDS processing" _is_ integrating; what AIMLESS does is called scaling.
3) what do you mean by "monomer NCS"? NCS implies two or more copies of the 
same molecule in the asymmetric unit. 
These copies often form dimers, trimers, tetramers, ... by making more-or-less 
strong and specific interactions.
4) you've advanced amazingly far and it sounds to me that with a combination of 
your refined MR model with the SAD data you
should be able to improve your solution. Look up the MR-SAD pipeline (for SAD 
after MR and for model rebuilding using anomalous 
data) of Crank2.

If you want me to take a look at your raw data, upload the best datasets 
(native and SeMet) to a cloud service and send me the link.

Good luck,
Kay

On Tue, 14 Nov 2023 21:25:30 +0530, Devbrat Kumar  
wrote:

>Hello everyone,
>
>The issue with the crystal is its multi-lattice nature; even the truncated
>protein, which has been crystallized, exhibits multi-lattice
>characteristics (detectable only after XRD).
>
>I have multiple native and selenium datasets with similar unit cell
>parameters. (One axis is excessively long.) The XRD images were processed
>using XDS in the P2 spacegroup, with unit cell parameters as follows: a =
>27.75 Å, b = 293.9 Å, c = 34.6 Å, and β = 113°. The XDS-processed data were
>integrated with the data reduction tool AIMLESS in the CCP4i2 suite. In
>CRANK2, the Estimation of Matthews coefficient (Program used: GCX)
>suggested the presence of monomer NCS with a solvent content of 63.6%. The
>FA estimation and substructure detection were performed by SHELXC, which
>detected a very weak signal below 3.4 Å. Substructure determination was
>carried out using SHELXD, yielding a maximum figure of merit of 27.8 after
>640 trials and suggesting 11 atoms in the substructure with an occupancy of
>at least 25%. Phasing and substructure refinement were conducted using the
>BP3 program, resulting in an FOM of 0.2. During hand determination, the
>programs suggested combined DM (density modification) FOM and phasing CLD
>score for hand one as 6.0 and for hand two as 4.783375. The tool didn't
>choose the hand because the value is less than the threshold. Density
>modification with Fourier recycling suggests that the final FOM for hand
>one and hand two is 0.428 and 0.482, respectively, while REFMAC5 gives the
>R factor and Rfree factor as 0.4262 and 0.4912.
>
>One of the MR templates (model with balbes) works(For MR, Identity with the
>PDB template is 21%), but R & Rfree are stuck at 33 & 37 for the 2.7
>Angstrom cut-off (the total resolution in the dataset is 2 Angstrom). The R
>& Rfree is not decreasing for the dataset. I have played with detector
>distances for spot resolution, but at one pHi the spots have merged as a
>single spot, while at 90 degrees will give us the streak of spots.
>
>Looking forward to hearing from you regarding dataset processing ideas for
>multi-lattice crystals(Native & Se dataset) and structure solution strategy.
>
>Thank you.
>Regards
>Devbrat
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
>list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
>https://www.jiscmail.ac.uk/policyandsecurity/
>



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/