Re: [ccp4bb] [xds] how to specify measuring angle

[Johan Hattne]

On 2020-10-09 01:59, Dirk Kostrewa wrote:

Dear Doo Nam Kim,

On 09.10.20 08:43, Doo Nam Kim wrote:
Since I don't know correct value of OSCILLATION_RANGE, I just changed 
to the example value (0.1) from (0.89976, I know it is not a 
positive multiple of 0.0001, but worked for ketone data).


without knowing the correct value for the OSCILLATION_RANGE, data 
processing might run through but produces non-sense results, independent 
of the data processing program you use. So, it is absolutely important 
to know the correct value for the oscillation range per frame.


For these data, the oscillation range should be 0.37 degrees, because 
the rotation rate is 0.09 degrees per second (as per SBGrid reprocessing 
instructions) and the time between successive frames is ~4.1 s (as 
determined by tvips2smv).


I just checked, and this is indeed what's in OSC_RANGE header item, 
assuming you actually used tvips2smv to make the SMV files.


// Cheers; Johan



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Re: [ccp4bb] [xds] how to specify measuring angle

[Jessica Bruhn]

Hi Doo Nam Kim,

If you do not know your OSCILLATION_RANGE, a good guess would be to take
your collection angle range (-60 to +60 or 120 degrees) and divide that by
the number of frames.

Best,
Jessica

On Fri, Oct 9, 2020 at 2:00 AM Dirk Kostrewa <
dirk.kostr...@lrz.uni-muenchen.de> wrote:

> Dear Doo Nam Kim,
>
> On 09.10.20 08:43, Doo Nam Kim wrote:
> > Since I don't know correct value of OSCILLATION_RANGE, I just changed to
> the example value (0.1) from (0.89976, I know it is not a positive
> multiple of 0.0001, but worked for ketone data).
>
> without knowing the correct value for the OSCILLATION_RANGE, data
> processing might run through but produces non-sense results, independent
> of the data processing program you use. So, it is absolutely important
> to know the correct value for the oscillation range per frame.
>
> Cheers,
>
> Dirk.
>
> --
>
> ***
> Dirk Kostrewa
> Gene Center Munich
> Department of Biochemistry, AG Hopfner
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:+49-89-2180-76998
> E-mail: dirk.kostr...@lmu.de
> WWW:www.genzentrum.lmu.de
>  strubio.userweb.mwn.de
> ***
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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>


-- 
Jessica Bruhn, Ph.D
Principal Scientist
NanoImaging Services, Inc.
4940 Carroll Canyon Road, Suite 115
San Diego, CA 92121
Phone #: (888) 675-8261
www.nanoimagingservices.com



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[ccp4bb] ONE WEEK TO APPLY: DLS/CCP4 Data Collection and Structure Solution Workshop, 30 Nov - 11 Dec 2020

[David Waterman]

Dear all,

Please note there is one week left to apply for this year's DLS/CCP4
workshop (details below).

Best wishes
-- David


On Tue, 6 Oct 2020 at 10:03, David Waterman  wrote:

> We are pleased to announce that the 7th joint Diamond-CCP4 Workshop on
> MX data collection and structure solution is open for applications.
>
> Bringing together leading experts in the field of MX to teach best
> practice in data collection and analysis, this course is aimed at PhD
> students, postdocs and early career scientists who have a focus on
> structural biology.
>
> The workshop will take place online via Zoom over the course of two
> full weeks, as well as a preparation day in advance of the workshop.
> It is essential that applicants commit to attending the workshop in
> its entirety. Please note below the workshop days and timings
> involved:
>
> - Preparation day: Monday 23 November 2020
> - Week 1: Monday 30 November to Friday 4 December 2020
> - Week 2: Monday 7 December to Friday 11 December 2020
> Each day will begin at 08:45 and will finish at 17:15 (GMT - UK Time)
>
> Some prior experience of crystallography and data collection is
> expected, and those who can bring an interesting project with them
> (crystals and possibly previously collected datasets) will be given
> priority.
>
> There is no fee to attend this online workshop, however attendance
> will be subject to an application process and a letter of support from
> the attendee's supervisor will be required. Both the application form
> and supervisor's letter of support will need to be submitted by 17:00
> (GMT) on Friday 16 October 2020.
>
> - The course homepage: https://www.ccp4.ac.uk/schools/DLS-2020/
> - Apply at the Diamond website:
>
> https://www.diamond.ac.uk/Home/Events/2020/Diamond-CCP4-Data-Collection-and-Structure-Solution-Workshop-2020.html
>
> *Disclaimer* Depending on the number of submissions we receive, we may
> need to close applications earlier than the deadline to allow the
> organisers time to process them. Applicants are therefore encouraged
> to apply as soon as possible with all the required details requested,
> including the letter of support - any incomplete applications will not
> be processed.
>
> -- David (on behalf of the organisers)
>



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[ccp4bb] Contouring Patterson map?

[Gloria Borgstahl]

What is the best way to display Harker sections these days?



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Re: [ccp4bb] [xds] how to specify measuring angle

[Dirk Kostrewa]

Dear Doo Nam Kim,

On 09.10.20 08:43, Doo Nam Kim wrote:

Since I don't know correct value of OSCILLATION_RANGE, I just changed to the 
example value (0.1) from (0.89976, I know it is not a positive multiple of 
0.0001, but worked for ketone data).


without knowing the correct value for the OSCILLATION_RANGE, data 
processing might run through but produces non-sense results, independent 
of the data processing program you use. So, it is absolutely important 
to know the correct value for the oscillation range per frame.


Cheers,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
WWW:www.genzentrum.lmu.de
strubio.userweb.mwn.de
***



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[ccp4bb] Scientist X-ray Crystallography at ZoBio in Leiden (NL)

[Denys Pogoryelov]

Scientist X-ray Crystallography at ZoBio in Leiden (NL)
ZoBio (www.zobio.com) was founded in 2004 and is located in Leiden, Netherlands. We offer innovative research services in the field of small-molecule drug discovery to the pharmaceutical and biotech industries. Our international team of 27 people covers four fields of expertise: Protein Engineering and Production, Assay Development and Screening, Structural Biology and Medicinal Chemistry.
We are currently looking to strengthen our team with an X-ray crystallographer with a track record in protein crystallography and a strong background in the X-ray crystallographic data analysis. In particular, experience in building and refinement of protein – small-molecule complexes would be extremely helpful.
The successful applicant will support our clients’ drug discovery programs by solving ligand-protein structures. You will work with minimal supervision but in a highly collaborative environment within the Structural Biology team and will effectively cooperate on a per-project basis with other research groups at ZoBio. This role requires working on multiple projects simultaneously and in a rapidly evolving environment. Team spirit and excellent organization and communication skills are essential.
RESPONSIBILITIES

High-throughput  crystallographic screening utilizing automation and robotics.
High-throughput and -quality structure elucidation and  interpretation of biological macromolecules in complexes with small  molecules of interest.
Utilization of X-ray crystallography pipelines with the  aid of computational structural biology tools to aid the efficient  structure elucidation of protein-ligand complexes.
Report results to the Head of Crystallography and  prepare presentations on the structural data for the project teams and  clients.
Maintain up-to-date understanding of the state-of-the-field  in X-ray crystallography in relation to modern drug discovery challenges.

REQUIREMENTS
·    PhD in relevant field with experience in an industrial or collaborative setting.  
·    Hands-on experience with ligand modelling into electron density maps and macromolecular model building and refinement in the context of Structure-Based Drug Discovery campaigns.
·    Hands-on experience in solving challenging X-ray crystallography cases (e.g. ab initio structure solution).
·    Experience with computational structural biology tools like ligand docking, virtual screening, molecular dynamics simulation would be considered as an advantage.
·    Experience in scripting and programming would be considered as an advantage.
·    Able to work in a team in a result-driven, goal-oriented environment.
It is fully expected that you will become a permanent and integral member of the ZoBio team, after an initial period of 12 months. Applicants at either the Senior Scientist or Scientist level will be considered. 
A tailored remuneration package will be proposed in line with individual qualifications and experience. The position is immediately available; the evaluation and assessment of candidates will run until the position is filled but not later than November 1st 2020. 
Please send your CV, motivation letter and names of potential referees at  with the subject: “Scientist position in X-ray Crystallography”.
--
Text version
Scientist X-ray Crystallography at ZoBio in Leiden (NL)
ZoBio (www.zobio.com) was founded in 2004 and is located in Leiden, Netherlands. We offer innovative research services in the field of small-molecule drug discovery to the pharmaceutical and biotech industries. Our international team of 27 people covers four fields of expertise: Protein Engineering and Production, Assay Development and Screening, Structural Biology and Medicinal Chemistry.
We are currently looking to strengthen our team with an X-ray crystallographer with a track record in protein crystallography and a strong background in the X-ray crystallographic data analysis. In particular, experience in building and refinement of protein – small-molecule complexes would be extremely helpful.
The successful applicant will support our clients’ drug discovery programs by solving ligand-protein structures. You will work with minimal supervision but in a highly collaborative environment within the Structural Biology team and will effectively cooperate on a per-project basis with other research groups at ZoBio. This role requires working on multiple projects simultaneously and in a rapidly evolving environment. Team spirit and excellent organization and 

Re: [ccp4bb] [xds] how to specify measuring angle

[Kay Diederichs]

Dear  Doo Nam Kim,

actually the results of XDS processing are deterministic for all practical 
purposes (to be nitpicking, the multi-processor version xds_par may result in 
slighly different output each time it is run, because for a few calculations 
the order of operations is influenced by the operating system's scheduler, but 
this only typically affects the last digit and is of no practical importance).

XDS needs to know the starting and end angle of each frame. It calculates these 
values internally, from STARTING_ANGLE and OSCILLATION_RANGE and the frame 
number (you specify the frames to process with DATA_RANGE for INTEGRATE, and 
with SPOT_RANGE for COLSPOT and IDXREF). If you don't specify STARTING_ANGLE, 
it will use 0 as the default. This does not affect the success of indexing, nor 
the data quality. There is no corresponding ENDING_ANGLE, because - as I said - 
the ENDING_ANGLE is anyway calculated internally; it is the end angle of the 
last frame.

Concerning completeness:
if your DATA_RANGE is specified correctly, AND the indexing succeeds, AND the 
space group is found (or given) correctly, then I see no reason why the 
completeness should not result in 60% for you, if someone else got 60%.

Apart from http://xds.mpimf-heidelberg.mpg.de, there is documentation and 
examples in XDSwiki at 
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_page

Hope this helps,
Kay



On Fri, 9 Oct 2020 07:43:22 +0100, Doo Nam Kim  wrote:

>Thank you Tim and Kay.
>
>
>
>"the indexing procedure is independent of the starting angle of the first 
>frame."
>--> I see, since XDS does indexing, I think that XDS is independent of the 
>starting angle of the first frame
>
>
>"Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
>per frame during data collection?"
>
>--> As I see 
>http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE=
>
>OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!)
>appears to designate 1 value, rather than 2 values (like min and max, e.g. 
>-60, 60).
>
>Since I don't know correct value of OSCILLATION_RANGE, I just changed to the 
>example value (0.1) from (0.89976, I know it is not a positive multiple of 
>0.0001, but worked for ketone data).
>
>Then, xds ran without error.
>
>Then, according to recommendtion, I changed from
>JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
>to
>JOB= DEFPIX INTEGRATE CORRECT
>
>and ran again.
>
>This time, it generated CORRECT.LP, but I see COMPLETENESS is only ~6%, while 
>my predecessor achieved ~60%
>
>I think that results of XDS are somehow random (not 100% deterministic). But I 
>didn't expect this big difference of COMPLETENESS (6% vs 60%).
>
>I think that I still entered a wrong option value somewhere in my XDS.INP.
>
>I think that I need to use well documented (with respect to needed xds.INP 
>parameters) microED dataset but I can't download from
>https://cryoem.ucla.edu/MicroED
>
>
>
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Re: [ccp4bb] [xds] how to specify measuring angle

[Doo Nam Kim]

Once I turned off my vpn, I could download from 
https://data.sbgrid.org/dataset/222/

Thank you for your help.



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Re: [ccp4bb] [xds] how to specify measuring angle

[Doo Nam Kim]

Thank you Tim and Kay.



"the indexing procedure is independent of the starting angle of the first 
frame."
--> I see, since XDS does indexing, I think that XDS is independent of the 
starting angle of the first frame


"Are you possibly looking for the OSCILLATION_WIDTH=, i.e. the degree
per frame during data collection?"

--> As I see 
http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#OSCILLATION_RANGE=

OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!)
appears to designate 1 value, rather than 2 values (like min and max, e.g. -60, 
60).

Since I don't know correct value of OSCILLATION_RANGE, I just changed to the 
example value (0.1) from (0.89976, I know it is not a positive multiple of 
0.0001, but worked for ketone data).

Then, xds ran without error.

Then, according to recommendtion, I changed from
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
to
JOB= DEFPIX INTEGRATE CORRECT

and ran again.

This time, it generated CORRECT.LP, but I see COMPLETENESS is only ~6%, while 
my predecessor achieved ~60%

I think that results of XDS are somehow random (not 100% deterministic). But I 
didn't expect this big difference of COMPLETENESS (6% vs 60%).

I think that I still entered a wrong option value somewhere in my XDS.INP.

I think that I need to use well documented (with respect to needed xds.INP 
parameters) microED dataset but I can't download from
https://cryoem.ucla.edu/MicroED



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