Re: [ccp4bb] CCP4i2 Export and Deposition task

[Martin Noble]

Thanks Huw: I am equally at fault for initiating a module without documenting 
it.


On 27 Nov 2020, at 11:32, Nikolas 
mailto:nikolas.ca...@gmail.com>> wrote:

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Dear Huw,

thanks a lot for your reply. Indeed the "Prepare and validate files for 
deposition" is the task I was using. My issue was accessing the output files, 
which was solved with your tutorial. I looking for the file in the folders when 
I should have saved it by clicking on the icons.

Thanks,
Nikolas

Il giorno gio 26 nov 2020 alle ore 23:43 Huw Jenkins 
<288da93ae744-dmarc-requ...@jiscmail.ac.uk>
 ha scritto:
Hi,

> On 26 Nov 2020, at 17:59, Nikolas 
> mailto:nikolas.ca...@gmail.com>> wrote:
>
> I am trying to prepare and export the files for a structure solved in CCP4i2 
> but so far the only tasks available are the "Prepare and validate" and "Merge 
> experimental data .." tasks.

Yes the first of these "Prepare and validate files for deposition" is the one 
you want.

> I have tried to look for the tutorial but both the icon and the input page 
> illustrated are different from the ones I can see in the software.

Is this the one found from "Help/Tutorials" - > "Task Documentation" within 
CCP4i2? Unfortunately that appears to be an outdated list of documentation and 
so links to the old (CCP4-7.0) "Prepare files for deposition" task. As you've 
spotted the interface has changed completely in CCP4-7.1.

Probably the closest thing to documentation for the new task is my presentation 
at this year's CCP4 study weekend 
here:https://www.youtube.com/watch?v=hd3pKgLpLM8=420

Apologies - writing documentation for this has been on my to-do list for a long 
time.

Best regards,


Huw


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Re: [ccp4bb] CCP4i2 Export and Deposition task

[Nikolas]

Dear Huw,

thanks a lot for your reply. Indeed the "Prepare and validate files for
deposition" is the task I was using. My issue was accessing the output
files, which was solved with your tutorial. I looking for the file in the
folders when I should have saved it by clicking on the icons.

Thanks,
Nikolas

Il giorno gio 26 nov 2020 alle ore 23:43 Huw Jenkins <
288da93ae744-dmarc-requ...@jiscmail.ac.uk> ha scritto:

> Hi,
>
> > On 26 Nov 2020, at 17:59, Nikolas  wrote:
> >
> > I am trying to prepare and export the files for a structure solved in
> CCP4i2 but so far the only tasks available are the "Prepare and validate"
> and "Merge experimental data .." tasks.
>
> Yes the first of these "Prepare and validate files for deposition" is the
> one you want.
>
> > I have tried to look for the tutorial but both the icon and the input
> page illustrated are different from the ones I can see in the software.
>
> Is this the one found from "Help/Tutorials" - > "Task Documentation"
> within CCP4i2? Unfortunately that appears to be an outdated list of
> documentation and so links to the old (CCP4-7.0) "Prepare files for
> deposition" task. As you've spotted the interface has changed completely in
> CCP4-7.1.
>
> Probably the closest thing to documentation for the new task is my
> presentation at this year's CCP4 study weekend here:
> https://www.youtube.com/watch?v=hd3pKgLpLM8=420
>
> Apologies - writing documentation for this has been on my to-do list for a
> long time.
>
> Best regards,
>
>
> Huw
> 
>
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Re: [ccp4bb] CCP4i2 Export and Deposition task

[Huw Jenkins]

Hi,

> On 26 Nov 2020, at 17:59, Nikolas  wrote:

> I have tried to look for the tutorial but both the icon and the input page 
> illustrated are different from the ones I can see in the software.

I have now updated the CCP4i2 documentation at 
https://ccp4i2.gitlab.io/rstdocs/index.html to reflect the updated task. 

Again I'm sorry this took so long.


Huw



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[ccp4bb] Position available: Beamline scientist at BioMAX (MAX IV)

[Ana Gonzalez]

Dear all,

I would like to draw your attention to the following position available at the 
MAX IV Laboratory:


BioMAX is the first operational beamline for macromolecular crystallography at 
MAX IV, which has been running within the MAX IV user program for the last 3 
years. The beamline is a state-of-the-art beamline geared towards 
high-throughput protein crystallography with high performance x-ray optics and 
control systems, goniometry, x-ray detectors and a cryogenic sample changer 
(See also: http://www.maxiv.se/biomax). The beamline is able to provide remote 
access to the users.


The beamline is operated by the international and interdisciplinary 
BioMAX-team, which is part of the MX group. Within the MX group we are also 
developing constructing  MicroMAX, a serial crystallography beamline for 
studying protein dynamics and the FragMAX project, which  operates a 
crystallographic fragment screening facility at MAX IV.

We are looking for a beamline scientist who enjoys working in an international 
and creative environment to join our team working at the BioMAX Beamline. As a 
beamline scientist, you will be involved in continuing development of the 
BioMAX beamline  and the scope of techniques that can be offered to our user 
community. User support will be an important part of the activity.  The MX 
environment will provide opportunities for collaborative work at the frontiers 
of the field.

For more information about this position, please see

https://lu.varbi.com/en/what:job/jobID:365824/


Best regards,


Ana


BioMAX Beamline Manager





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[ccp4bb] Instruct Internship call open

[Claudia Alén Amaro]

Dear All

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These researchers will be able to integrate different technologies to open up 
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to Instruct Centres. 
Internships cover travel plus subsistence of the intern for pre-doctoral and 
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Instruct research groups applying techniques that are not available in the 
applicant's laboratory and the longer duration of awards allows interns to gain 
in depth experience in the host laboratory.



Applications should specifically focus on the benefit to the applicant's 
research. Incomplete applications will not be considered, this includes the 
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online. The applicant needs to have discussed in detail with the Instruct 
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If due to the coronavirus, new unexpected restrictions occur after the 
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More complete guidelines are available 
here.



Due to the COVID-19 pandemic, applications are invited for submission at any 
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Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

[Clemens Vonrhein]

Dear Nika,

as a possible alternative or second opinion, you could have a look at
the ligand-detection modes [1] in BUSTER too - see e.g.

  https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes

It's very similar to the Phenix Polder maps - so might not tell you
anything different, but looking at results from different
implementations can be useful as a check.

Anyway, one of the main problems handling partially occupied ligands
(and let's ignore the possibility of partial disorder for
"simplicity") is that you might have a mixture of three models within
your binding site: (1) compound, (2) waters (at ordered positions when
the ligand is not bound) and (3) bulk solvent (at disordered positions
when the ligand is not bound).

What can be useful is to include at least the alternative ordered
water model (from a well refined APO model?) and then refine the
(grouped) occupancies:

  OCC(compound) + OCC(waters) = 1.0

This way you give the refinement the option to chose between two
alternative interpretations [2]. To avoid any bias in that refinement
procedure, you could start from two extremes: once with
OCC(compound)=0.9 and once with 0.1. If the OCC(compound) refines to a
small value (say <0.2 or such) in both cases, it is possibly not really
there.

Cheers

Clemens

[1] Vonrhein, C. and Bricogne, G., 2005. Automated structure
refinement for high‐throughput ligand detection with
BUSTER‐TNT. Acta Crystallogr. Sect. A, 61, p.c248.
[2] 
http://www.globalphasing.com/pipermail/buster-discuss/2015-August/000255.html

On Tue, Nov 24, 2020 at 11:28:42AM +, Nika Žibrat wrote:
> Hello,
> 
> 
> I have a question about protein-ligand, of which ligand displays an ambiguous 
> electron density. I am solving a structure of protein with ligand  which was 
> obtained via soaking. Structural characteristics indicate the ligand is 
> present however the electron density is quite vague and too small for the 
> size of the whole ligand. I did a Polder map which showed much larger area of 
> green density. After insertion of my ligand into the green density in Polder 
> I ran phenix.refine and there is a lot of red on the spot where the ligand is 
> which was to be expected. This leaves me wondering how, if even do I 
> incorporate the polder map data into my refine input.
> 
> 
> My question is, how do I continue refining and validating the structure in 
> this case?
> 
> 
> Thank you,
> 
> 
> Nika Žibrat
> 
> 
> 
> 
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-- 

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



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