[ccp4bb] PostDoc position in time-resolved crystallography

[Schulz, Eike-Christian]

Dear all,

There is an opening for a PostDoc position in my group. Funding is generously 
provided by an ERC Synergy Grant for the DynaPLIX project, wherein we aim to 
understand the dynamics of protein ligand interaction via an integrative 
approach combining NMR-spectroscopy (Mikael Akke, Lund University, 
MD-simulations (Kresten Lindorff-Larssen, University of Copenhagen) and 
time-resolved crystallography (Eike C. Schulz, UKE Hamburg).

https://cordis.europa.eu/project/id/101071843

Directly located on the DESY Campus (Petra-III synchrotron/EU-XFEL), we will be 
making ample use of our recently developed HARE and LAMA methods but also 
explore the foundations of protein function via multi-dimensional 
crystallography. Further pushing technology and method development in the field 
I am also terribly excited about our most recent toy, the spitrobot - a 
crystal-plunger that enables cryo-trapping with a time-resolution in the ms 
domain.

Candidates interested in a PostDoc position, motivated to push the boundaries 
in time-resolved (serial) crystallography should reach out directly to me 
(ec.sch...@uke.de), exciting projects are ahead.

Recent pre-prints:
The spitrobot: https://www.biorxiv.org/content/10.1101/2022.09.20.508674v1
Multi-dimensional crystallography: 
https://www.biorxiv.org/content/10.1101/2021.11.07.467596v2

Recent publications:
SSX vs SFX (Science Advances 2021): 
https://www.science.org/doi/10.1126/sciadv.abf1380
Allosteric communication (Science 2019): 
https://www.science.org/doi/10.1126/science.aaw9904
LAMA (Nature Methods 2019) https://www.nature.com/articles/s41592-019-0553-1
HARE (Nature Methods 2018) https://www.nature.com/articles/s41592-018-0180-2


With best regards,

Eike




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[ccp4bb] Postdoc and PhD positions in time-resolved crystallography

[Schulz, Eike-Christian]

Dear all,

Since July 1st I have started a tenure track group leader position at the 
University medical center (UKE) in Hamburg, with my lab located directly at the 
DESY campus. Funding is generously provided by the BMBF program junior research 
groups in infection research 
https://www.gesundheitsforschung-bmbf.de/de/nachwuchsgruppen-in-der-infektionsforschung-12245.php.
 The aim of my group is to understand the catalytic mechanisms of enzymes 
involved in antibiotic resistance via time-resolved crystallography.

We will be making ample use of our recently developed HARE and LAMA methods but 
also explore the foundations of protein function via multi-dimensional 
crystallography. Further pushing technology and method development in the field 
I am also terribly excited about our most recent toy, the spitrobot - a 
crystal-plunger that enables cryo-trapping with a time-resolution in the ms 
domain.

Candidates interested in PostDoc or PhD positions in time-resolved 
crystallography should reach out directly to me 
(ec.sch...@uke.de), exciting projects are ahead.

Recent pre-prints:
The spitrobot: https://www.biorxiv.org/content/10.1101/2022.09.20.508674v1
Multi-dimensional crystallography: 
https://www.biorxiv.org/content/10.1101/2021.11.07.467596v2

Recent publications:
SSX vs SFX (Science Advances 2021): 
https://www.science.org/doi/10.1126/sciadv.abf1380
Allosteric communication (Science 2019): 
https://www.science.org/doi/10.1126/science.aaw9904
LAMA (Nature Methods 2019) https://www.nature.com/articles/s41592-019-0553-1
HARE (Nature Methods 2018) https://www.nature.com/articles/s41592-018-0180-2


Best regards,

Eike


Dr. Eike C. Schulz
Universitätsklinikum Hamburg-Eppendorf
Zentrum für Experimentelle Medizin | Institut für Biochemie und 
Signaltransduktion | Martinistrasse 52, Gebäude N45, 20246 Hamburg
Visiting Adress:  DESY | Bldg. 610 (HARBOR) | Luruper Chaussee 149 | 22761 
Hamburg | Germany





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[ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

[Schulz, Eike-Christian]

Dear all,

I am considering to purchase a chromatography system for routine protein 
purification. The device is supposed to be used in a multi-user environment, 
hence ease of use, ease of training and ease of maintenance is important. I am 
rather looking for a robust system people like to use than a system that comes 
with many bells and whistles that no one dares to touch.


  *   Is there any particularly _bad_ experience with either system?


  *   Is there any specific advantage of one system over the other?


  *   Does anyone have experience about (long-term) stability / performance of 
the systems?


  *   Do you think the higher price-point of the Aekta systems is justified?


With best regards,

Eike






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Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

Dear Paul, 

sorry for the delay. 

I did not answer your previous questions in detail, because going back to coot 
0.8 did solve the problem for me, which kept me busy. But of course, to do sth. 
about the situation you need to understand a lot better what is going on. 

What I have is a “phenotype” (coot 0.9) that presents differently than the 
previous generation (coot 0.8) and since it’s not possible for me to revert any 
of the mutations its hard to pinpoint the cause of the problem. The most 
general description I can come up with: in coot 0.9 the model moves “funny” – 
different from coot 0.8. Some (new?) restraints seem to act on the atoms 
preventing them to stay where I put them. This "hidden-thinking" coot 0.9 
appears to apply confuses me. 

*I don’t think this description is a major improvement from before, maybe 
someone else (Georg?, Eleanor? Herman?) can give it a try?

However, I have a hunch that the root of our communication trouble is that the 
way you and I are using coot is very different. Therefore, I think it maybe 
best if (a) I told you how I use it most of the time and (b) provide you with a 
specific example (off-list). Maybe you can reproduce the trouble if you follow 
my procedure. 

Staying in the picture of your Ferrari/bus metaphor, I think I am probably 
walking to work:

I am predominantly using the real-space refine options, going through the 
structure bit by bit, putting the model where (I think) it belongs. I also make 
use of the stepped-refine procedure, but I know more than one colleague who 
considers that “cheating” already or do not know about that option at all. Of 
course, I am making use of the validation, measurement, map and model tools, 
but hardly of any automation (§). No special key-binding, no scripts - just out 
of the box, default settings, iterative cycles with refinement. That may not be 
what you have intended, but the people in my echo chamber just do the same. 

Eigen-flip, jiggle-fit, pepflip, JED-flip, backrub, interactive contact dots, 
acedrg – sorry I’ve never heard of them. 

You mentioned a blog and/or other coot info before. With coot 0.9 I tried 
finding more information but your coot-website and the included tutorials 
appear to be a bit older https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/. 

Is there a new source of info somewhere? - I am happy to look into it. 

Best, 

Eike


§ automatic building of alternate conformations for HR-structures would be 
really helpful though. 


-Original Message-
From: CCP4 bulletin board  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Tuesday, 8. September 2020 at 17:44
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] AW: Going back to Coot 0.8

On 08/09/2020 16:25, Georg Zocher wrote:
>
>
> we have the same experience in our lab.


What experience is that? I am still in the dark about you think is now 
worse.


> Personally, I did would not like to judge here, as so far, I did not 
> have had enough time to get into the new RSR of coot 0.9.x by myself. 
> But many colleagues did not like the new refinement module maybe just 
> as they are used to the method in all coot versions before.


You have a Ferrari parked beside your house but you want to to take the 
bus to work because that's what you've always done. Or maybe the Ferrari 
is parked around the back and you don't know it's there?


>
> I just thought if it wouldn't be an option to let the user decide what 
> kind of RSR implementation she/he would like to use and give them the 
> choice via an option in coot preferences?


That would be possible but not easy. Unlike much of the CCP4 suite, Coot 
is Free Software. But, again... why would you want to take the bus? Explain.


regards,


Paul.



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

Dear Paul, 

Thanks for the detailed response. The reason for me being a bit annoyed is 
really simple: basic model building did work well in coot 0.8.x and (for me and 
others) it does not work anymore in coot 0.9. Because I like coot (and because 
most computer problems are usually 30cm in front of the screen) I have tried to 
get used to it for a few month, but on the weekend I have switched back to coot 
0.8 *  –>  problem(s) solved, what a relief. 

I realize that I have not been particularly helpful in bug-fixing, but the 
changes appear to be rather comprehensive and thus I can only comment on the 
user experience. This is (naturally) a subjective experience but what I hear 
from my colleagues tells me that I am not alone with my frustration. 

Try to look at it from my point of view: 
-   the previous version of coot does what I want, 
-   I see few advantages of the new version,
-   the basic functionality (that I am used to) appears to be gone in the 
new version.

Since I am not convinced - why should I switch ?

Best regards, 

Eike


* thanks to Bill Scott for the pre-compiled mac-binaries 
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot

-Original Message-
From: CCP4 bulletin board  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Saturday, 5. September 2020 at 02:05
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

Dear Eike,

Yes, it helps a little.

Changing weights on switching refinement maps is inconvenient, but not a 
point of failure.

Alternative conformations may need some assistance - pin an atom using 
anchoring.

When Coot starts a refinement it tells you in the terminal about the bad 
bonds and non-bonded contacts that it found in the model. Do you 
perceive that to be wrong or missing interactions?

There are many ways to skin a covalent ligand complex. I use the 
Acedrg-Coot interface (as described in my blog). Do you?

If you wish, you can calculate an average map, the tool for that can be 
found in Calculate -> Map Tools -> Average Maps...

Perhaps it would be useful to have an alert "You're not looking at the 
map into which you are trying to fit the model" - maybe the background 
should go pink - or something.

I feel that you are annoyed but I still don't understand why. As Phil 
used to like to say, the devil's in the details.

I see that previously I didn't answer your question. So let me correct 
that now:

(i) You can turn on interactive contact dots ("Contact Dots On") using 
Refinement Tools from Curlew. This is a validation tool however and 
doesn't describe what is going on with the refinement energy inside 
Coot's head. I have it turned on by default for myself, FWIW.
(ii) There is no way to turn on "Old Style" refinement in 0.9 - although
"proportional editing" in 0.9.1 will bring some of that non-refined 
initial displacement of surrounding atoms [1]
(iii) 0.8.2 is the best release for the 0.8.x series. I did quite a bit
of work on 0.8.3 but I never released it. Most (not all) of the updates 
have been folded into 0.9.x.

Paul.

[1] it was seeing that Tristan had added to ISOLDE something like the 
tool I had intended that that actually made me write it for Coot [2] - 
it is a useful technique when shoving around domains in cryo-EM.
[2] That and watching Blender tutorials.

On 04/09/2020 19:04, Schulz, Eike-Christian wrote:
> Dear Paul,
> 
> thanks for your comprehensive response in spite of my rather general 
comment. And thanks for listening! I hope you see this as constructive 
criticism and not only as blunt complaining (a national tradition ;) ):
> 
> Instead of a screencast I'd like to give at least a few more details on 
the trouble on my end.
> 
> The problems mainly arise when:
> 
> - switching maps e.g. from 2Fo-Fc to Fo-Fc, or omit maps (X-ray 
restraints ?)
> - modelling alternative / low occupancy conformations
> - modelling covalent ligand complexes (atom clashes ?)
> - parts of the solution are in either of the maps (maybe map averaging 
would help?)
> 
> --> which is practically all I am doing, and the result is often a model 
next to but not inside of the density. I am a long-term practitioner of 
ctrl-drag, but with little help in these cases.
> 
> With respect to sophisticated solution and the "method developers’ 
intention", I would like to answer with some experience from our own serial 
crystallography method development.
> 
> For even distribution of micro-crystal slurries, we developed a 
custom-multichannel pipette adapter, went through different iterations, adapted 
and improved the design added more

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

lustrates the problem, then I would be very 
interested to view it.

Regards,

Paul.


On 04/09/2020 10:05, Schreuder, Herman /DE wrote:
> Dear Paul,
> 
> Here I fully agree with Eike. With the real space refinement in the 
> new coot the ligand often goes everywhere, except where it should go. 
> Changing the Xray weight helps sometimes, but not always. In many 
> cases I do not real-space refine and leave it to Buster to do the 
refinement. It would be very good if the old behavior could be reinstalled.
> 
> Best regards,
    > 
> Herman
> 
> *Von:*CCP4 bulletin board  *Im Auftrag von 
> *Schulz, Eike-Christian
> *Gesendet:* Freitag, 4. September 2020 10:36
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] Going back to Coot 0.8
> 
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk 
> <mailto:owner-ccp...@jiscmail.ac.uk>
> 
> Dear Paul,
> 
> I have been working with coot for over 10 years now with little reason to 
complain.
> 
> However, in spite of trying for a few months now, I am not getting warm 
with coot 0.9.
> 
> I like the new eye-candy, and the more organized menus. But fitting 
> residues and ligands into ED, has never before been so difficult, and 
> frankly it annoys me that previously simple tasks have become an 
> effort. It seems as if coot and I see different minima and we always 
disagree where to put the residue. At the moment all my data are at convenient 
resolutions of 1.7Å or better, so there is little ambiguity on that side.
> 
> I am using all default settings, but maybe there is something that needs 
to be changed?
> 
>   * Is there a way to go back to the old (0.8-style) fitting functions in 
coot 0.9? If so how?
>   * If not, which of the last coot versions
> 
(https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_=DwIDaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM=5NsBSHjvi7V_A6kImjIckNzc50syFHFMZyXcv7xVvNA=
> 
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_=DwMGaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA=_vveOeCJ42OXDKFFrxFP_yaBEA0xSQBIGW2RWy8kmAk=>)
> would you recommend?
> 
> With best regards,
> 
> Eike
> 
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[ccp4bb] Going back to Coot 0.8

[Schulz, Eike-Christian]

Dear Paul,

I have been working with coot for over 10 years now with little reason to 
complain.

However, in spite of trying for a few months now, I am not getting warm with 
coot 0.9.

I like the new eye-candy, and the more organized menus. But fitting residues 
and ligands into ED, has never before been so difficult, and frankly it annoys 
me that previously simple tasks have become an effort. It seems as if coot and 
I see different minima and we always disagree where to put the residue. At the 
moment all my data are at convenient resolutions of 1.7Å or better, so there is 
little ambiguity on that side.

I am using all default settings, but maybe there is something that needs to be 
changed?


  *   Is there a way to go back to the old (0.8-style) fitting functions in 
coot 0.9? If so how?
  *   If not, which of the last coot versions 
(https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/) would 
you recommend?

With best regards,

Eike






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[ccp4bb] coot scripting advise for beginners

[Schulz, Eike-Christian]

Good evening,

I am looking for some advice wrt. coot scripting. Unfortunately, I have never 
done it, and I have to admit I did not find the ccp4-wiki particularly helpful 
to get started - but that is certainly linked to my generally very limited 
scripting experience.

What I have in mind seems super simple to me:
to improve a semi-automatic refinement script, I would like to include coots 
“stepped refine” and then return to another round of refinement.

What would you recommend is an easy way to implement this in a shell (or 
python) script ?

Many thanks in advance,

Eike






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[ccp4bb] SFALL change (?) affecting END_RAPID ?

[Schulz, Eike-Christian]

Dear all,

Yesterday, I have updated to the most recent version of CCP4. Today the 
END_RAPID scripts give me following error message:

[…]

Optimize H/D positions using phenix.geometry_minimization
phenix.geometry_minimization "/bla/refined.updated.pdb" 
use_neutron_distances=False output_file_name_prefix=refined.updated 
selection="element H or element D" write_geo_file=False 
fix_rotamer_outliers=False silent=True correct_hydrogens=True
generating phenix models...
no solvent
sharp solvent
regular
making sfall map for vacuum level reference
mapmask:   rcards - error in AXIS card
ERROR: unabel to run sfall
usage:
/opts/end.rapid/END_RAPID.com phenixrefine.eff

[…]

Was there any change that could lead to this error ?

Best,

Eike




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[ccp4bb] ECM32 Satellite workshop on fixed-target serial crystallography

[Schulz, Eike-Christian]

Dear all,

We would like to bring to your attention that there will be a satellite 
workshop on the ECM32 focusing on fixed-target serial crystallography. As there 
are only a limited number of places available, please register as soon as 
possible. If you would like to present a poster please  submit an abstract by 
June30th . We will then let you know if we are able to accommodate you by July 
10th 2019.

Please submit your poster abstract to: 
ecm32.fixed.tar...@gmail.com

Abstracts sent to other addresses can unfortunately not be considered. The 
registration fee is 50 €.

Further information can be found at 
https://www.ecm2019.org/satellites/fixed-target-methods/

The following areas will be covered primarily in talks and informal round table 
discussion:

  *   Introduction to fixed targets
  *   Making fixed-target methods reliable for routine user operation
  *   Implementation at different facilities
  *   SSX applications beyond TRX
  *   Fixed target parameters / dimensions / materials
  *   Translation stage systems and integration of control software into 
beamline software
  *   Fixed-target mounting solutions (e.g. magnetic mounts, robots, etc.)
  *   Fixed-target storage and shipment options
  *   Auto Processing/Workflows and Pipelines

Looking forward to meeting you in Vienna,

The organizing team:

Arwen Pearson, Jennifer Wierman, Pedram Mehrabi, Eike Schulz


Dr. Eike C. Schulz
Max Planck Institute for the Structure and Dynamics of Matter
Luruper Chaussee 149 | 22761 Hamburg | Germany
Building 99 (CFEL) | Office O2.101
Phone +49 (0)40 8998-6264 | Fax +49 (0)40 
8994-6264 | Website 
www.mpsd.mpg.de





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[ccp4bb] wanted: Hampton Research Glucose Isomerase Crystals

[Schulz, Eike-Christian]

Dear all,

For a comparative experiment we are looking for the glucose isomerase crystals 
Hampton Research used to sell:
https://hamptonresearch.com/.../hr005720_7-102_user_guide.pdf
We ran out of stock before the experiment was completed and unfortunately they 
don’t sell these anymore. We asked Hampton for leftovers but they did not 
respond ☹.

Does anybody have some spare crystals remaining? We wouldn’t mind if they were 
old. Of course we would cover original purchase and shipment costs.

Best regards,

Eike




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Re: [ccp4bb] using CC1/2 to define resolution limit in Xscale

[Schulz, Eike-Christian]

The ideas was to cut all datasets at say 30% CC1/2 to see how they differ in 
resolution I/sigI etc. for that given CC1/2 …

From: Eleanor Dodson <eleanor.dod...@york.ac.uk>
Date: Friday, 27. October 2017 at 23:12
To: "Schulz, Eike-Christian" <eike.sch...@mpsd.mpg.de>
Cc: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] using CC1/2 to define resolution limit in Xscale

Do you mean the CC1/2 for the 15 merged data sets? Doesnt AIMLESS give you this 
- treat each one as a seperate run, and you get the stats for each run, as well 
as the overall result.

Then you can check where CC1/2 reaches your chosen limit..\

Eleanor

PS - not sure if it is an absolute criteria - it might depend to some extent on 
multiplicity..

On 27 October 2017 at 21:31, Schulz, Eike-Christian 
<eike.sch...@mpsd.mpg.de<mailto:eike.sch...@mpsd.mpg.de>> wrote:
Dear all,

I would like to compare > 15 datasets and would like to use a common CC1/2 
value as an objective criterion to determine the resolution cut-off.

All data were integrated in XDS.

Is there a convenient way to apply this in XSCALE or in any of its alternatives?

With best regards,

Eike

[ccp4bb] using CC1/2 to define resolution limit in Xscale

[Schulz, Eike-Christian]

Dear all,

I would like to compare > 15 datasets and would like to use a common CC1/2 
value as an objective criterion to determine the resolution cut-off.

All data were integrated in XDS.

Is there a convenient way to apply this in XSCALE or in any of its alternatives?

With best regards,

Eike

[ccp4bb] Lysozyme soaked with GlcNac?

[Schulz, Eike-Christian]

Dear all,

There are several structures in the PDB that show Lysozyme (mutants) in complex 
with GlcNac (or similar compounds). However, all of those structures seem to 
originate from co-crystallization experiments. I was wondering whether anybody 
knew a successful case of complex formation by soaking. But maybe the solvent 
channels are too small …

I would be very happy if anybody could point me to a reference but I could also 
live with anecdotal evidence.

With best regards

Eike

[ccp4bb] structure determination from a hollow crystal

[Schulz, Eike-Christian]

Dear all,

Is there a documented case of a structure determination from a hollow crystal? 
We have the unfortunate situation that a protein only crystallizes as a hollow 
tube, where the inside is filled with solvent, which ruins the diffraction 
patterns.

I was often confronted with similar situations, but in the previous cases I 
could always find a suitable crystal (part) or a different crystallization 
condition saved me.

If anybody had general advise on how to proceed or could point me to relevant 
literature it would be much appreciated.

With best regards

Eike

[ccp4bb] edit CBF file header

[Schulz, Eike-Christian]

Dear all, 


I am looking for a tool, which allows me to edit the header of CBF-files. In a 
large set of files (~175K) the beam-centre is put incorrectly and I would 
prefer a fairly automated way. I know that XDS et al. can correct for this but 
my problem is posed differently. I was considering a regular expression script 
but I suppose this would not work with the binary files … ?

Thanks a lot for your advice 

Best regards

Eike