[ccp4bb] Postdoctoral position in cryoEM at KU Leuven (Belgium)

[Sergei Strelkov]

Applications are invited for a postdoctoral opening in the Laboratory for 
Biocrystallography at KU Leuven (Belgium), to work on two ongoing projects 
mainly using cryoelectron microscopy.

KU Leuven is a leading Belgian University, located in the charming town of 
Leuven just 20km east of Brussels. Laboratory for Biocrystallography, led by 
Prof. Sergei Strelkov, is active in structural biology and rational drug 
design. The working language is English. In addition to superb facilities for 
molecular biology and X-ray crystallography, there are two brand-new 200kV 
cryoelecton microscopes on campus and a good access to 300kV microscopes in 
Brussels and at European facilities.

The new postdoctoral researcher will focus on cryoEM studies of intermediate 
filament proteins and a novel protein target for cancer drug development. The 
successful candidate will have a track record in structural biology, experience 
with cryoEM and a capacity to work independently. Support on molecular biology 
and computation will be provided by other team members.

The contract will be up to three years, with yearly extension. Please send your 
motivation letter, including a detailed CV and a list of publications, to: 
sergei.strel...@kuleuven.be<mailto:sergei.strel...@kuleuven.be>

Lab page: https://pharm.kuleuven.be/Biocrystallography




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Re: [ccp4bb] Synergy-R vs Synergy-S

[Sergei Strelkov]

Dear Wu,

Just as you say there is an order of magnitude difference in intensity (one is 
a sealed tube and another is a rotating anode). Our experience with MicroMax007 
is that it is often possible to collect a full dataset from a medium-sized 
crystal overnight. With a sealed tube, this would have been five days which is 
clearly impractical. The choice is yours, but a system suitable for screening 
only and a system occasionally capable of full data collection are two 
different things.

HTH,
Sergei


Prof. Sergei V. Strelkov
Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU 
Leuven
O, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Phone: +32 16 33 08 45, mobile: +32 486 29 41 32, skype sergei.strelkov
Lab pages: 
http://pharm.kuleuven.be/Biocrystallography

From: CCP4 bulletin board  On Behalf Of Wu, Jinhua
Sent: Tuesday, January 25, 2022 11:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Synergy-R vs Synergy-S


Dear all,

Does anyone have experience on the two new Rigaku systems, Synergy-R and 
Synergy-S?  It seems that Synergy-R has one order of magnitude higher intensity 
than Synergy-S. But Synergy-S does not need an external water chiller and is 
maintenance free. Do you think if Synergy-S enough for crystal screening in 
most cases (nonmembrane proteins)? Anything should be aware of with the two 
models? Thanks for sharing your thoughts.

Best,

Jinhua Wu

Fox Chase Cancer Center



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[ccp4bb] Characterising potential drug-binding pockets

[Sergei Strelkov]

Dear everyone,


In a drug discovery project where our aim is to interfere with some PPIs, we 
could obtain binding of drug-like fragments in several potentially interesting 
pockets on our target. We would like to make a projection on how promising 
these individual pockets are. One way of doing this is through the Sitemap 
program (Halgren, T. A. Identifying and characterizing binding sites and 
assessing druggability. J. Chem. Inf. Model 49, 377-389 (2009)). Are there 
other tools around to do this? In particular, we would like to have accurate 
numbers for the pocket volume, surface, no. of H-bond donors and acceptors, 
average hydrophobicity, etc etc.


Thank you,

Sergei




Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography



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Re: [ccp4bb] microscope camera

[Sergei Strelkov]

Moticam 5 has been working well for us for a few years now (installed on a 
Leica binocular)


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera

Forgive the off topic subject:

Has anyone got any experience with moticam microscope cameras?
We are looking into cheap cameras for record keeping etc and this supplier 
looks good but...

Cheers in advance

Sent from Mail for Windows 10




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Re: [ccp4bb] coiled coil molecular replacement - PS

[Sergei Strelkov]

> 1. Try our coiled-coil modelling server
> https://pharm.kuleuven.be/apps/biocryst/ccfold.php

Some more explanation here. This server runs our CCFold algorithm (Guzenko & 
Strelkov (2017) Bioinformatics, article btx551). CCFold is a threading-type 
algorithm which was specifically designed to model coiled coils from amino-acid 
sequence. This is why it is fundamentally faster than generic algorithms like 
Quark or Rosetta. CCFold is also trivial to run using our web server or a local 
installation if you prefer. The modelling accuracy of CCFold was discussed in 
the Guzenko and Strelkov paper cited above.

Sergei


From: CCP4 bulletin board  on behalf of Sergei Strelkov 

Sent: Tuesday, October 8, 2019 14:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coiled coil molecular replacement

Dear Tommi,

With coiled coils you certainly want to use the best search model possible. 
Coiled coils are elongated structures and a small local inaccuracy of your 
search model may result in large differences (in terms of overall rmsd) with 
respect to the true structure. Two suggestions:

1. Try our coiled-coil modelling server
https://pharm.kuleuven.be/apps/biocryst/ccfold.php

2. Prepare a set of partial models (corresponding to various parts/lengths e.g. 
50-60% of the total length) and attempt MR with each of them. In our experience 
the standard algorithms (MolRep/Phaser) can also work well. It depends a lot on 
the space group and particular packing of your dimers (dense packings being the 
most challenging).

Hope this helps,
Sergei


Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, KU Leuven
O, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Phone: +32 16 33 08 45, mobile: +32 486 29 41 32
Lab pages: http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Kajander, Tommi 
A 
Sent: Monday, October 7, 2019 23:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] coiled coil molecular replacement

Hello,

We have a bit tricky case of coiled coil protein with good data (2.05Å) for 
dimeric coiled coil (dimer in AU)  - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet 
if there is a clear how-to manual)

Some technical tips on usage for generation of fragments for AMPLE would be of 
help, not completely on top of that… (running the QUARK server, the real 
sequence is bit over 200 aa so not sure what is the best approach here? 
Rosetta? any how-to for that.. well i am running Robetta fragments too).

with AMPLE can I do this with the online server or better run locally (need 
Rosetta installed I take it?)

Suppose I could try Rosetta-MR also, but to my recollection that requires some 
kind of a phaser hit first to be improved, and i dont think I am there.

Thanks for any comments,

Best,
Tommi






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Re: [ccp4bb] coiled coil molecular replacement

[Sergei Strelkov]

Dear Tommi,

With coiled coils you certainly want to use the best search model possible. 
Coiled coils are elongated structures and a small local inaccuracy of your 
search model may result in large differences (in terms of overall rmsd) with 
respect to the true structure. Two suggestions:

1. Try our coiled-coil modelling server 
https://pharm.kuleuven.be/apps/biocryst/ccfold.php

2. Prepare a set of partial models (corresponding to various parts/lengths e.g. 
50-60% of the total length) and attempt MR with each of them. In our experience 
the standard algorithms (MolRep/Phaser) can also work well. It depends a lot on 
the space group and particular packing of your dimers (dense packings being the 
most challenging).

Hope this helps,
Sergei


Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, KU Leuven
O, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Phone: +32 16 33 08 45, mobile: +32 486 29 41 32
Lab pages: http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Kajander, Tommi 
A 
Sent: Monday, October 7, 2019 23:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] coiled coil molecular replacement

Hello,

We have a bit tricky case of coiled coil protein with good data (2.05Å) for 
dimeric coiled coil (dimer in AU)  - looks like AMPLE might be a way
to solve such cases, if you know other good programs please suggest (Better yet 
if there is a clear how-to manual)

Some technical tips on usage for generation of fragments for AMPLE would be of 
help, not completely on top of that… (running the QUARK server, the real 
sequence is bit over 200 aa so not sure what is the best approach here? 
Rosetta? any how-to for that.. well i am running Robetta fragments too).

with AMPLE can I do this with the online server or better run locally (need 
Rosetta installed I take it?)

Suppose I could try Rosetta-MR also, but to my recollection that requires some 
kind of a phaser hit first to be improved, and i dont think I am there.

Thanks for any comments,

Best,
Tommi






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Re: [ccp4bb] design specs/tolerances for crystallization rooms?

[Sergei Strelkov]

Dear Frank and everyone,


Thanks for useful tips. Snow in liquid nitrogen has been annoying us on a 
regular basis in fact. During some synchrotron sessions, a large percentage of 
crystals were covered with snow. We could never fully figure out how to get rid 
of it, although filtering LN2 before filling the vessel for freezing seemed to 
help a bit...


Would installing a dehumidifier in a standard 20C crystallization room (where 
we mount most of our crystals) be a good idea? Any experiences there? I guess 
the downside would be that small crystallization drops would be drying more 
quickly...


Best wishes,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Frank Von Delft 

Sent: Wednesday, September 25, 2019 7:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] design specs/tolerances for crystallization rooms?

My colleague Opher Gileadi gave us an excellent tip when we were designing our 
4C harvesting room, over a decade ago:  set it to 7C.  The crystals are 
unlikely to mind, but it's SO much more comfortable to be in for hours.

I seem to remember he mentioned something like a comfort inflection point as 
you approach 4C.

Install low-flow fans.  Fridge people seem to default to installing hurricane 
machines, you have to tell them that a very very small flow is enough.

Get strong light - probably even those daylight things (we don't have them).  
Being cold is miserable enough already, there's no need to compound it with 
weak light.

Vibration - that dwindles to insignificance if the air flow goes down.

Humidity - we installed (at considerable expense) a low humidity air supply - 
really hard to know just how much it helps, but a few years ago when I had it 
turned it off to help save energy, very quickly I heard complaints about snow 
in the liquid nitrogen becoming a major hassle.  So based on that set of 
anecdotes, I conclude it probably is worth having dry air.

It's much cheaper though if they can design it into the building's 
infrastructure, if it's a new building;  retrofitting turned out to be super 
expensive (in our case).

As dry as possible.  Look at and understand the psychrometric chart (google 
it):  if you're in even vaguely warm or temperate regions (or seasons), cooling 
the intake air to 4C brings it to below dew point, and then condensation and 
snow are guaranteed.

Size - make it as big as you can get away with, with lots of bench and shelf 
space.  Your students will already be miserably cold, no need for them to be 
cramped too.

Good luck!
Frank





On 24/09/2019 23:40, Scott, Emily wrote:
Anyone out there specifically design rooms for (protein) crystallization at ~22 
deg and 4 deg C?  If you have successes or failures and can share any design 
specs with regard to vibration, temperature, and humidity tolerances, it would 
be much appreciated to pass on to the architects for our new laboratory.

Sincerely,
Emily Scott

--
Emily Scott, Ph.D.
Professor, Medicinal Chemistry/Pharmacology/Biophysics
Faculty Director, BioNMR Core Lab
University of Michigan
428 Church Street
Ann Arbor, MI 48109-1065
Phone:  734-764-3530
https://pharmacy.umich.edu/people/scottee
Lab webpage:  http://scottlab.info



**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues



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Re: [ccp4bb] MR for coiled coil structure

[Sergei Strelkov]

Dear Shengyuang,


Some further suggestions. To create a model towards MR searches, you could try 
our server for modelling coiled coils:

https://pharm.kuleuven.be/apps/biocryst/ccfold.php

It takes a few seconds to run.

The reference is here: https://www.ncbi.nlm.nih.gov/pubmed/28968723


I recommend trying a full-length model but also truncated versions (e.g. 1/2 of 
the total length; those may be more accurate locally).


Another thought, if you happen to have data for several crystal forms do try 
them all towards MR. The success of MR with coiled coils is highly dependent on 
the packing/space group. Some discussion on the matter can be found here:

https://www.ncbi.nlm.nih.gov/pubmed/28101862


HTH,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Shengyang Jin 

Sent: Wednesday, July 10, 2019 10:00
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MR for coiled coil structure

Dear all,

We recently acquired a data set (2.0 A, P222) for a coiled coil protein 
(according to Itasser, QUARK, Robetta, and Phaser).
Matthews coefficient indicates 1 copy of protein per ASU. Sequence of the 
protein is quite novel with no apparent homolog in PDB.
We tried to to MR with various models (ab initio or homology based) but with 
little success.

We then tried to use AMPLE, but in ccp4 it always returned this error:
__main__.py: error: unrecognized arguments: -use_arpwarp True
(if we untick arpwarp and choose buccaneer instead, it returns -use_arpwarp 
False)

Could anyone help?

Thank you very much.


Shengyang Jin
Nanyang Technological University
Singapore



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Re: [ccp4bb] Fo-Fc density close to cysteine residue

[Sergei Strelkov]

Dear Lumbini,


Certainly not a proof but your density looks like (di)methyl-arsinoyl-cysteine 
(PDB residue type CAF). This modification can happen when the protein has been 
exposed to cacodylate buffer. You can find such residues (and maps) in the PDB 
entries 3LPT or 5MDI.


Best wishes,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Lumbini Yadav 

Sent: Wednesday, July 10, 2019 13:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fo-Fc density close to cysteine residue

Thank you for the valuable input

On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Well - that more or less proves the residue is a CYS - there is a peak in the 
PHAN map right on the S.
And that the extra density does not contain an anomalous scatterer so is 
probably not a metal or a sulphate or...

But that still doesnt explain WHAT it is . Sorry not to be more help..

Eleanor

On Wed, 10 Jul 2019 at 11:32, Lumbini Yadav 
mailto:lumbin...@gmail.com>> wrote:
No I am using ccp4i. I tried doing SAD refinement in refmac and the output 
image is attached below .
I do not seen density near cysteine that was visible in Fo-Fc map

On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
The key word for refmac is ANOM MAPONLY
Are you using GUI2?
Eleanor

On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav 
mailto:lumbin...@gmail.com>> wrote:
I have soaked my crystals in  sodium dithionite a reducing agent. I have not 
done mass spec but sequence is confirmed

On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel 
mailto:dbon...@som.umaryland.edu>> wrote:
Have you mass-speced the protein before crystallization to make sure it wasn't 
derivatized during expression and/or purification, or compared the mass spec of 
the crystals verses purified protein? Any fancy reagents or other reductants 
used during purification?
What about S-Acetyl-cysteine (3-letter code: SCY).

Best,

Dan

Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457


From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Lumbini Yadav
Sent: Tuesday, July 09, 2019 5:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fo-Fc density close to cysteine residue

Dear all,

We have found a huge Fo-Fc density close to cysteine residue (see attached 
image) in the structure with resolution of 1.2A. In the crystallization 
condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and 
protein was in Tris and NaCl. Before freezing the crystals were soaked in 
mother liquor containing sodium dithionite.

I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD, 
CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in all the 
screenings we do see some part of Fo-Fc density unaddressed at 3 sigma.

Does anyone have an idea about what this density could be? Covalent 
modification?

Thanks.



Kind regards,
Lumbini



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Re: [ccp4bb] Interesting pattern on a crystallization drop

[Sergei Strelkov]

Artem (and Beatriz),


Me bad, could have thought about that! I think you are right.


There were initially bubbles in each drop (7 in one case, 4 in the other).

At some point the bubbles exploded (it was an instantaneous process, not just 
shrinking).


Kind regards,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography


From: CCP4 bulletin board  on behalf of Artem Evdokimov 

Sent: Thursday, March 28, 2019 1:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop

Neat!

Looks like multiple adjacent bubbles that were initially touching but 
eventually shrunk down to the central cores - the connectors are protein 
filaments (skin on the bubbles) left over from when bubbles had contact points.

Artem

On Wed, Mar 27, 2019, 19:39 Marshall, Bevan (Manufacturing, Parkville) 
 wrote:
Looked up the condition on C6 (https://c6.csiro.au/C6.asp) and that condition 
is found in both Index and JCSG screens as well as Classics II.


Bevan Marshall
Staff Scientist | Collaborative Crystallisation Centre
Manufacturing
CSIRO
E bevan.marsh...@csiro.auT +61 3 9662 7492
343-351 Royal Parade, Parkville, VIC 3052
www.csiro.au | https://c3.csiro.au
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From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
LEGRAND Pierre
Sent: Thursday, 28 March 2019 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interesting pattern on a crystallization drop

Dear Beatriz,

Nice drops :-))
Could it be that there is a reaction going on in these drops ?
The conditions are quite "exotic" with possibilities of coordination or 
oxydoreduction (Co2+/Co3+) or polymerization...
Do you have reductants with the protein buffer ?
Is the protein an enzyme or a metalloprotein ?
Just some ideas.

Best wishes,
Pierre


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
de la part de Beatriz Gomes Guimaraes 
[beatriz.guimar...@fiocruz.br]
Envoyé : mercredi 27 mars 2019 19:44
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Interesting pattern on a crystallization drop

Dear all,



I would like to share with you a surprising pattern I found when examining some 
crystallization plates (attached figures).



It is less obvious looking the photos, but apparently the "lines" are formed by 
precipitated protein and there are some "bubbles" with small drops inside. I 
wish they were microcrystals but I do not think this is the case.

I was suprised by the symmetry !



And it is not completely random because for the same condition the difference 
between the two drops are : protein alone ("hexagon") and protein + ligand 
("rhombus")


crystallization condition is:

0.01 M Cobalt(II) chloride hexahydrate

0.1 M Tris pH 8.5

20% w/v Polyvinylpyrrolidone K 15



Have you seen anything similar before?



Thank you for your comments!

Beatriz




--
Beatriz Guimarães
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ Paraná
Rua Prof. Algacyr Munhoz Mader, 3775   Bloco C
CIC 81350-010
Curitiba - PR, Brasil
Tel.:+55(41)3316-3225/2104-3438



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Re: [ccp4bb] Should we still keep copies of all raw data?

[Sergei Strelkov]

Dear John,


I certainly agree with your point. This would indeed be an argument to

keep copies of all datasets -- even though we are not any likely to look

at them ever again, beyond 1% of the more difficult cases.


Regards,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven <http://pharm.kuleuven.be/anafar>


From: John R Helliwell 
Sent: Friday, July 13, 2018 12:07
To: Sergei Strelkov
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Should we still keep copies of all raw data?

Dear Sergei,
Re "all". As a researcher my perspective is that one's funding agency 
requirement for a data management plan will be the core of what you would need 
to follow. Your employer may have additional policies and requirements placed 
on you as an employee. Eg the UK funding agency EPSRC requires data be retained 
for 10 years. My employer, University of Manchester, has a policy which regards 
data loss as research malpractice.
Central facility data retention policies vary from facility to facility so you 
would need to check ie for the ones you use.
For publication IUCr encourages raw data underpinning a publication be archived 
and its doi cited. That doi can also be entered into the relevant PDB 
deposition.
Best wishes,
John


Emeritus Professor John R Helliwell DSc

On 13 Jul 2018, at 10:30, Sergei Strelkov 
mailto:sergei.strel...@kuleuven.be>> wrote:


Dear All,


I believe this question may be of some interest.

In the past, we always stored all raw data ever collected by the lab.

With the recent advances, such as

(a) automated/on-the-fly processing offered by some (European) synchrotrons, and

(b) an ongoing discussion on centralized raw data archiving,

I wonder if it is time to revise the strict policy of keeping all data

(before we invest in a new NAS system... )


Best wishes,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven <http://pharm.kuleuven.be/anafar>



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[ccp4bb] Should we still keep copies of all raw data?

[Sergei Strelkov]

Dear All,


I believe this question may be of some interest.

In the past, we always stored all raw data ever collected by the lab.

With the recent advances, such as

(a) automated/on-the-fly processing offered by some (European) synchrotrons, and

(b) an ongoing discussion on centralized raw data archiving,

I wonder if it is time to revise the strict policy of keeping all data

(before we invest in a new NAS system... )


Best wishes,

Sergei


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven 



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[ccp4bb] Postdoctoral opening in structural biology (protein crystallography and drug discovery) at KU Leuven, Belgium

[Sergei Strelkov]

Postdoctoral opening in structural biology (protein crystallography and drug 
discovery) at KU Leuven, Belgium


There is an opening for a PhD level structural biologist (postdoc / senior 
postdoc) in my laboratory

(http://pharm.kuleuven.be/Biocrystallography). KU Leuven, ranked the 35th best 
university world-wide,

is a major node of biomedical research in Flanders, situated within a short 
drive from Brussels.

We are looking for candidates with a strong interest and track record in 
structural biology

(especially X-ray crystallography) and new drug discovery. A thorough command 
of crystallographic

computing, structural bioinformatics and/or rational drug design as well as 
ability to guide PhD

students are expected.


Please address further questions and submit your detailed CV (including a full 
publication list and

contact details of persons who could provide a recommendation) to 
sergei.strel...@kuleuven.be,

as soon as possible and before August 21.


Strong candidates will be invited to prepare an application towards the Maria 
Sklodowska-Curie

European Fellowship (IF) and/or internal KU Leuven postdoctoral fellowship, 
both before a September 14

deadline. This will include writing a research proposal in a close 
collaboration with us as host laboratory.

The overall topic should normally revolve around the structure-based drug 
design for several targets

that we are working on, in accordance with particular research interests of the 
candidate.

Prof. Sergei V. Strelkov
Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU 
Leuven
http://pharm.kuleuven.be/Biocrystallography

[ccp4bb] Retired Rigaku RU-H2R system

[Sergei Strelkov]

We are about to recycle an old Rigaku RU-H2R rotating anode system
(Cu anode, Yale mirrors). In case anyone is interested in some parts,
please contact me as soon as possible.

Regards,
Sergei

--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Lab pages: http://pharm.kuleuven.be/Biocrystallography

Re: [ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Sergei Strelkov]

I wanted to thank everyone who responded,
for a whole bunch of advice and suggestions!
Sergei



On 29-Jul-13 12:22 PM, Sergei Strelkov wrote:

Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete 
NFS-based

cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei



--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

[ccp4bb] Advice on setting up / maintaining a Ubuntu cluster

[Sergei Strelkov]

Dear all,

In old times I, just like about any protein crystallographer,
used to work on a cluster of SGI/IRIX workstations with complete NFS-based
cross-mounting of hard disks.

A typical operation included:
1. A single home directory location for every user:
if my home directory was on workstation X, I would by default use
it after logging on any of the workstations in the cluster.
2. A single location for all software for general use.
(And, obviously, 3. The ability to log on any node from
any terminal; today this is done via the 'ssh -X' command).

I wondered if someone could give us an advice on a painless
setup enabling 1. and 2., for a small cluster of Ubuntu computers.
We (will) have about five similar Dell computers in a local (192.168.*.*)
network (wired/wireless). Any tips on the hardware (especially the
LAN and network disks) are also welcome.

Many thanks,
Sergei

--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven
Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845   Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] Detwin

[Sergei Strelkov]

Dear Careina,

Could you please let us know what your cell parameters are?
And what is the twin law ('transformation') that you suspect?

Best wishes,
Sergei



Dear CCP4

I have data that is twinned with an L statistic of 0.43. It seems all 
the crystals that I produced were twinned sadly. Is there anything I 
can do to twinned data to make it easier to analyse?
I have tried to use the detwin software but it won't let me input a 
twinning operator for a standard transformation. I am not sure why? My 
space group is P21.

Thanks for your help
Careina

Re: [ccp4bb] asking for a reference for cacodylate decomposition in protein crystals upon X-ray exposure

[Sergei Strelkov]

Dear Tatyana,

We once had a project where the crystallization
condition contained cacodylate. The crystals diffracted
to 1.9A and survived reasonably well under the beam
(maybe there was indeed some colour change upon
exposure, I do not remember exactly).

We were working with drug soaks. The original structure is 1HYV.
The most interesting result of cacodylate presence
is modification of Cys residues. It was interpreted
as S-dimethylarsinoyl  cysteine.

Best wishes,
Sergei


On 30-Jul-12 12:53 AM, Tatyana Sysoeva wrote:

Hi!

I heard a couple of times that use of cacodylate buffers in 
crystallization is bad, and not only because of the compound toxicity.


As I understood, presence of the cacodylate in a protein crystal will 
cause a particular crystal degradation pattern upon X-ray exposure - 
darkening of the crystals, gas formation

I tried to find some references on that and failed in doing so.
I found some earlier discussions like this one:
http://www.proteincrystallography.org/ccp4bb/message23691.html
but don't have anything to reference in literature. I would appreciate 
if someone can point me to a right direction.


I am sorry if this question is out of the groups topic range.

Thank you in advance!
Sincerely,
Tanya



--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
ON2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845  Fax: +32 16 323469 OR +32 16 323460
Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

[Sergei Strelkov]

Dear Napoleão,

Thank you for updating everyone on your
efforts, and also acknowledging the advice.

I wanted to respond to your question regarding maps.
I know that many people who try to figure out
whether or not their MR solution is the right one
would ask the same question.

So first of all if you wonder why you actually get very
decently looking maps the answer is a classical one:
because 'the phases are more important than amplitudes'.
The appearance of your map is defined by
your model phases, and hence a good match between the
model and the map /may not/ be taken as
a sign of a correct solution. Once again: /never ever!/

On the contrary, at least in your coil1.jpg
image I clearly see that the density exactly follows
the model which is almost entirely poly-Ala.
Unless your protein is really poly-Ala this should be
alarming. If you had a correct solution they you
would hope to see the (difference)density for
at least some missing side chains.

And a second point. Unless your model contains
the complete chain (which is rarely the case, especially
for the coiled coils, as discussed already)
a sign of the correct solution would be the appearance
of extra density near the N- and/or C-terminus of
the model. If it is not there, it is almost certainly not
a solution.

And you should not be worried about the R-factors being
very high at this stage. If the solution is correct then
you should see at least some extra features in the map.

Kind regards,
Sergei



Thank you all for the replies.

Sorry for taking so long to reply, I was actually trying some of your
interesting ideas (and I'm still trying).

I tried using the low resolution data sets for the molecular replacement
(thanks to Yuriy Patskovsky), I also improved and increased my coiled
coil database and employed it in many approaches using EPRM (interesting
program I was not aware of), which I found to produce lots of data,
hopefully addressing at some extent the helixes bent (thanks to Bernhard
Rupp). I also tried some more tweaking in Phaser, although not sure if
did it properly (thanks to Randy Read).

There is no twinning as far as I can tell (thanks to Ed Pozharski for
the tip). Using a data set with enough completeness (360 degrees @
Brookhaven) and processing in P1 did not help me because in this space
group there is most likely 2-3 helixes in the asymmetric unit, which
complicates the problem (and it takes a lot of time for Phaser to run).
Automated approaches also did not yield a better result (as far as I can
tell). I'm convinced that the space group is C2221, but I may be wrong.

Thanks to Sergei Strelkov for the numerous useful suggestions on how to
approach the problem.

One of the big issues for me is to discriminate between a lot of
similarly good density maps. For example:

http://www.fullonline.org/coils/coil1.jpg
http://www.fullonline.org/coils/coil2.jpg

I have hundreds of solutions like these and I think they are all wrong.

I couldn't manage to run Arcimboldo, could not find a tutorial on it
either. It was highly recommended here (and elsewhere), so I'm
definitely willing to give it a try (thanks Isabel Uson).

You guys opened my eyes about a series of issues that I should learn
about and approach, I'm most thankful for that.
Best regards,
   Napo



--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
ON2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845  Fax: +32 16 323469 OR +32 16 323460
Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

[Sergei Strelkov]

Dear Napoleão,

I will try to summarize our experience and give some suggestions.

Few reasons why MR with coiled coils can be very tricky, such as
their asymmetric shape and their ability to overlap onto themselves
upon a shift and rotation (for a heptad-based coiled coil, this would be a
shift by 7 residues) have been already mentioned.
And I can add two more.

First, we very often see that coiled coils get bent due to
crystal contacts. This means that the conformation may be
quite different compared to your search model.
Second, many coiled coil sequences were seen to
assemble into structures different to what
they were supposed to be. Examples I know include
a trimer when a dimer was expected, an antiparallel
coiled coil when a parallel one was expected,
a monomer when a a dimer was expected,
chains offset with respect to each other, etc etc

We were able to phase several short (40-60 residues)
coiled coils by MR in the past. The paper
Strelkov SV et al (2002) EMBO Journal describes
two such cases (please look at the Methods section
which provides a fairly detailed explanation of what
we did). Both were done with Molrep.

I do have to say that we also failed on MR
miserably in many other cases, whatever we tried.
One recent example of a coiled coil fragment
that assembled to something entirely different
than we expected it to, is in Nicolet S et al (2010)
J. Struct. Biol. There, we really had to use heavy atoms.




I collected
various data sets (home source, Brookhaven and Diamond), including some
at the resolution of 1.65 A, for which the space group appears to be
C222 or C2221.


You have collected many data sets and you are still not sure
about the space group - ? Have you looked at the systematic absences
carefully? If you are still missing the (00l) axis then you
probably could try collecting it again while considering the
orientation of your crystal.

Knowing the correct space group is a valuable
information. Yes there are cases when you can not
distinguish between two space groups from the diffraction pattern
(e.g. P61 and P65) and then you /have/ to run your MR search
twice in both groups. Yes modern programs will do
it almost by default for you. But if you do know your correct space
group (for instance C2221 and not C222) then when you
do the MR search in the two space groups you /may/ (with some
luck) see better results with the first than with the second.
This /may/ be a hint that your C2221 solution is correct.




  I have tried A LOT of Molecular Replacement using Phaser and Phenix
AutoMR.
As mentioned already, is really advisable to try other MR programs 
(MolRep, epmr etc),

as in fact they are all based on different algorithms.


I'm using a 80% identity coiled coil helix as search model.
  Regarding the search model, I already tried trimming some or all
side chains and removing 2, 3 or 5 residues on each/both sides.


From your description I am guessing that you use a monomeric helix
currently - ?

Indeed you really should try different models, anything you can
get your hands on. In fact this is a number one factor to
get MR to work.

On one hand, you should indeed try shortening your
model (even systematically trimming one residue at a time).
Do not hesitate to use much shorter models (less than
half of your full helix). You can trim the wrong side chains
but I would not advise chopping off all of them.

With a short helix, once you have the first candidate
solution, try searching for a second copy with the packing penalty
switched off. If you get another helix overlapping with your first
solution (with some offset) this may be a sign of success.
(see the EMBO J paper)

On the other hand, our experience shows that in many cases
you can only get a solution if you use a full coiled coil
(dimer, trimer,...) and not a monomeric helix.

If your real structure is a non-crystallographic dimer etc,
then you should definitely search with a dimer etc.
If your oligomer is due to a crystallographic axis, then
you may try this as well, after switching off the
packing penalty. But beware that the oligomer
will almost certainly land on the axis, even for a wrong solution.

Hope this will help, and best of luck with your MR
searches -- which are fun, since they still require
some thinking!
Sergei

--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
ON2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845  Fax: +32 16 323469 OR +32 16 323460
Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

[ccp4bb] Postdoctoral Position in Structural Bioinformatics at the University of Leuven, Belgium

[Sergei Strelkov]

Postdoctoral Position in Structural Bioinformatics at the University of Leuven, 
Belgium

We have an opening for a computational scientist interested in protein 
structure.
The successful candidate should have a degree in computational mathematics,
bioinformatics or a related field. S/he is expected to have a thorough knowledge
of computational methods and scientific programming as well as previous
experience with analysis and modelling of biomolecules.

The successful candidate will play a key role in several collaborative projects.
The computational efforts of the new member will be supported by our ongoing
experimental work including protein crystallography and further biophysical
techniques. Topics to work on will include in particular modelling and analysis
of intermediate filaments and coiled-coil proteins as well as analysis of small-
angle X-ray scattering data from protein solutions. The expected output is both
 the creation of new software and gaining of novel biostructural knowledge by
 means of existing computational tools.  

Please address further questions and submit your CV (including a full 
publication
list and contact details of persons who could provide a recommendation) to Prof.
Sergei Strelkov, preferably before August 7, 2011. Applications from highly
experienced candidates with previous postdoctoral experience and excellent track
record are particularly welcome.

Selected publications:

Kuehnel K et al (2004) The VASP tetramerisation domain is a right-handed coiled
coil based on a 15-residue repeat. Proc. Nat. Acad. Sci. USA 101, 17027-17032.

Sokolova A et al (2006) Monitoring intermediate filament assembly by small-angle
 X-ray scattering reveals molecular architecture of assembly intermediates.
Proc. Nat. Acad. Sci. USA, 103, 16206-16211.

Herrmann H et al (2007) Intermediate filaments: from cell architecture to
nanomechanics. Nature Reviews Molecular Cell Biology 8, 562-73. 

Baranova EV et al (2011) Three-dimensional Structure of a-Crystallin Domain 
Dimers
of Human Small Heat Shock Proteins HSPB1 and HSPB6.  J. Mol. Biol. 411, 110-122.

Laboratory web page: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] SFCHECK produces incomplete postscript

[Sergei Strelkov]

April 1st, 2011


Dear Andy,

We have observed the same problem before,
and just today we could finally find an explanation.

Apparently, a new (still undocumented) functionality
was quietly introduced into few widely used oscillation data
processing programs, enabling the recording of the scattering
from antimatter atoms traditionally ignored in crystallography
(see a related discussion on this BB earlier today!).

While obviously a welcomed improvement, the inclusion
of antimatter SFs in the calculations has resulted in
aberrant behaviour of some other programs. This apparently
includes SFCHECK which attempts to calculate the R-factor and
further statistics, but since the data for matter and antimatter
cancel out, all you get is a blank output.

I wonder if Alexei already has a new version of SFCHECK
that outputs the matter and antimatter SF statistics separately - ?

HTH,
Sergei




Dear all,

I have been trying to compare a model that I'm refining against the native SFs using 
SFCHECK.  SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps 
files), but produces a postscript file with only the first page of output (and it is mostly blank). 
 There is the typical light-grey panels on a dark-grey background format that I'm used to for 
SFCHECK postscript files, but there are no figures or data.  Also, my mouse icon indicates it is 
hung trying to load/read the file (i.e. it's a moving busy icon under 
Linux).

I've tried other postscript viewers without luck.  I can successfully run SFCHECK 
on a completely different model/MTZ pair without problem though.  So does anyone know of 
circumstances that would lead to a hung postscript file from SFCHECK?

Thanks for your help,
-Andy

Re: [ccp4bb] while on the subject of stereo

[Sergei Strelkov]

Dear Dave,

Here come my five pence...
I personally found stereo graphics useful in two cases.

1. When you first introduce students to biomolecular
structure and/or biocrystallography. Showing stereo
certainly helps 'building up' the initial fascination,
which is very important of course. But since we do not
have a classroom stereo setup, I am just speaking
of seating a new/prospective (graduate) student
in front of a stereo workstation.

2. When one performs more difficult tasks while
doing research (although it was not your question).
This includes building difficult regions in poor/low resolution
maps as already mentioned, but maybe even more
importantly when trying to make sense of a difficult
MR case and finally when dealing with protein docking.

However:
1. In my experience, what at least the better students
do is to look at a structure using a simple program
like Swiss PDB Viewer or Rasmol and their 300 euro
laptop. No arguments can persuade them
to use the 3000 euro lab stereo setup -- because they
can manage to see what they want to see by just
rotating the molecule...

2. For both teaching purposes and publications,
I remain an adept of printed stereo pairs.
Get each of your students a 5 euro stereo viewer
and give them a handout full of stereo pairs
rather than mono images. The very important
this is that, on paper, one can make
notes and drawings. An active digestion
of the teaching material (rather than passive
starring at your screen) has been known to help
efficient learning since long ago...

I can summarize my view as follows:
for /most/ purposes, you should be fine
by using one of the two:
simple mono graphics to achieve
the 3D effect by rotation -- or printed
stereo pairs.

HTH
Sergei


Thanks for the comments, I do appreciate them.  I guess we went off in a
direction I wasn't thinking of - related to your personal like or
dislike of stereo.  What I am really looking for is an answer to a
simple question in that is stereo a nice thing from a pedagogy
standpoint for showing students complex biomolecules.

I am in a chemistry department - undergraduate only.  We focus on
3-dimensional shape and the importance of shape of chemical
function/reactivity/etc...  With small molecules (PF5, etc...), it's
easy to see how shape works by simply rotating the molecule.  The
molecules are small enough, the concept of 3D can be visualized easily
in these systems.  Furthermore, they can make a simple model using your
standard organic or inorganic model kit, no worries.

Now, bring in a huge protein, or a protein-protein complex.  The issue
of 3Dness becomes fuzzier.  It's not so easy to see which hydrogen will
get plucked off during a chemical reaction, even with careful zooming
and mouse manipulation.  So my question still is, how many of you feel
stereo is important from a pedagogy standpoint (not looking at maps,
just structures that are huge and complex).  Is it something that we
need to try to bring to the classroom, or is it just a cool toy like the
3D TV that hopefully is going nowhere and will soon fade out like the
viewmaster of old.  I know a large percentage of people cannot see
stereo (at least the way we present it), and so it isn't for everybody.
But, does it help, and if so, does it help when done in a huge classroom
or when put on an individual screen.  Has anybody tried to assess this
(there's a horrible word for you).

That's what I was wondering about.  Presenting the stereo is a different
issue (how is that done), but I think there are lots of avenues for that
depending on your particular situation.

Thanks again

Dave

Re: [ccp4bb] helix translation

[Sergei Strelkov]

Dear Young-Tae,

The program Twister (Strelkov and Burkhard, 2002) can calculate this,
among other things. If you are interested I would gladly send you
the program.

Of course one should look into the reason for your helix having
an aberrant geometry. If it is just a slightly distorted a-helix
then you should still see the classical hydrogen bonding pattern between
the mainchain atoms.

Best wishes,
Sergei




Dear colleagues,

I am analyzing a helical segment that looks a bit off from the 
traditional alpha-helix. Does anyone knows a program for calculating 
alpha helix translation per residue along the helical axis?


Thanks,
Young-Tae

Young-Tae Lee, Ph. D.
Research Associate
David Goodin lab
Dept. of Molecular Biology
The Scripps Research Institute

Re: [ccp4bb] High Rmerge with thin frames

[Sergei Strelkov]

Dear All,

first of all, I would like to thank the many
good people who have responded to my query.
Yet another truly interesting discussion on this BB!

As a partial summary, two points:

1. Few people suggested that our high Rmerge problem
could be caused by experimental troubles
like phi angle imprecision rather than the crystal itself.
Thus far we could not find indications for that but maybe
we did not look carefully enough. However, the
frames ARE weak, and I tend to think
that this is the main cause of the problem.

2.  Few people argued that data processing programs
(XDS in particular) 'should' handle thin frames
as efficiently as thicker frames...
After digesting these (very useful!) arguments,
I still tend to think that the best proof would be in the pudding,
i.e. trying to pool thin frames into thicker frames
(but I do not have an immediate means of doing this... )

Sergei




Dear All,

I am processing a dataset collected (not by me) with 0.1 degree
oscillations.
The diffraction is quite weak even though there is a clean diffraction
pattern to about 3A.

Either Mosflm or XDS processes the data readily with +/- default settings
but both yield a high overall Rmerge of about 0.23 in the expected symmetry.
Processing in P1 yields an overall Rmerge of ~0.18, but what is
especially disappointing
is that Rmerge is as high as 0.15 at ~5A resolution already.

The question is, how can we process the data so that the merging statistics
becomes more reasonable?

Apparent mosaicity turns out to be ~0.5A. My naive way of thinking is
to try treating each five consecutive frames as a single 0.5 degree frame.
Does anyone have experience with this?

Many thanks in advance,
Sergei





--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
ON2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845  Fax: +32 16 323469 OR +32 16 323460
Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

[ccp4bb] High Rmerge with thin frames

[Sergei Strelkov]

Dear All,

I am processing a dataset collected (not by me) with 0.1 degree 
oscillations.
The diffraction is quite weak even though there is a clean diffraction 
pattern to about 3A.


Either Mosflm or XDS processes the data readily with +/- default settings
but both yield a high overall Rmerge of about 0.23 in the expected symmetry.
Processing in P1 yields an overall Rmerge of ~0.18, but what is 
especially disappointing

is that Rmerge is as high as 0.15 at ~5A resolution already.

The question is, how can we process the data so that the merging statistics
becomes more reasonable?

Apparent mosaicity turns out to be ~0.5A. My naive way of thinking is
to try treating each five consecutive frames as a single 0.5 degree frame.
Does anyone have experience with this?

Many thanks in advance,
Sergei

Re: [ccp4bb] coiled coil question

[Sergei Strelkov]

  

  
Dear all,

 Is anyone aware of a structure where the individual alpha helical
chains of a coiled coil are related by a crystallographic axis? Or does
anyone know of a coiled coil structure (dimer or higher order
oligomer) that is perfectly symmetric at least in terms of the
protein backbone or alpha carbon atoms?

Thanks and best regards,
Xie

  

  
  

Dear Xie,

there is a plenty of coiled coils that sit on crystallographic 2, 3...
-folds.
Examples: 1x8y (dimer), 1ox3 (trimer), ...
Why do you ask? ;)

Sergei

[ccp4bb] In-house X-ray systems: what is your experience

[Sergei Strelkov]

Dear All,

following a good discussion recently on the crystallization
imaging systems, I wanted to start a discussion with respect
to choosing a new in-house X-ray source (rotating anode).

Bruker is there with Microstar-H and Microstar Ultra.
Rigaku has 007HF and FR-E+.

I wondered if people who have recently considered or bought
such systems could express their opinions with regard to few
points, including (1) true intensity, (2) reliability, (3) ease of service
such as alignment, filament chance, anode rebuild...

I will post a summary afterwards.
Many thanks in advance!
Sergei Strelkov


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

[ccp4bb] Vacancy posting: PhD student position in structural biology / protein crystallography

[Sergei Strelkov]

A PhD student position in protein
crystallography / structural
biology is available in the
Laboratory for
Biocrystallography, Department of Pharmaceutical Sciences, University of Leuven, Belgium
(http://pharm.kuleuven.be/anafar/).


The PhD student will participate in one or more
high-impact
medically-oriented structural biology 
projects carried out in
intramural and
international collaboration. The activities of the successful
 candidate
will include recombinant
protein isolation, crystallization, X-ray crystallographic
 and
small-angle
solution scattering studies as well as modelling.


The applicant should have a MSc or a
BSc diploma in
biochemistry, biophysics, bioinformatics
 or a related field. A record
of
research experience is a scientific laboratory is a must. Strong
interest
 in computational methods is a plus. The working language will be
English.


Our laboratory is hosted in a brand-new building
and is
fully equipped with an X-ray diffractometer 
(Rigaku/Mar),
crystallization
facilities, wet labs and a computer cluster. Leuven is a university
town
 located 20 km east of Brussels.
The University of Leuven is ranked among the top centres for

biomedical
research in Belgium.
Rich history, remarkable architecture and proximity of Brussels,

Paris and London
make
Leuven an outstanding location. 

The search for suitable candidates is open
immediately and
will continue until the position is filled. 
The target starting date is
September
1st, 2008, but can be negotiated.  Please
address any further 
questions and/or your application, including a
detailed CV,
publication list and a list of referees, 
to Prof. Sergei Strelkov via
e-mail.


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.

[ccp4bb] Job advert: Postdoctoral and PhD student posts at the University of Leuven, Belgium

[Sergei Strelkov]

1. A postdoctoral position is available to work with Prof. Sergei 
Strelkov in
the Laboratory for Biocrystallography, Department of Pharmaceutical 
Sciences,
Catholic University of Leuven. The successful candidate should have 
considerable
experience in protein crystallography, especially including cloning, 
purification and crystallization
of recombinant proteins, as well as a strong publication record. Good 
communicational
skills and ability to guide junior group members are essential. The post 
is fully funded by the
University of Leuven 'OT' grant for a period of up to four years, 
pending sufficient progress.


The main research project will be aimed at elucidating the 
three-dimensional structure
of intermediate filaments using X-ray crystallography, small-angle X-ray 
scattering
and other biophysical methods. For background information see Strelkov 
et al

(2002) EMBO J 21, 1255-1266; Strelkov et al (2003) Bioessays 25, 243-251;
Herrmann et al (2007) Nature Reviews Molecular Cell Biology, 8, 562-573.
In addition, the postdoctoral fellow will participate in further 
collaborative,

high-impact medically-oriented projects focussed on protein structure.
Our laboratory is hosted in a brand-new building and is fully equipped with
an X-ray diffractometer (Rigaku/Mar), crystallization facilities, wet 
labs and a computer cluster.


2. In addition, a PhD student ('assistent') post in protein 
crystallography is available.
The applicants should have a BSc or MSc diploma in biophysics, 
bioinformatics or a related field
and at least some experience in research. The post is funded for a 
period of up to five years.
NB: the PhD student will participate in the teaching of undergraduate 
students; correspondingly,

proficiency in Dutch is required!

The search for suitable candidates is open immediately and will continue 
until the positions are
filled. The target starting date for either post is October 1st, 2007, 
but can be negotiated.
Please send your application, together with a detailed CV, publication 
list and a list of referees,
to: sergei.strelkov(at)pharm.kuleuven.be. Leuven is a university town 
located 20 km
east of Brussels. Rich history, remarkable architecture and proximity of 
both Brussels

and the North sea make Leuven an outstanding location.

Laboratory homepage is at http://pharm.kuleuven.be/anafar
(currently undergoing a major overhaul, to be competed in a few weeks' 
time).


--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Catholic University of Leuven
Campus Gasthuisberg, ON2 Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 33 08 45  Fax: +32 16 32 34 69
Mobile: +32 486 29 41 32


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

[Sergei Strelkov]

Many thanks to good people who have responded
to my message! Apparently I have to apologize for not formulating
my question clearly enough. Here is more explanation.

According to Ewald construction, diffraction images
collected by oscillation method correspond to thin 'curved' slices of the
reciprocal space. What I am looking for is a program to generate the 
reciprocal

space (as a 3D map) from these 'slices' directly, *without* any indexing or
integration of I's. This is a simple purely geometrical calculation.

This is *not* anything routinely done for normal high-quality crystal data.
For a good dataset, such a conversion should simply yield a lattice
with distinct points. For our partially-ordered crystals, this should 
help us

visualizing the actual 'shapes' of our reflections (many of them
are smeared/overlapping).

My guess that folks working with semi-ordered systems, such as liquid 
crystals

or lipid bilayers, should have some programs like that...
any ideas?

Thank you again,
Sergei.



Dear All,

we are dealing with a difficult case of a 'partially ordered' protein 
crystal.

Here it would be very useful to view the reciprocal space
as a 3D map. Is anyone aware of a program that would convert
standard oscillation data (one-degree frames, mar225)
into such a map? What we need is a direct conversion.
There is a program in CCP4 that is able to 'visualize' the reciprocal
space, but it requires hkl's as input.

Thank you,
Sergei Strelkov




--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Catholic University of Leuven
Campus Gasthuisberg, ON2 Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 33 08 45  Fax: +32 16 32 34 69
Mobile: +32 486 29 41 32
E-mail:  [EMAIL PROTECTED] 



Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm