Re: [ccp4bb] Question about CCP4 monomer dictionaries

[Steiner, Roberto]

Hi Stephen

A value of 1.48 A sounds reasonable to me. For H2O2
https://cccbdb.nist.gov/exp2x.asp?casno=7722841=0
Also in the paper below we have the structure of a peroxide derivative pretty 
much at atomic resolution and the O-O distance refined at 1.47 A
Bui et al. Direct evidence for a peroxide intermediate and a reactive 
enzyme-substrate-dioxygen configuration in a cofactor-free 
oxidase.
Angew Chem Int Ed Engl. 2014 Dec 8;53(50):13710-4. doi: 10.1002/anie.201405485. 
Epub 2014 Oct 14.

HTH

Best wishes
Roberto

__
Professor Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab


roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
Viale G. Colombo 3
35131 Padova, Italia
Telefono 0039 049 8276409

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From: CCP4 bulletin board  on behalf of 
"stephen.c...@rc-harwell.ac.uk" <8f3604def7f0-dmarc-requ...@jiscmail.ac.uk>
Reply to: "stephen.c...@rc-harwell.ac.uk" 
Date: Monday, 28 November 2022 at 18:29
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Question about CCP4 monomer dictionaries

You don't often get email from 8f3604def7f0-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important
Dear CCPBB,

I have a question regarding the origin of the monomer libraries in CCP4.  I ask 
because I have quoted the bond length listed in the monomer library describing 
peroxide in a manuscript and a referee has asked for a reference since they 
seem to disagree with the quoted value of ~1.48 A. My understanding is that 
parameters describing bond length, angles etc are derived from structures in 
the CSD is this the case?  Is there an appropriate reference out there 
somewhere?

Thanks very much in advance,
Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
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Re: [ccp4bb] Highest resolution of X-ray / neutron / electron crystallography, cryo EM

[Steiner, Roberto]

Just queried the PDB and found 4AR3 for neutron at 1.05A.

Best
Roberto


On 9 Jun 2020, at 14:46, Tobias Beck 
mailto:tobiasb...@gmail.com>> wrote:

Dear all,

Thanks for the link to the latest BioRxiv papers! So for cryo EM it is 1.2 now. 
Any numbers for neutron?

Best, Tobias.

Tobias Beck mailto:tobiasb...@gmail.com>> schrieb am Di. 
9. Juni 2020 um 15:35:
Dear all,

I was asked by a student what the highest resolution is, for each of the four 
methods listed above. Maybe someone has researched the current numbers 
previously and would like to share them? For X-ray, I found 0.48 A in the PDB. 
For EM method details, the PDB gives me 0.6 A, but it is actually for electron 
diffraction. I found a structure with 1.8 A for Cryo EM.

I am aware that resolution is only one parameter and that high resolution may 
not correspond to high data quality. However, maybe someone knows the record 
holders, either for biomacromolecules or small molecules or for both.

Thanks!

Best, Tobias.






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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London






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Re: [ccp4bb] powdery residue on pucks?

[Steiner, Roberto]

Fully agree with what others have said. When ’the dust’ happened to us we had 
to replace that particular shipping dewar as T was not holding for very long.

Best wishes
Roberto

On 22 Feb 2020, at 00:33, Emilia C. Arturo (Emily) 
mailto:ecgart...@gmail.com>> wrote:

Hi All,

We have been noticing lately that our crystal pucks return from different 
beamlines coated with the same powdery material. For the record, we typically 
undo our pucks, clean the assemblies and dry out the pucks within a day of 
receiving the shipping dewar, but notice the same thing regardless of how long 
between receiving the dewar and disassembling the pucks. Have any of you 
experienced this sort of thing, or have suggestions of what might be the cause 
and/or the powdery material?

Regards,
Emily.

--
"Study as if you were going to live forever; live as if you were going to die 
tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May 
Alcott




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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London






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Re: [ccp4bb] Shipping samples for neutron diffraction

[Steiner, Roberto]

Dear Stephen

I guess the first thing to understand is whether you have a RT or cryo NMX 
planned. In my personal experience the transition from RT to cryo NMX is not 
necessarily straightforward. If you (and the beam line scientist) are sure that 
cryocooled xtals will give you an experiment then this is the easiest option 
for an anaerobic sample. However, I would certainly suggest a RT backup.

If you go for RT, given that your xtal will sit in front of neutrons for days I 
would certainly make sure that once outside your shipping airtight contained 
your sample is anaerobic for a sufficient length of time. Air diffusion will 
happen to some extent but it might not be necessarily too bad. That will depend 
on how sensitive your particular system is to O2. This can also be tested on a 
X-ray home source after your capillary have been left sitting in air for, let’s 
say, a week.

Best of luck with those deuterons.
Roberto

On 19 Feb 2020, at 10:22, 
stephen.c...@rc-harwell.ac.uk 
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear CCP4 community,


I have an impending trip to a neutron source and was wondering how people tend 
to ship their samples prior to beam time?  Is sending something frozen best or 
is sealed in a capillary more sensible or is there another better way?  One 
caveat is that ideally my sample should remain anaerobic which has me leaning 
towards frozen, but I guess in pcr type tubes sealed in gas tight vessels is 
also a viable option?


Any thoughts or suggestions are very much appreciated.


Best wishes,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
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Re: [ccp4bb] Errors reading mmcif files when trying to deposit coordinates to pdb

[Steiner, Roberto]

I assume you’re using ccp4i and not i2. If you use the latter the mmcif coords 
file produced should be ok.
I have had the same problem a few days ago.

Best wishes
Roberto


On 25 Sep 2019, at 15:00, 
stephen.c...@rc-harwell.ac.uk 
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:

Dear ccp4ers,


I have refined several structures using refmac5 within ccp4i and tried to 
upload the output mmcif files to the pdb in order to deposit the 
coordinates/structure factors.

However, during the initial upload process when the files are scanned I get the 
following errors:


ERROR - Read file 'input_file_1' failed:

syntax error at line 30421

ERROR - syntax error at line 30426

Warning - Duplicate category name chem_comp_atom at line 30428

Warning - Duplicate category name chem_comp_bond at line 30446

Warning - Duplicate category name chem_comp_angle at line 30467

ERROR - syntax error at line 30581

ERROR - syntax error at line 30585


These all lie after the coordinates in the dictionary part of the file.  When I 
have investigated this I cannot see any duplicated category names that would 
result in the above warnings and the syntax errors are not a result of anything 
obvious.  I have checked for hidden characters, found none, and can see nothing 
else wrong.  Finally, line 30585 does not exist, the file stops at 30584.


Has anyone had similar problems or any suggestions that might solve this?


Thanks,


Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
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Guy's Campus
SE1 1UL
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Re: [ccp4bb] select from a pdb file a sphere of atoms

[Steiner, Roberto]

pymol?

example
S1 around 12.3  a.  Atoms with centers within 12.3 Angstroms of the center 
of any atom in S1
Best wishes
Roberto

On 3 Apr 2019, at 15:18, Stephen Cusack mailto:cus...@embl.fr>> 
wrote:

Dear All,

 I am looking for an accessible programme that allows selection of atoms from a 
PDB file

within a sphere of inputted radius from a central atom.

Thanks for any help,

Stephen Cusack

--

**
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Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

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Professor Roberto Steiner
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London










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[ccp4bb] Faculty positions in cryoEM at King's College London

[Steiner, Roberto]

Dear Colleagues

I would like to draw your attention on the following Lecturer/Senior Lecturer 
positions in cryoEM available at King’s College London. Closing date for the 
application is 11-Apr-2019.

https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=011466

https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=011489

With best wishes

Professor Roberto Steiner
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London









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Re: [ccp4bb] Crystallization problems using MPD (2-Methyl-2,4-pentanediol)

[Steiner, Roberto]

Hi js

It happened to us as well with a 1:1 protein complex with decent affinity (Kd 
about 1 uM). The MPD-based condition (quite high % MPD if I recall correctly) 
would break the complex apart and only one of the two components formed a 
crystal (effectively allowing crystallisation of a sample with 50% purity). In 
the end we did not do anything particularly clever. Changed the construct a bit 
and the complex gave crystals in a different set of conditions.

Best of luck.

Roberto


On 1 Feb 2019, at 16:42, Jorg Stetefeld 
mailto:jorg.stetef...@umanitoba.ca>> wrote:


Hi everyone,



this is Joerg Stetefeld.



I would like to approach the community in a peculiar case of 
2-Methyl-2,4-pentanediol (MPD)
impacting our crystallisation experiments.



We are working on extracellular ligand-receptor complexes, which we 
characterize in advance to crystallisation attempts very thoroughly 
(SEC-MALS/AUC/MST/iSCAMS a.o.). It happens frequently that whenever MPD is part 
of the setup the complexes are disrupted and just one of the molecules forms a 
single crystals. Solving these structures shows always a very distinct, 
spiral-like pore assembly of this respective molecule and the other binding 
partner cannot be detected. Attempts to “find” and characterize the MPD binding 
site(s) failed.



Remarkably, these phenomena can also be detected in solution and EM images are 
indicating the same behavior.



Did anyone experience similar cases and how can this be avoided?



Your advise is appreciated.



js





Jörg Stetefeld, PhD


https://stetefeldlab.ca/






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Roberto A. Steiner
Professor of Biomolecular Structure
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London




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Re: [ccp4bb] Refinement with native and anomalous data

[Steiner, Roberto]

Dear Piotrek

You can find some info on the use of prior phase information in refinement with 
Refmac in

Acta Crystallogr D Biol 
Crystallogr. 2011 
Apr;67(Pt 4):355-67. doi: 10.1107/S0907444911001314. Epub 2011 Mar 18.
REFMAC5 for the refinement of macromolecular crystal structures.
Murshudov 
GN1,
 Skubák 
P,
 Lebedev 
AA,
 Pannu 
NS,
 Steiner 
RA,
 Nicholls 
RA,
 Winn 
MD,
 Long 
F,
 Vagin 
AA.

and references therein.

As stated in the paper (paragraph 2.2.2), the incorporation of prior phase 
information by the refinement function is especially useful in the early and 
middle stages of model building and at all stages of structure solution at 
lower resolutions, owing to the improvement in the observation-to-parameter 
ratio.
Refinement in Refmac is very fast therefore the best thing (as you just did) is 
to try both options and see.

With best wishes
Roberto



On 4 Jan 2019, at 09:55, Piotr Wilk 
mailto:wilk.piot...@gmail.com>> wrote:

Dear Eleanor,

I have used the ACORN previously for structure solution but I will have to read 
more about its functionality in structure refinement.
I have run two Refmac jobs using either native or anomalous data with otherwise 
default parameters resulting in R/Rfree of 0.2013/0.2458 and 0.1862/0.2274 
respectively for crystal diffracting to ~1.85A. This seems to me, that using 
anomalous signal in refinement can be useful at least in some cases.

Regards,
  Piotrek


Hmm - you can certainly generate "MAD" phases using the anom signal from one 
data set, and then PARROT or some such density modification tool to extend 
those phases for the higher resolution reflections..
Or ACORN can work well if he data resolution is high enough to give good phases 
for all the data


Then you can use those phases in the initial refinement procedure - the usual 
idea is to use them till the R factor drops below 30% or 35% then just refine 
against the Fobs, phasing just from the model .

But I dont think it is ever worth working at a limited resolution..


Dear Eleanor,

thank you for your comment. My crystals of interest diffract with dmin usually 
between 1.4 and 1.9 A (in high energy data set) and significant anomalous 
signal extends usually to approx. 4 A (in low energy data set).
Certainly I do agree, that in "EITHER, OR" situation one can check both 
approaches, compare the results and take the more convincing one. I can easily 
do that in Refmac running one job against data with Friedel pairs merged and 
parallel one against data with Friedel pairs unmerged. I was considering rather 
an "AND" scenario in which in addition to high resolution data (FP) I'd include 
information from anomalous signal (F+ F-, DANO). I understand that this should 
increase number of observations from a given sample and therefore help to 
refine positions, occupancies and perhaps ADPs for at least a fraction of atoms 
in a model (Mn ions and S in my case). I imagine it as somehow analogical to 
adding geometrical restrains derived from very high resolution data to 
refinement protocols.
I was wondering first of all if my reasoning is sensible and if there is an 
existing protocol to try this?

With kind regards,
 Piotrek

czw., 3 sty 2019 o 22:00 Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> napisał(a):
Hmm - you can certainly generate "MAD" phases using the anom signal from one 
data set, and then PARROT or some such density modification tool to extend 
those phases for the higher resolution reflections..
Or ACORN can work well if he data resolution is high enough to give good phases 
for all the data


Then you can use those phases in the initial refinement procedure - the usual 
idea is to use them till the R factor drops below 30% or 35% then just refine 
against the Fobs, phasing just from the model .

But I dont think it is ever worth working at a limited resolution..

eleanor

On Thu, 3 Jan 2019 at 20:40, Piotr Wilk 
mailto:wilk.piot...@gmail.com>> wrote:
Dear Eleanor,

thank you for your comment. My crystals of interest diffract with dmin usually 
between 1.4 and 1.9 A (in high energy data set) and significant anomalous 
signal 

[ccp4bb] PhD opportunity

[Steiner, Roberto]

Dear all

An exciting computational PhD position is available to extend the current 
capabilities of Refmac5, one of the flagship programs of the CCP4 suite, to the 
field of neutron crystallography.
Details for the application can be found at 
https://www.kcl.ac.uk/health/study/studentships/div-studentships/randall/steiner.aspx
Please feel free to contact 
roberto.stei...@kcl.ac.uk or 
ga...@mrc-lmb.cam.ac.uk for informal details.

With best wishes
Roberto



Professor Roberto A. Steiner
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London




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Re: [ccp4bb] XQuartz and High Sierra OSX

[Steiner, Roberto]

Yes. Things are now fine using 2.7.11. I just had to play a bit with the Apple 
Thunderbolt Display which was causing XQuartz to behave funny.
Problem solved.

Cheers
Roberto


On 4 Dec 2017, at 13:39, Engin Özkan 
<eoz...@uchicago.edu<mailto:eoz...@uchicago.edu>> wrote:


Hi,

I have been using Xquartz 2.7.11 (the latest release) perfectly fine on High 
Sierra. We did not have to downgrade to 2.7.8. CCP4i and Coot works perfectly 
fine with XQuartz 2.7.11 on multiple iMacs and MacBook Pros we have in the lab.

Best,

Engin

On 12/4/17 4:49 AM, Martin Montgomery wrote:
Dear Roberto,

You can install Xquartz 2.7.8 which is still available from the xquartz web 
site.  This was the last version where Xquartz behaved properly and it runs 
fine on High Sierra.

Regards

MGM


Martin G Montgomery
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mrc-mbu.cam.ac.uk=01%7C01%7Croberto.steiner%40KCL.AC.UK%7C06113be020af498f49b308d53b1fd0e7%7C8370cf1416f34c16b83c724071654356%7C0=EBaOqIeiudEp2d42gZQUOyWuxXEX7VlQ6r5eEWNlDY8%3D=0>

On 2 Dec 2017, at 00:04, Steiner, Roberto 
<roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>> wrote:

Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
fresh installation) does not longer behave properly. Essentially, X11 does not 
seem to understand touchpad actions (for example cannot close X11 windows, 
cannot drag them around, etc.). This problems also affects programs that rely 
on X11. Has anyone experienced (and ideally solved) this problem?

Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London




Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] XQuartz and High Sierra OSX

[Steiner, Roberto]

Solution: I noticed yesterday that XQuartz was behaving normally when my laptop 
was not connected to the Apple Thunderbolt Display. Resetting the Thunderbolt 
Display solved the problem.

Roberto

On 2 Dec 2017, at 00:04, Steiner, Roberto 
<roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>> wrote:

Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
fresh installation) does not longer behave properly. Essentially, X11 does not 
seem to understand touchpad actions (for example cannot close X11 windows, 
cannot drag them around, etc.). This problems also affects programs that rely 
on X11. Has anyone experienced (and ideally solved) this problem?

Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London



Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk<mailto:roberto.stei...@kcl.ac.uk>
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

[ccp4bb] XQuartz and High Sierra OSX

[Steiner, Roberto]

Hi all

Since my recent upgrade to High Sierra, XQuartz (most recent version 2.7.11 - 
fresh installation) does not longer behave properly. Essentially, X11 does not 
seem to understand touchpad actions (for example cannot close X11 windows, 
cannot drag them around, etc.). This problems also affects programs that rely 
on X11. Has anyone experienced (and ideally solved) this problem?

Thanks in advance
Roberto

Roberto A. Steiner, PhD
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] A polite reminder to xia2 users

[Steiner, Roberto]

shocking ! it should have been Steiner, RA (not Steiner R or Steiner, RS,)

plus the most recent one is missing from the list….!

REFMAC5 for the refinement of macromolecular crystal structures.
Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, 
Long F, Vagin AA.
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. 


Cheers
Roberto (A.)



> On 5 Nov 2015, at 16:22, Keller, Jacob  wrote:
> 
> I have a general question about this: many programs in CCP4 have 
> interdependencies, so does one have to ferret out and cite all dependencies? 
> For example, I recently was looking up the citation for Refmac, and was 
> astonished to see the list below. Now, are we really supposed to cite all 
> nine of these for each time Refmac is used/mentioned (provided those features 
> were used)? I certainly understand the reasoning for accumulating citations 
> for continued funding, but, well...really?
> 
> JPK
> 
> Refmac
> 
> "Application of Maximum Likelihood Refinement" G. Murshudov, A.Vagin and 
> E.Dodson, (1996) in the Refinement of Protein structures, Proceedings of 
> Daresbury Study Weekend.
> "Refinement of Macromolecular Structures by the Maximum-Likelihood method" 
> G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) in Acta Cryst. D53, 240-255.
> "Incorporation of Prior Phase Information Strengthen Maximum-Likelihood 
> Structure Refinemen" N.J.Pannu, G.N.Murshudov, E.J.Dodson and R.J.ReadA 
> (1998) Acta Cryst. section D54, 1285-1294.
> "Efficient anisotropic refinement of Macromolecular structures using FFT" 
> G.N.Murshudov, A.Lebedev, A.A.Vagin, K.S.Wilson and E.J.Dodson (1999) Acta 
> Cryst. section D55, 247-255.
> "Use of TLS parameters to model anisotropic displacements in macromolecular 
> refinement" M. Winn, M. Isupov and G.N.Murshudov (2000) Acta Cryst. 2001:D57 
> 122-133
> "Fisher's information matrix in maximum likelihood molecular refinement." 
> Steiner R, Lebedev, A, Murshudov GN. Acta Cryst. 2003 D59: 2114-2124
> "Macromolecular TLS refinement in REFMAC at moderate resolutions," Winn MD, 
> Murshudov GN, Papiz MZ. Method in Enzymology, 2003:374 300-321
> "Direct incorporation of experimental phase information in model refinement" 
> Skubak P, Murshudov GN, Pannu NS. Acta Cryst. 2004 D60: 2196-2201
> "REFMAC5 dictionary: organisation of prior chemical knowledge and guidelines 
> for its use." Vagin, AA, Steiner, RS, Lebedev, AA, Potterton, L, McNicholas, 
> S, Long, F and Murshudov, GN. Acta Cryst. 2004 D60: 2284-2295
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme 
> Winter
> Sent: Thursday, November 05, 2015 9:07 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] A polite reminder to xia2 users
> 
> Dear xia2 users on the CCP4bb,
> 
> While we of course welcome any recognition of the use of xia2 in structure 
> depositions and publications, we would like to gently remind users that xia2 
> uses other software *on your behalf* for example but not limited to XDS, 
> pointless, aimless, mosflm, DIALS, CCP4. Please could you also include the 
> citations for these packages in your publications and depositions, so that 
> the software used on your behalf gets appropriate recognition :)
> 
> This is made slightly easier for you as xia2 writes out appropriate citations 
> for the packages it has used as illustrated here
> 
> http://xia2.blogspot.co.uk/2015/11/xia2-citing-software-xia2-has-used.html
> 
> If you have found xia2 *and* XDS useful (say) in a PDB deposition where the 
> processing was performed with xia2 -3d, then appropriate text could be
> 
> REMARK 200  INTENSITY-INTEGRATION SOFTWARE : xia2/XDS
> REMARK 200  DATA SCALING SOFTWARE  : xia2/XSCALE
> 
> or
> 
> 
> REMARK 200  INTENSITY-INTEGRATION SOFTWARE : xia2/MOSFLM
> 
> REMARK 200  DATA SCALING SOFTWARE  : xia2/AIMLESS
> 
> since this would recognise the contributions of the program authors while 
> making it clear that the "blame" for any poor choices made in the processing 
> belonged to xia2.
> 
> We appreciate in some cases (not limited to Diamond Light Source) the MTZ 
> file from your data may appear "by magic" and you may not have run the 
> software yourself - even in this case it should be straightforward to find 
> out from the log file, which should be looked at, which packages were used.
> 
> We appreciate your help with this, it makes our relationship with other 
> program authors *much* easier.
> 
> Thanks & best wishes Graeme
> 
> -- 
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail 

Re: [ccp4bb] A polite reminder to xia2 users

[Steiner, Roberto]

For ‘standard refinement’ I typically cite the most recent general paper. In 
the case of Refmac: 

> REFMAC5 for the refinement of macromolecular crystal structures.
> Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn 
> MD, Long F, Vagin AA.
> Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. 

With best wishes
RAS


> On 5 Nov 2015, at 17:40, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> 
> Yes it seems there are some typos, like "refinemen[sic]."
> 
> But the general question remains: should authors really cite all of these 
> papers when Refmac is used? What's the best practice?
> 
> JPK
> 
> -Original Message-
> From: Steiner, Roberto [mailto:roberto.stei...@kcl.ac.uk] 
> Sent: Thursday, November 05, 2015 11:42 AM
> To: Keller, Jacob
> Cc: <CCP4BB@JISCMAIL.AC.UK>
> Subject: Re: [ccp4bb] A polite reminder to xia2 users
> 
> shocking ! it should have been Steiner, RA (not Steiner R or Steiner, RS,)
> 
> plus the most recent one is missing from the list….!
> 
> REFMAC5 for the refinement of macromolecular crystal structures.
> Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn 
> MD, Long F, Vagin AA.
> Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. 
> 
> 
> Cheers
> Roberto (A.)
> 
> 
> 
>> On 5 Nov 2015, at 16:22, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
>> 
>> I have a general question about this: many programs in CCP4 have 
>> interdependencies, so does one have to ferret out and cite all dependencies? 
>> For example, I recently was looking up the citation for Refmac, and was 
>> astonished to see the list below. Now, are we really supposed to cite all 
>> nine of these for each time Refmac is used/mentioned (provided those 
>> features were used)? I certainly understand the reasoning for accumulating 
>> citations for continued funding, but, well...really?
>> 
>> JPK
>> 
>> Refmac
>> 
>> "Application of Maximum Likelihood Refinement" G. Murshudov, A.Vagin and 
>> E.Dodson, (1996) in the Refinement of Protein structures, Proceedings of 
>> Daresbury Study Weekend.
>> "Refinement of Macromolecular Structures by the Maximum-Likelihood method" 
>> G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) in Acta Cryst. D53, 240-255.
>> "Incorporation of Prior Phase Information Strengthen Maximum-Likelihood 
>> Structure Refinemen" N.J.Pannu, G.N.Murshudov, E.J.Dodson and R.J.ReadA 
>> (1998) Acta Cryst. section D54, 1285-1294.
>> "Efficient anisotropic refinement of Macromolecular structures using FFT" 
>> G.N.Murshudov, A.Lebedev, A.A.Vagin, K.S.Wilson and E.J.Dodson (1999) Acta 
>> Cryst. section D55, 247-255.
>> "Use of TLS parameters to model anisotropic displacements in 
>> macromolecular refinement" M. Winn, M. Isupov and G.N.Murshudov (2000) 
>> Acta Cryst. 2001:D57 122-133 "Fisher's information matrix in maximum 
>> likelihood molecular refinement." Steiner R, Lebedev, A, Murshudov GN. 
>> Acta Cryst. 2003 D59: 2114-2124 "Macromolecular TLS refinement in 
>> REFMAC at moderate resolutions," Winn MD, Murshudov GN, Papiz MZ. 
>> Method in Enzymology, 2003:374 300-321 "Direct incorporation of 
>> experimental phase information in model refinement" Skubak P, 
>> Murshudov GN, Pannu NS. Acta Cryst. 2004 D60: 2196-2201
>> "REFMAC5 dictionary: organisation of prior chemical knowledge and 
>> guidelines for its use." Vagin, AA, Steiner, RS, Lebedev, AA, 
>> Potterton, L, McNicholas, S, Long, F and Murshudov, GN. Acta Cryst. 
>> 2004 D60: 2284-2295
>> 
>> 
>> 
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Graeme Winter
>> Sent: Thursday, November 05, 2015 9:07 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] A polite reminder to xia2 users
>> 
>> Dear xia2 users on the CCP4bb,
>> 
>> While we of course welcome any recognition of the use of xia2 in 
>> structure depositions and publications, we would like to gently remind 
>> users that xia2 uses other software *on your behalf* for example but 
>> not limited to XDS, pointless, aimless, mosflm, DIALS, CCP4. Please 
>> could you also include the citations for these packages in your 
>> publications and depositions, so that the software used on your behalf 
>> gets appropriate recognition :)
>> 
>> This is made slightly easier for you as xia2 writes out appropriate 
>> citations for the packages it has used as illustrated here
>

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

[Steiner, Roberto]

SITUS is another good option.

R

From my iPhone

On 26 Jun 2015, at 08:20, Deborah Harrus har...@free.fr wrote:

 Dear Weifei,
 
 You might want to use SUPCOMB from the ATSAS suite.
 http://www.embl-hamburg.de/biosaxs/supcomb.html
 
 Cheers,
 
 Deborah.

[ccp4bb] I

[Steiner, Roberto]

From my iPhone

Re: [ccp4bb] Bulk solvent

[Steiner, Roberto]

On 12 Jan 2015, at 10:09, Bernhard Rupp 
b...@ruppweb.orgmailto:b...@ruppweb.org wrote:

What still evades me is, why exactly is the Babinet immune to these effects of 
excluding/masking-out unmodelled parts?
The Babinet correction is also a function of the MODELLED part, just the 
opposite sign. So an incomplete model
de facto equals an over-estimated solvent. Is it just the high effective 
dampening of this correction (B ~200) as
Pavel said that makes it less susceptible because the higher resolution 
reflections are less affected and
therefore have a chance to correct/overcome the inadequate (implicit) masking?

I have the feeling that this might be the case.
More details on the two bulk-solvent correction methods available in Refmac 
(with formulae) are in Murshudov et al (2011) Acta Cryst D67, 355-367 - Section 
2.4

Best wishes
Roberto



Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor 
Dodson
Sent: Sonntag, 11. Januar 2015 17:05
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Bulk solvent

Yes. If the model is incomplete it is obviously not sensible to use the mask 
based solvent - you will tend to lose the unmodelled features. It also gives 
unrealistically low R factors for a crystal with high solvent content. However 
the best test would be to analyse maps and try to decide if  when the 
different procedures work best.. A project for a student dissertation perhaps??
  Eleanor

On 9 January 2015 at 20:13, Roberts, Sue A - (suer) 
s...@email.arizona.edumailto:s...@email.arizona.edu wrote:
I always try both methods - usually there is little difference.  However,

For CueO (multicopper oxidase) where there are about  25 disordered (unseen) 
residues in a loop,  using Babinet scaling instead of the default refmac 
scaling reduced the R factors by about 2% (both R and Rfree) and improved the 
quality of the maps substantially.

From Dirk's comment, I'd guess this is because the mask-based solvent model is 
putting solvent where there is (disordered) protein, which is different from 
real bulk solvent.

Sue

Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1306 E. University Blvd,  Tucson, AZ 85721
Phone: 520 621 4168tel:520%20621%204168
s...@email.arizona.edumailto:s...@email.arizona.edu



-Original Message-
From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent

Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction 
instead of mask based scaling?
Armando



Roberto A. Steiner, PhD
Randall Division of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

[ccp4bb] J

[Steiner, Roberto]

From my iPhone

Re: [ccp4bb] Classification of Ig-like domains

[Steiner, Roberto]

Dear Thomas 

There are several Ig-like domains that do not contain S-S bridges . 
I am not aware of a software tool that does what you'd like. However, two key 
papers on the Ig-like fold (old but still very relevant) that might be useful 
to you are:

(1) Bork, Holm  Sander - The Immunoglobulin Fold. Strcutural Classification, 
Sequence Patterns and Common Core - J.Mol.Biol (1994) 242, 309-320.

(2) Harpaz  Chothia - Many of the Immunoglobulin Superfamily Domains in Cell 
Adhesion Molecules and Surface Receptors Belong to a New Structural Set Which 
is Close to That Containing Variable Domains - J. Mol. Biol. (1994), 238, 
528-539.

With best wishes
Roberto


On 9 Oct 2014, at 08:42, Thomas Krey tk...@pasteur.fr wrote:

 Dear all,
 
 I was wondering, if there is a tool out there that allows the easy 
 classification of immunoglobulin and Ig-like domain subclasses based on a 
 given pdb file. As far as I am aware the state-of-the-art for immunoglobulin 
 domains is to determine the distance (in amino acids) between the two 
 cysteines forming the canonical disulfide bond between strands B and F. 
 However, I am facing a couple of Ig-like domains that do not contain this 
 disulfide bond !
 Any help will be highly appreciated.
 
 Best regards
 Thomas
 
 Dr. Thomas Krey
 Institut Pasteur
 Structural Virology Unit
 25-28 Rue du Docteur Roux
 75015 Paris
 France
 tk...@pasteur.fr


Roberto A. Steiner, PhD
Randall Division of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine 
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Re: [ccp4bb] Metal ion differentiation - reg

[Steiner, Roberto]

If you have a access to a synchrotron you can try double difference anomalous 
DDANO maps see Than et al. Acta Cryst. (2005). D61, 505–512 for an example


Best
Roberto

On 1 Jul 2014, at 16:10, Dhanasekaran Varudharasu 
dhana...@gmail.commailto:dhana...@gmail.com wrote:

Dear all,

  I have solved a structure (using molecular replacement) of 
metallo-enzyme  which may have Zn or Ni at its active site. I  collected data 
at in-house CuKa radiation. Now, I am able to locate the active site metal ion 
preciously but I am not able to differentiate whether it is Zn or Ni. I 
computed anomalous difference map and I got good anomalous map also. But still 
there is ambiguity, since Zn and Ni have closest F values at CuKa radiation ( 
For Zn = 0.68 and For Ni = 0.51). But both, Zn and Ni have different F' values 
at CuKa radiation ( For Zn = -1.61 and For Ni = -3.07).

My question is that,

Can we used F' value information to differentiate metal ions?.

Is it possible to find whether I have Zn or Ni at active site of my enzyme 
using  crystallographic technique?.

Thanks in advance

--
Dhanasekaran Varudharasu
Post-Doctoral Fellow
Department of Oral Biology
Rutgers school of Dental Medicine
Rutgers Biomedical and Health Sciences
Newark, NJ 07103
USA




Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Refining Metal Ion Occupancy

[Steiner, Roberto]

Straightforward in Refmac...(a CCP4 package)...

From my iPhone

On 6 May 2014, at 18:02, Chris Fage cdf...@gmail.com wrote:

 Hi Everyone,
 
 In my 2.5-angstrom structure, there is negative Fo-Fc density
 surrounding a metal ion after refining in Phenix. From anomalous
 diffraction I am certain of the metal's identity and position in each
 monomer. Also, the ion is appropriately coordinated by nearby side
 chains. Should I be refining the occupancy of the ion in attempt to
 flatten the negative density? I am considering soaking the metal ion
 into crystals or cocrystallizing and collecting additional datasets.
 
 Thanks for your help!
 
 Regards,
 Chris

Re: [ccp4bb] Phasing with Many Monomers/AU

[Steiner, Roberto]

In my experience translational NCS also can a part when one has many molecules 
in the a.u. If MR is an option, modern packages are rather good in dealing with 
TNCS.
We used Molrep + Refmac at 3.x A (still unpublished) for a case with 18 
complexes (36 monomers) in the a.u. and things weren't as bad as I originally 
thought.

BTW, we later made the construct 3 aa longer and we got 1 dimer in the a.u. 
with xtals diffracting to 2 A. I would consider playing a bit with your 
construct (not only the tag).

Good luck!

R

On 18 Jan 2014, at 17:14, Chris Fage 
cdf...@gmail.commailto:cdf...@gmail.com wrote:

Hello Everyone,

I am currently trying to phase a structure with an asymmetric unit predicted to 
contain 20-24 monomers (space group P1). The native crystals, while beautiful 
in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and 
SeMet-derived crystals grow with poor morphology (small needles). Also, based a 
fluorescence scan, I know that mercury does not bind appreciably. Other than 
screening for a new space group, what options might I have for phasing this 
many monomers at lower resolution? Is there any real chance of solving the 
structure in this space group?

Thank you in advance for any suggestions!

Regards,
Chris
Crystals.jpg

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

[Steiner, Roberto]

Many (more) reviewers  - [panic on Roberto's face] 
Isn't real peer-review just a question of standing the test of time? 
A piece of work blatantly wrong will sooner or later be picked up by someone 
(although I acknowledge that wrong papers can have serious consequences on 
one's ability to 
get funding).  Limitations on a piece of research due to whatever reason will 
be hopefully lessened by other authors or the next generation(s) of scientists. 
Overall, I don't think the current system is really that bad. 

Cheers
Roberto

On 10 Oct 2013, at 06:57, miguel miguel.ortiz-lombar...@afmb.univ-mrs.fr
 wrote:

 (Sorry if you get this twice. The first time as marked as junk by our email 
 server. Well, it may be junk after all...)
 
 Hi Marco,
 
 Impact factor is the last refuge of the publishing system as it is.
 Precisely because in this ocean of untrusted publications we tend to
 believe that high impact factor journals deserve our respect. This is
 more or less all right: among those who have investigated the issue some
 are more pessimistic than others about the quality of papers published
 in those journals. Yet, it is hard to believe that their papers are
 generally worse than those of not-so-high impact factor journals. But
 from a scientific point of view, taking into account the evolution of
 research and publishing, the trust that we give to high impact journals
 is, in my opinion, wishful thinking.
 
 Concerning peer-reviewing, I don't think that adding more opacity will
 help. On the contrary. What I believe, but I don't have any proof of it,
 is that peer-reviewing is useful only if it is more transparent, engages
 in a real scientific discussion (understood as a conversation, not as an
 exchange of messages separated by weeks) and is open to (many) more
 reviewers. But that alone will not help if the way research is done does
 not evolve at the same time.
 
 On Wed, 9 Oct 2013 18:56:32 -0700, Marco Lolicato wrote:
 Hi scientists,
 this interesting topic brought back to my mind a similar discussion I
 had with a colleague of mine and now I want to share it with you guys.
 As Vale already pointed out, the peer-review process seems to be far
 from an ideal system: there are many papers in which one of the author
 is himself the editor of the journal in which the paper is published;
 the impact factor of a journal is becoming the only way to judge the
 quality of a paper (and of the authors) [example:  one of the European
 Commission grants has as mandatory eligibility criterium that the
 applicant should have at least one paper published in a high IF
 journal...I'm asking...Why?].
 I have also the suspect (from my insignificant experience) that some
 papers are accepted in really high IF journals without a clear
 peer-review process, but basing the decision mostly on the authors
 listed in that paper.
 Anyway, for those reasons and more, I was wondering if maybe is
 nowadays needed to revisit the peer-review process. One thing that
 immediately came out was: the authors of a papers should be hidden to
 both the reviewers and the editors, so that paper will be judged only
 on the intrinsic quality and not from the names on it or from the
 country.
 
 I'm looking forward to see your opinion.
 
 
 Marco
 
 
 
 
 Il giorno 09/ott/2013, alle ore 15.00, Miguel Ortiz Lombardia ha scritto:
 
 Hi denizens,
 
 Now that Biology has gone missing, at least in the programs of the
 funding agencies in this part of the world, the reflections that I'm
 going to expose concern at best that even smaller field of natural
 philosophy that we euphemistically call, not without a twist of candour,
 biomedicine. At worst, they only concern the world whose limits are
 the limits of my language.
 
 As I understand it, the main purpose of really existing peer-reviewing
 is to act as a filter. By selecting those papers deemed publishable it
 spares us the herculean task of reading every possible piece emanating
 from our overheated brains. This actually reveals a big problem of
 really existing research (with the caveat expressed in the first
 paragraph). But I'm not going to venture into that problem: more clever
 minds have drowned in its muddy waters. Back to the point, if the need
 of publishing were not such a strong source of inspiration and we
 researchers would feel the compelling necessity of publishing only when
 we could write well-structured and thoughtful papers, full of useful
 data and rich in new ideas and hypotheses, we could then read a
 reasonable percentage of the papers concerning our fields of interest.
 In that utopia, peer-reviewing could be a continuous, transparent and
 open process that would involve a relevant part of the community. Not
 likely to happen and probably for good: knowledge seems to progress by a
 combination of slow accretion of small steps and sudden
 (re)interpretations of those steps.
 
 But what is interesting to see in that utopian/dystopian possibility is
 that really 

Re: [ccp4bb] Concerns about statistics

[Steiner, Roberto]

BTW there's a also an earlier paper (properly cited in Karplus  Diederichs 
2012) showing the benefit of weak 'high-resolution' reflections.

Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):988-1000. doi: 
10.1107/S0907444910029938. Epub 2010 Aug 13.
Inclusion of weak high-resolution X-ray data for improvement of a group II 
intron structure.
Wang J.
Department of Molecular Biophysics and Biochemistry, Yale University, New 
Haven, CT 06520, USA. jimin.w...@yale.edu

Abstract
It is common to report the resolution of a macromolecular structure with the 
highest resolution shell having an averaged I/sigma(I)  or = 2. Data beyond 
the resolution thus defined are weak and often poorly measured. The exclusion 
of these weak data may improve the apparent statistics and also leads to claims 
of lower resolutions that give some leniency in the acceptable quality of 
refined models. However, the inclusion of these data can provide additional 
strong constraints on atomic models during structure refinement and thus help 
to correct errors in the original models, as has recently been demonstrated for 
a protein structure. Here, an improved group II intron structure is reported 
arising from the inclusion of these data, which helped to define more accurate 
solvent models for density modification during experimental phasing steps. With 
the improved resolution and accuracy of the experimental phases, extensive 
revisions were made to the original models such that the correct tertiary 
interactions of the group II intron that are essential for understanding the 
chemistry of this ribozyme could be described.

Best wishes
Roberto

On 14 Jun 2013, at 10:43, Dirk Kostrewa kostr...@genzentrum.lmu.de
 wrote:

 Dear Andrea,
 
 I agree with Tim and still cut the resolution at I/sigma=2. In my 
 experience, including higher resolution shells with poorer signal-to-noise 
 never changed the apparent resolution of the electron density maps.
 In addition, the high resolution limit at I/sigma=2 coincides very well 
 with the point where the Fo vs. Fo +Gauss(0,1)*sigma(Fo) correlation 
 coefficient curve, reported by BUSTER, crosses the recommended lower limit of 
 0.9.
 
 And please note, CC*=0.5 corresponds to CC(1/2)=0.143. In my very limited 
 experience, I/sigma=2 corresponds to roughly CC(1/2)~0.7.
 
 Although I'm very excited about the CC(1/2) or CC* paper by Karplus  
 Diederichs, I still prefer to be on the save side, until it has been verified 
 in numerous cases, that choosing high resolution cutoffs based on CC(1/2) 
 really leads to higher resolution structures. The recommended procedure to 
 include small resolution increments in refinement to decide the high 
 resolution cutoff is very time-consuming.
 
 Best regards,
 
 Dirk.
 
 
 Am 13.06.13 17:15, schrieb Andrea Edwards:
 Hello group,
 I have some rather (embarrassingly) basic questions to ask. Mainly.. when 
 deciding the resolution limit, which statistics are the most important? I 
 have always been taught that the highest resolution bin should be chosen 
 with I/sig no less than 2.0, Rmerg no less than 40%, and %Completeness 
 should be as high as possible. However, I am currently encountered with a 
 set of statistics that are clearly outside this criteria. Is it acceptable 
 cut off resolution using I/sig as low as 1.5 as long as the completeness is 
 greater than 75%? Another way to put this.. if % completeness is the new 
 criteria for choosing your resolution limit (instead of Rmerg or I/sig), 
 then what %completeness is too low to be considered? Also, I am aware that 
 Rmerg increases with redundancy, is it acceptable to report Rmerg (or Rsym) 
 at 66% and 98% with redundancy at 3.8 and 2.4 for the highest resolution bin 
 of these crystals? I appreciate any comments.
 -A
 
 -- 
 
 ***
 Dirk Kostrewa
 Gene Center Munich
 Department of Biochemistry
 Ludwig-Maximilians-Universität München
 Feodor-Lynen-Str. 25
 D-81377 Munich
 Germany
 Phone:+49-89-2180-76845
 Fax:  +49-89-2180-76999
 E-mail:   kostr...@genzentrum.lmu.de
 WWW:  www.genzentrum.lmu.de
 ***
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

Dear Kavya

What about using occupancy refinement in refmac?
link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy 
refinement.

R


On 12 Apr 2013, at 17:12, Kavyashree Manjunath ka...@ssl.serc.iisc.in
 wrote:

 Dear users,
 
 Is it advisable to refine the occupancy of
 a ligand for a 2.0Ang data by approximately
 changing the values of occupancy based on
 its b-factor?
 After refinement, there were some negative
 densities appearing in some parts of the
 ligand, like at the centre of a pyrimidine
 ring, so I expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.
 
 Thanking you
 With Regards
 Kavya
 
 
 -- 
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Ligand occupancy refinement ~2.0Ang

[Steiner, Roberto]

So there is a CCP4 GUI

Just prepare a txt file with the relevant occupancykeywords and use it in the 
GUI under 'Refmac keyword file'

Best
R

From my iPhone

On 12 Apr 2013, at 19:50, Kavyashree Manjunath ka...@ssl.serc.iisc.in wrote:

 Respected Sir,
 
 I saw this option in refmac5 - 5.6.0037, (I use
 refmac5-5.6.0117), but is this option present in
 GUI?
 
 Thanking you
 With Regards
 Kavya
 
 Dear Kavya
 
 What about using occupancy refinement in refmac?
 link http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ follow occupancy
 refinement.
 
 R
 
 
 On 12 Apr 2013, at 17:12, Kavyashree Manjunath ka...@ssl.serc.iisc.in
 wrote:
 
 Dear users,
 
 Is it advisable to refine the occupancy of
 a ligand for a 2.0Ang data by approximately
 changing the values of occupancy based on
 its b-factor?
 After refinement, there were some negative
 densities appearing in some parts of the
 ligand, like at the centre of a pyrimidine
 ring, so I expected that the problem is with
 the occupancy. (the crystal was obtained by
 co-crystallisation method).
 Kindly provide some suggestions.
 
 Thanking you
 With Regards
 Kavya
 
 
 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 
 
 Roberto A. Steiner
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London
 roberto.stei...@kcl.ac.uk
 
 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL
 London
 
 Phone 0044 20 78488216
 Fax0044 20 78486435
 
 
 
 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 
 
 
 
 
 -- 
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.
 

Re: [ccp4bb] delete subject

[Steiner, Roberto]

I fully agree that questions should keep coming. In addition it might be worth 
pointing out that CCP4 (and others) organise great crystallographic schools 
which are ideal for this sort of problem. Most of the schools ask you to bring 
your own data (!) and you can sit down with developers and experts who will 
help at length with practical and theoretical questions.

Roberto



From my iPhone

On 28 Mar 2013, at 04:47, Frank von Delft 
frank.vonde...@sgc.ox.ac.ukmailto:frank.vonde...@sgc.ox.ac.uk wrote:

mistake?  I beg to differ, violently:  a student had an honest question and 
did exactly what the ccp4bb exists for:  posted his question there.  Moreover, 
when asking he showed he had thought about it, and provided complete background 
-- that's what we all want, right?

  *   I disagree with Tassos:  the email was not rude, on not one of the counts 
he listed.  (I concede he may have had a bad day... I had one on Monday :-)
  *   I disagree (slightly) with Tim:  the teasing was not malicious.
  *   And I share Mark's dream...

Students:  please don't stop asking your questions here!!!

phx.




On 27/03/2013 22:47, VAN RAAIJ , MARK JOHAN wrote:
Dear Tom,
don't feel too bad about it - everyone can make a mistake.
Some of the replies give crystallographic tips that may be useful to other 
beginning and not-so-beginning crystallographers. Although I agree the 
attachments to the first mail would perhaps better be deleted from the records.
Greetings,
Mark


Quoting Tom Van den Bergh 
mailto:tom.vandenbe...@student.kuleuven.betom.vandenbe...@student.kuleuven.bemailto:tom.vandenbe...@student.kuleuven.be:

Is it possible to delete my post: refinement protein structure from ccp4 bb, i 
get too many bad reactions. I think its bettter to just delete the whole topic.

Greetings,

Tom

Re: [ccp4bb] refinement protein structure

[Steiner, Roberto]

we should all chip in a water molecule or two and the second author becomes 
the CCP4 community….

On 27 Mar 2013, at 17:22, Antony Oliver antony.oli...@sussex.ac.uk
 wrote:

 At the risk of being somewhat cheeky - perhaps I could claim second author?
 I too have successfully solved the structure - and I totally concur with Phil.
 Placing a second molecule in the asymmetric unit, essentially resolves the 
 perceived R-factor problem.
 
 A good thorough manual inspection and rebuilding is *ALWAYS* good practice 
 for newcomers to the field.
 
 Tony.
 
 
 On 27 Mar 2013, at 17:14, Petr Leiman petr.lei...@epfl.ch
 wrote:
 
 Since this is now public domain knowledge and if this gets ever published, 
 Phil has my vote to be the first author!
 
 Petr
 
 
 On Mar 27, 2013, at 6:09 PM, Phil Jeffrey wrote:
 
 That's quite brave - shipping your entire structure to people that could be 
 actual competitors.  But it was fun to play at 1.4 Angstrom over lunch.
 
 Practical points:
 
 * not everyone loves 12Mb of attachments in one email in their inbox, so if 
 you do this again please put the files on a webserver and point us there
 
 Structural points:
 
 * the map looks pretty good, but I think the sequence is misassigned in 
 some regions (e.g. A118-A122 etc).  Automation is a good tool but a poor 
 master, and extreme caution is required before taking the results too 
 literally.  Usually you'd expect a 1.4 Angstrom to be easy to autobuild but 
 I recently had a sequence misassignment at just that resolution. That map 
 was trivial to interpret with the correct sequence however - one of the 
 joys of working with Arp/wArp at 1.4 Angstrom.
 
 * the large number of positive difference density blobs and water molecules 
 clustered in what otherwise would be the solvent void strongly suggest that 
 there's a second molecule present.
 
 
 If I take redfluorescentprotein_refine_10.pdb (waters removed) and 
 exptl_fobs_phases_freeR_flags.mtz and ask Phaser to look for two molecules, 
 it finds them quite successfully.  (for the record an LLG of 15111 using 
 nominal sequence identity of 90%).  I will send this to you off-list.  
 Please note that Phaser is using a different origin for this molecular 
 replacement solution so the coordinates and your previous map do not 
 overlap.
 
 This rather nicely explains why your structure had an R-factor in the 40's 
 despite being a half-way decent model.  The new MR solution has an R-free 
 in the 30's in the phenix.refine job I'm running right now.
 
 
 Going forward I suggest you utilize the Arp/wArp program to autobuild your 
 structure for you, starting from the molecular replacement solution (or, 
 perhaps with it stripped to ALA).  While you could use Autobuild, this is 
 the CCP4 list and so you should use CCP4 programs.
 
 Phil Jeffrey
 Princeton
 
 
 On 3/27/13 12:22 PM, Tom Van den Bergh wrote:
 Dear members of ccp4bb,
 
 I need some help with the refinement of my structure of a variant of
 mRFP (monomer red fluorescent protein, sequence in attachment). I have
 done molecular replacement with phaser with model 2VAD of protein
 database. Then i have done some model building phenix.autobuild. (2
 pdb's (overall...), freeR flags and log file attached) When i refine
 with phenix.refine my structure i get a R-value of 0,42 which is still
 way too high. (redfluorescent protein.pdb, .mtz and logfile attached)
 When i look at the structure in coot i find many unmodelled blobs and
 many outliers in density analysis and rotamer analysis. The problem is
 that there are so many problems with my structure, that i dont know
 where to begin. Could you try some refinement for me, because this is
 first structure that i need to solve as a student and i dont have too
 many experience with it.
 
 Greetings,
 
 Tom
 
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] first use of synchrotron radiation in PX

[Steiner, Roberto]

Nice account on the subject

J Synchrotron Radiat. 2010 July 1; 17(Pt 4): 433–444.
Published online 2010 May 14. doi:  10.1107/S0909049510011611
Impact of synchrotron radiation on macromolecular crystallography: a personal 
view

Zbigniew Dauter,a,* Mariusz Jaskolski,b,* and Alexander Wlodawer,c,*


On 13 Mar 2013, at 19:22, DUMAS Philippe (UDS) p.du...@ibmc-cnrs.unistra.fr 
wrote:

 Jean Witz  (now deceased) once told me that the following paper is the first 
 one mentionning data collection on a synchrotron.
 The journal is not really obscure and the paper should easily be found.
 The work was done in Germany, if I remember well.
 
 G. Rosenbaum, K.C. Holmes and J. Witz, Synchrotron radiation as a source for 
 X-ray diffraction, Nature, 230, 434-437 (1971). 
 
 Philippe Dumas
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] CCP4 Update 014

[Steiner, Roberto]

I can only echo Kay's comments. The CCP4 update system is just great.
 
Together with a few others I was one of the initial beta testers of the update 
system. Beta-testing could not have not been easier. The thing just worked!

Congratulations on an brilliant and extremely useful piece of software.

Roberto

On 20 Jan 2013, at 11:32, Kay Diederichs kay.diederi...@uni-konstanz.de
 wrote:

 Hi Andrey, Eugene and others -
 
 it is time to say that this new system is extremely useful, and so easy to 
 use at the same time! Gone are the times when one had to worry about manually 
 updating parts of CCP4. 
 I just wonder why there should ever be a need for a CCP4 6.4.0 release; a 
 rolling update seems just adequate to me - but that's just a user's 
 perspective, and probably this has been discussed somewhere although I'm not 
 aware of it.
 
 thanks for making this available, and the hard work to make it so perfect!
 
 Kay
 
 On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev 
 andrey.lebe...@stfc.ac.uk wrote:
 
 Dear CCP4 Users
 
 A CCP4 update has just been released, consisting of the following changes.
 
 All systems:
 
 *   Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on 
 request, or when have tNCS or twinning
 *   Othercell: Various bug fixes
 *   PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex 
 situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
 empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper
 
 Linux and Mac only: *)
 
 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)
 
 *)  Corresponding changes for Windows have been already included in update 
 No 13
 
 Windows only:
 
 *   Phaser.ensembler: Corrected path to syminfo.lib
 
 
 If you do not currently receive updates, consider re-installing your CCP4 
 setup using the latest binary packages, which now have CCP4 Update manager 
 (ccp4um) integrated.
 
 Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
 therefore upgrade if necessary. Please report any bugs to 
 c...@stfc.ac.ukmailto:c...@stfc.ac.uk
 
 
 Many thanks for using CCP4.
 
 Andrey Lebedev
 
 
 -- 
 Scanned by iCritical.
 

Roberto A. Steiner
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London
roberto.stei...@kcl.ac.uk

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London

Phone 0044 20 78488216
Fax0044 20 78486435

Re: [ccp4bb] Pisa application

[Steiner, Roberto]

Maybe

Nat 
Protoc.http://www.ncbi.nlm.nih.gov/pubmed?term=Predicting%20protein-protein%20interactions%20on%20a%20proteome%20scale%20by%20matching%20evolutionary%20and%20structural%20similarities%20at%20interfaces%20using%20PRISM#
 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367.
Predicting protein-protein interactions on a proteome scale by matching 
evolutionary and structuralsimilarities at interfaces using PRISM.
Tuncbag 
Nhttp://www.ncbi.nlm.nih.gov/pubmed?term=Tuncbag%20N%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Gursoy 
Ahttp://www.ncbi.nlm.nih.gov/pubmed?term=Gursoy%20A%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Nussinov 
Rhttp://www.ncbi.nlm.nih.gov/pubmed?term=Nussinov%20R%5BAuthor%5Dcauthor=truecauthor_uid=21886100,
 Keskin 
Ohttp://www.ncbi.nlm.nih.gov/pubmed?term=Keskin%20O%5BAuthor%5Dcauthor=truecauthor_uid=21886100.
Source
Center for Computational Biology and Bioinformatics, College of Engineering, 
Koc University, Rumelifeneri Yolu, Sariyer Istanbul, Turkey.
Abstract
Prediction of protein-protein interactions at the structural level on the 
proteome scale is important because it allows prediction of protein function, 
helps drug discovery and takes steps toward genome-wide structural systems 
biology. We provide a protocol (termed PRISM, protein interactions bystructural 
matching) for large-scale prediction of protein-protein interactions and 
assembly of protein complex structures. The method consists of two components: 
rigid-body structural comparisons of target proteins to known template 
protein-protein interfaces and flexible refinement using a docking energy 
function. The PRISM rationale follows our observation that globally different 
protein structures can interact via similar architectural motifs.PRISM predicts 
binding residues by using structural similarity and evolutionary conservation 
of putative binding residue 'hot spots'. Ultimately,PRISM could help to 
construct cellular pathways and functional, proteome-scale annotation. PRISM is 
implemented in Python and runs in a UNIX environment. The program accepts 
Protein Data Bank-formatted protein structures and is available at 
http://prism.ccbb.ku.edu.tr/prism_protocol/.


On 8 Aug 2012, at 07:33, Careina Edgooms wrote:

Dear ccp4ers

I just wonder whether anybody knows if the PISA software could be used/modified 
to detect potential interfaces of interaction of different proteins? This would 
be very useful as a tool to validate protein-protein interactions detected by 
in vivo methods such as yeast 2 hybrid screens. If PISA is not quite there yet, 
does anyone know of other software that could do a similar thing?

Best
Careina

Roberto Steiner
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry

[Steiner, Roberto]

My understanding is that ML functions in the presence of pseudo-translational 
symmetry are suboptimal (see a very short discussion in Acta Cryst. (2011). 
D67, 355–367. Acta Cryst. (2008). D64, 99–107 is also a good reading).
Having said that if your crystal/dataset exhibits twinning on top of 
pseduo-translation you should activate the twin refinement option in Refmac.

Roberto

On 31 Jul 2012, at 10:47, Qixu Cai wrote:

Dear all,

Can I use the twin refinement to refine the pesudo-translational symmetry 
dataset?

Thanks a lot for your help.

Best wishes,

Qixu Cai

Roberto Steiner
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Alternative conformation of Phe and Tyr?

[Steiner, Roberto]

Or refine the occupancies with Refmac...

Roberto

From my iPhone

On 27 Jul 2012, at 11:04, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear Ngo Duc Tri,
 
 I would manually set the occupancy of chain A to about 30% and chain
 B's to 70% and try again.There is density for chain A present in the
 second picture, it is just weaker.
 
 Cheers,
 Tim
 
 
 On 07/27/12 10:01, Tri Ngo wrote:
 Dear ccp4bb,
 
 
 I am working on refinement of an enzyme structure. I notice an
 alternative conformation (gauche+ and gauche-) on both residues Phe
 and Tyr.
 
 
 Here is the image of electron density before refinement. Based on
 the different map intensity, I am quite sure there is an
 alternative conformation on both positions.
 
 
 http://i50.tinypic.com/29zaoap.jpg
 
 
 However, after running occupancy refinement by Phenix, I don't see
 the density map at the gauche- conformation of Tyr residue. Please
 take a look at the image 2.
 
 
 http://i50.tinypic.com/anzfrn.png
 
 
 So do you think the gauche- conformation of Tyr exists in this
 structure. Should I keep it in the final model because there is no
 positive map there?
 
 
 
 Thank you very much for your input.
 
 
 
 - -- 
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
 
 iD8DBQFQEmd7UxlJ7aRr7hoRAsy8AKCKlbHZxS+jR3JMIZbzhFQnRD13/ACeJk1D
 T7WJvAy48cOevzV6pJF4t2M=
 =lpal
 -END PGP SIGNATURE-

Re: [ccp4bb] Does anyone have used DelPhi to calculate the Electrostatic potentials of DNA ？

[Steiner, Roberto]

Dear Eleanor

I (capital!) believe the original poster means 
http://compbio.clemson.edu/delphi.php

Best wishes
Roberto

On 11 Jul 2012, at 09:54, Eleanor Dodson wrote:


On 11 Jul 2012, at 03:36, dengzq1987
 don't understand the question really.  What DELPHI do you mean?

Many programs output DELPHI (refmac,  SigmaA etc ) and they are usually used as 
input to a difference map using FFT
Eleanor


Hi all,
recently，I want to use DelPhi to calculate the Electrostatic potentials of 
DNA.but in the manual,i can not find the method to create the inputfile fort.11 
、fort.12 and fort.13.Does anyone have experience on this?  Please suggest

Thank you in advance

Sincerely
dengzq


Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Phaser Fatal runtime error.

[Steiner, Roberto]

Don't know where the exact problem is. However, it is definitely possible to 
use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have 
done a few times.
I am sure you will be able to get help from Agilent people. If not, feel free 
to get back to me.

Best
Roberto


On 26 Jun 2012, at 18:34, Stephen Carr wrote:

 Dear CCP4bb
 
 I have collected a data-set using the supernova x-ray generator from Agilent 
 and taken the mtz file generated by the data processing software in crysalis 
 pro forward for structure solution.  The data collection was straight forward 
 and the software seemingly processed the data successfully - space-group 
 P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  Truncate 
 converted the intensities to structure factors with no problems, but when I 
 tried to use the data for molecular replacement with Phaser it produced the 
 following error:
 
 FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry
 
 I'm not sure how to proceed from here as other programs in the suite do not 
 seem to detect this problem.  Also when this error has been mentioned in the 
 past on the bb it was with a data set collected on a Bruker home source and 
 the data processed with Denzo/scalepack, and the suggested solution was to 
 use the Bruker software to process the data.
 
 I am currently attempting to reprocess the data with mosflm, but that is 
 likely to be the subject of another post!
 
 Any suggestions will be gratefully received.
 
 Best wishes,
 
 Steve
 
 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.uk
 tel 01235 567717

Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics 
King's College London

Room 3.10A 
New Hunt's House 
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit

[Steiner, Roberto]

We solved recently a structure with 18 dimers in the a.u. related by 
translational symmetry. Molrep did a great job
at quickly placing all molecules but few. The missing ones were found later by 
map inspection. We found rather important to play with the resolution cutoff.

I understand new versions of Phaser can also handle pseudotranslation very 
effectively.

Good luck.
R



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ke, Jiyuan 
[jiyuan...@vai.org]
Sent: Monday, April 30, 2012 4:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies per 
asymmetric unit

Dear All,

I have a question regarding solving a crystal structure by molecular 
replacement. It is a single protein with a molecular weight of 25.5 kDa. The 
cell dimension is rather big from the diffraction data ( 90.9 Å, 143.9 Å, 
216.3Å, 90°, 90°,  90°). The possible space group is P212121. With such a big 
unit cell, we predicted that there are 8-10 molecules per asymmetric unit. We 
have a decent model with sequence similarity of 49%. I tried several times with 
Phaser search with the current model and had difficulty to find any clear 
solution. Has anyone seen such cases and any suggestions to solve the 
structure? Thanks!

Jiyuan Ke, Ph.D.
Research Scientist
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503

[ccp4bb] X-ray equipment available

[Steiner, Roberto]

Full Rigaku R-axis IIC  Image Plate X-ray diffraction system
We would like to offer a complete macromolecular diffraction system free of 
charge to anyone prepared to pay (up-front) the shipping costs from our 
laboratory to theirs.
The system consists of a R-axis IIC area detector, Rigaku RU-200BH rotating 
anode X-ray generator with Yale mirrors together with an Oxford cryosystems 600 
series cryostream and associated dewars.  The system includes a purpose built 
enclose made of lead-rated perspex, obviating the need for a walk in enclosure. 
 The footprint of the X-ray generator cabinet 810cm (D) x 1100cm (W) x 900cm 
(H),  the footprint of the radiation enclosure is 1400cm (D) x 1750cm (W) x 
1000cm (H). The weight of the X-ray generator is  (550kg) and the HV 
transformer (450kg), RaxisIIC (150kg), enclosure (80kg) and table (80kg).
We wish to give away the whole system and not break it down to parts, so 
requests should be for the complete system.
Please contact Marty Rajaratnam (Randall division of Cell and Molecular 
Biophysics, King’s College London) email 
r.rajarat...@kcl.ac.ukmailto:r.rajarat...@kcl.ac.uk if you are interested in 
acquiring this system.

With best wishes
_
Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] twin refinement in refmac

[Steiner, Roberto]

On 2 Mar 2012, at 08:01, arka chakraborty wrote:

Hi all,

I will like to know, as a follow up of what Prof. Randy Read said, what should 
be done to do the refinement against the measured data and not the detwinned F( 
which refmac outputs in the mtz after twin refinement), during subsequent 
refinements.

Operationally, don't put in the MTZ in field of the GUI something that Refmac 
generated for you in a previous run as MTZ out file. Always use as MTZ in 
your original data file.

And also, I would like to know how to ensure that the free R generated takes 
twinning into account if I am not using phenix.

Refmac does take in consideration the twin law(s) when handling free 
reflections . This is the case even if you have generated your free reflections 
randomly. Internally Refmac will modify your Free set in such a way that twin 
related reflections are in the same group (free or working) -- classes 
mentioned by Garib

The good thing about this is that twin-related reflections are handled properly 
during refinement irrespective of your Free-set choice.
The bad thing (Garib please correct me if I am wrong here) is that you might 
end up depositing a Free set which is not that actually used in refinement.

Best wishes
Roberto



Thanks in advance,

Regards,

ARKO

On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read 
rj...@cam.ac.ukmailto:rj...@cam.ac.uk wrote:
I'm worried when you say that you use the initial job's output MTZ. Refmac 
replaces F with a detwinned F in the output file so you wouldn't be refining 
against your measured data in the subsequent round.

Best wishes

Randy Read


Randy J. Read

On 2 Mar 2012, at 02:00, wtempel wtem...@gmail.commailto:wtem...@gmail.com 
wrote:

 Dear CCp4ers,
 A good morning to everyone.
 Today, I have a structure that I initially refined in space group P6522, 
 1mol/asu.
 Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; I/sigma  3
 2.61-2.55A: Rsym=39.6%, I/sigma  10
 50.00-6.13: Rsym=6.4%
 Some mild anisotropy in the resolution limits is apparent on the diffraction 
 images. Say, visible spots at 2.2A in one direction, 2.6A in the other.
 Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A 
 resolution, with some difference density for loops that cannot be interpreted 
 with reasonable geometry.
 Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage 
 does not suggest merohedral twinning.
 Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad'd 
 them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my 
 model to a homotetramer and ran Refmac with amplitude based twinning. (Would 
 this be a reasonable input to twin refinement?)
 From the output coordinates:
 REMARK   3  TWIN DETAILS
 REMARK   3   NUMBER OF TWIN DOMAINS  :4
 REMARK   3  TWIN DOMAIN   :1
 REMARK   3  TWIN OPERATOR :  H,  K,  L
 REMARK   3  TWIN FRACTION : 0.269
 REMARK   3  TWIN DOMAIN   :2
 REMARK   3  TWIN OPERATOR : -K, -H, -L
 REMARK   3  TWIN FRACTION : 0.171
 REMARK   3  TWIN DOMAIN   :3
 REMARK   3  TWIN OPERATOR :  K,  H, -L
 REMARK   3  TWIN FRACTION : 0.258
 REMARK   3  TWIN DOMAIN   :4
 REMARK   3  TWIN OPERATOR : -H, -K,  L
 REMARK   3  TWIN FRACTION : 0.302
 Does this establish twinning versus underestimated symmetry? And what do I 
 need to know about my free-R? Did refmac assign a new flag? Whereas the 
 output file's flags are all 1s and 0s, the input file had 0 ... 19. During 
 the first run, Rfree dropped to 28%. But on a subsequent run, Rfree was 
 stuck 30% when I used the initial job's output MTZ.
 Many thanks in advance for your helpful comments.
 Wolfram Tempel




--

ARKA CHAKRABORTY
CAS in Crystallography and Biophysics
University of Madras
Chennai,India


Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Movements of domains

[Steiner, Roberto]

I believe ESCET was designed to answer your kind of question

Best
Roberto

On 21 Nov 2011, at 22:03, Filip Van Petegem 
filip.vanpete...@gmail.commailto:filip.vanpete...@gmail.com wrote:

Dear crystallographers,

I have a general question concerning the comparison of different  structures.  
Suppose you have a crystal structure containing a few domains.  You also have 
another structure of the same, but in a different condition (with a bound 
ligand, a mutation, or simply a different crystallization condition,...).  
After careful superpositions, you notice that one of the domains has shifted 
over a particular distance compared to the other domains, say  1-1.5 Angstrom.  
 This is a shift of the entire domain.  Now how can you know that this is a 
'significant' change?  Say the overall resolution of the structures is lower 
than the observed distance (2.5A for example).

Now saying that a 1.5 Angstrom movement of an entire domain is not relevant at 
this resolution would seem wrong: we're not talking about some electron density 
protruding a bit more in one structure versus another, but all of the density 
has moved in a concerted fashion.  So this would seem 'real', and not due to 
noise.   I'm not talking about the fact that this movement was artificially 
caused by crystal packing or something similar. Just for whatever the reason 
(whether packing, pH, ligand binding, ...), you simply observe the movement.

So the question is: how you can state that a particular movement was 
'significantly large' compared to the resolution limit?  In particular, what is 
the theoretical framework that allows you to state that some movement is 
signifcant? This type of question of course also applies to other methods such 
as cryo-EM.  Is a 7A movement of an entire domain 'significant' in a 10A map? 
If it is, how do we quantify the significance?

If anybody has a great reference or just an individual opinion, I'd like to 
hear about it.

Regards,

Filip Van Petegem

--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: mailto:filip.vanpete...@gmail.com 
filip.vanpete...@gmail.commailto:filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/http://crg.ubc.ca/VanPetegem/

Re: [ccp4bb] Distinguish NH4 from Na?

[Steiner, Roberto]

Bond valence sum

Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better 
than 1.8 A)


R

On 16 Nov 2011, at 18:20, Jacob Keller wrote:

 Dear Crystallographers,
 
 I have crystals containing 666mM NH4 and 540mM Na, and there appears
 to be a water which is only about 2.2 Ang from some polar atoms. It
 is currently reasonably happy as a Na, but is there any reasonable way
 to decide which cation is there?
 
 JPK
 
 -- 
 ***
 Jacob Pearson Keller
 Northwestern University
 Medical Scientist Training Program
 email: j-kell...@northwestern.edu
 ***

Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A 
New Hunt's House 
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.uk

[ccp4bb] Postdoctoral Position at King's College London

[Steiner, Roberto]

A three-year postdoctoral position in the field of mechanistic enzymology is 
immediately available in the Steiner Laboratory of King’s College London. The 
salary is £33,193 per annum inclusive of London allowance.
The project aims at studying the intriguing biological process of 
cofactor-independent oxygenation catalysis (1). To understand how dioxygen 
chemistry takes place in a cofactor-less manner we will use enzymes for which 
we have recently obtained structural information in various catalytically 
relevant states (2).
The ideal candidate has a strong biochemistry/chemistry background, extensive 
experience in structural biology focused on enzyme mechanisms and an interest 
in molecular dynamics (MD). The MD work will be carried out in collaboration 
with Prof. Ceccarelli of the University of Cagliari, Italy, where the postdoc 
will be able to spend some time to improve his/her skills in MD techniques. The 
postdoc will also be in close contact with the Manchester group of Prof. 
Scrutton where complementary spectroscopic and kinetic studies will be carried 
out.
This project will equip the post-holder with a rare and sought-after skill-set 
as well as a comprehensive overview of an inter-disciplinary study.
To apply for this position go to 
http://www.kcl.ac.uk/depsta/pertra/vacancy/external/pers_detail.php?jobindex=10871.
 Please make sure you quote the reference number G6/JKA/772/11-JT.
Informal enquiries are welcome at 
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk. The closing date 
for this application is 24 Nov. 2011.

(1) Fetzner S. and Steiner RA (2010). Cofactor-independent oxidases and 
oxygenases. Appl. Microbiol. Biotechnol. 86, 791-804.
(2) Steiner RA, Janssen HJ, Roversi P, Oakley OJ, Fetzner S (2010). Structural 
basis for cofactor independent dioxygenation of N-heteroaromatic compounds at 
the •/•-hydrolase fold. Proc. Natl. Acad. Sci. USA, 107, 657-662.

Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] hkl2map on Mac OSX 10.6

[Steiner, Roberto]

I only managed to get it working using zsh.
All other shells were giving me errors.

Ciao
R.



On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote:


Hi all,
has anybody managed to have hkl2map running on an intel-based Mac?

I have downloaded and installed the shelx programs, which I have aliased in my 
.bashrc, and will run from the command line.
I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that 
does open hkl2map windows.

However, when type hkl2map, I get this:

Screen shot 2011-07-15 at 11.39.22 AM.png


Any ideas on how to solve the problem?
Thanks a lot in advance,
best,
s

--
Sebastiano Pasqualato, PhD
Crystallography Unit
IFOM-IEO Campus
Cogentech - Consortium for Genomic Technologies
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5172
fax +39 02 9437 5990







Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] hkl2map on Mac OSX 10.6

[Steiner, Roberto]

...and in zsh for me

r
On 15 Jul 2011, at 14:56, Harry Powell wrote:

and in tcsh for me...

On 15 Jul 2011, at 14:48, Bosch, Juergen wrote:

works fine in bash for me
On Jul 15, 2011, at 5:51 AM, Steiner, Roberto wrote:

I only managed to get it working using zsh.
All other shells were giving me errors.

Ciao
R.



On 15 Jul 2011, at 10:40, Sebastiano Pasqualato wrote:


Hi all,
has anybody managed to have hkl2map running on an intel-based Mac?

I have downloaded and installed the shelx programs, which I have aliased in my 
.bashrc, and will run from the command line.
I also have downloaded and aliased the 'wish hkl2map-0.2-dist' command, that 
does open hkl2map windows.

However, when type hkl2map, I get this:

Screen shot 2011-07-15 at 11.39.22 AM.png


Any ideas on how to solve the problem?
Thanks a lot in advance,
best,
s

--
Sebastiano Pasqualato, PhD
Crystallography Unit
IFOM-IEO Campus
Cogentech - Consortium for Genomic Technologies
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5172
fax +39 02 9437 5990







Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk




..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH

http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011


Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

Re: [ccp4bb] low resolution refinement

[Steiner, Roberto]

Dear CAI Qixu

Refmac does an excellent job at low resolution. Many of the features available 
in version 5.6.x are described in a very recent Refmac paper

Murshudov et al. REFMAC5 for the refinement of macromolecular crystal 
structures.
Acta Crystallogr D Biol Crystallogr (2011) vol. 67 (Pt 4) pp. 355-67

Guidelines for Refmac use (including new functions) can be found at 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html

For example:
Jelly body restraints are controlled by

ridge distance sigma value # Default 0.1
ridge distance dmax value  # Default 4.2
ridge atoms sigma
ridge bvalue sigma

keywords. You will find info on this under Harmonic distance restraints (Ridge 
regression)

External restraints (distance) are controlled by a syntax like that below:

exte dist first chain A residue   78 atom  O   second chain A residue   82 atom 
 N   value 3.000 sigma 0.05

More information at under External restraints. As Rob pointed out ProSMART can 
generate the above type of restraints for you.
Phenix can also provide a list of external distance restraints which can be 
interpreted by Refmac
phenix.secondary_structure_restraints model.pdb format=refmac


Best wishes
Roberto



On 9 Jul 2011, at 17:44, CAI Qixu wrote:

Hi,

Thank you for your suggestion.
Could you tell me what is riding hydrogens?
And it seems there is not reference model function in refmac5.6?



2011/7/9 Robbie Joosten 
robbie_joos...@hotmail.commailto:robbie_joos...@hotmail.com
Dear Qixu,



refamac 5.6 works well at these resolutions. You can add commands to your 
refinement in CCP4i by using the 'Run and view command script' (or something 
like that) option and just typing in the extra commands. Jelly-body has worked 
very well for me (although I use tigheter restraints than the default). Also 
local NCS works well (provided you have NCS). I never used reference 
structures, but I heared good things about it. Don't forget to use riding 
hydrogens, for some reason it is not the deafault.
 Perhaps you should also switch of the automatic X-ray weighting in favour of 
optimizing the matrix weight yourself (start with 0.05 and compare refinements 
for higher and lower values).



HTH,

Robbie





 Date: Sat, 9 Jul 2011 16:59:29 +0800
 From: caiq...@gmail.commailto:caiq...@gmail.com
 Subject: [ccp4bb] low resolution refinement
 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK

 Dear all,

 Recently, I refine two low resolution structures in refmac 5.5. Their
 resolutions are 3A and 3.5A respectively.
 For 3A structure, after MR by phaser and rigidbody refinementrestraint
 refinement by refmac5.5, I got R factor 25% and R free 35%. And then
 each time, after my model building in coot and restraint refinement by
 refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%.
 For 3.5A structure, the R factor stays 27%, but R free increases from
 37% to 42% after my slightly model building in coot.
 Could you help me to find the reason?

 Maybe the reason is the overfit of the structure? I found that new
 version of refmac 5.6 has many new features for low resolution
 refinement, such as jelly boy, secondary structure restraints. But I
 don't know how to use these new features in old version ccp4i (6.1.13)?

 I also used phenix.refine with the reference model ( I have high
 resolution model for one domain of the low resolution protein) and
 secondary structure restraints, but it seams the same. Any suggestion?

 BTW, is that simulator annealing not suitable for low resolution
 structure? I used the simulator annealing method of CNS and
 phenix.refine, but the geometry of the structure is always destroyed
 seriously.

 Could you help me?

 Thank you very much!


Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk

[ccp4bb] Postdoctoral Position Available in London

[Steiner, Roberto]

Dear CCP4-ers,
_
Postdoctoral position in reactive oxygen species (ROS) biology

A postdoctoral position supported by the King’s College London British Heart 
Foundation Centre of Excellence is available at King’s College London in the 
field of ROS biology. The project is a collaborative effort amongst the groups 
of Prof Ajay Shah MD (Cardiovascular Division, King’s College London), Dr Conte 
and Dr Steiner (Randall Division of Cell and Molecular Biophysics, King’s 
College London) aimed at elucidating the molecular mechanism of controlled ROS 
production in higher organisms.

The project is highly interdisciplinary and will combine structural biology 
(X-ray and NMR) with biophysical (ITC), biochemical and cell biology work. The 
post requires experience in molecular biology/protein biochemistry. Proven 
prior experience in protein expression using the baculovirus system is also 
considered very important. Additional experience with biophysical methods 
complementary to structural biology and/or oxygen biochemistry is welcomed.

The post is available immediately and funding is initially available for 18 
months. Salary will be commensurate to prior experience and qualifications. 
Interested applicants should contact Dr Roberto A Steiner 
(roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk ) directly by 
submitting their CV together with the names of three referees. Informal 
inquiries are welcome.
Deadline for this application is 21st March 2011.
_

Best wishes
Roberto

Re: [ccp4bb] disulfide bridge in red density

[Steiner, Roberto]

Hi Sadaf

It is also possible that the features you observe are also due to anisotropy of 
the ADPs. At 1.3A resolution you can perform anisotropic refinement. Give it a 
go and se if it helps.

Best
Roberto

On 6 Mar 2011, at 18:57, sadaf iqbal wrote:

Hello everyone,

Recently, i have solved a protein structure at 1.3 Å resolution. I have 
encountered one problem in this structure while refining in COOT. There are 
three disulfide bridges in my structure and if i used 2.0 Å resolution range in 
refmac then the density around disulfide bridges is ok but if i used 1.3 Å 
resolution range in refmac then red density is appeared along with blue one. 
Can anybody help me in this regard? I already played by increasing temperature 
factor of sulfur atoms but red density is still there.

Thanks in advance

Sadaf Iqbal
PhD Scholar
ICCBS, University of Karachi, Pakistan.
 Visiting Scientist
University of Hamburg, Germany.

Re: [ccp4bb] Micromatrix seeding using the mosquito

[Steiner, Roberto]

Dear Maria

In our hands Mosquito MMS worked by adding 2x protein solution + 1x seed 
solution + 1x reservoir. The reason for doing this was two-fold:

I) ratio protein/reservoir is similar to the condition that generated the seed 
stock
II) a deliberate bias toward the initial condition is given

I) and II) might not always be helpful and possibly other ratios should be 
explored.

Best wishes
Roberto

On 20 Sep 2010, at 08:55, Maria Håkansson 
maria.hakans...@maxlab.lu.semailto:maria.hakans...@maxlab.lu.se wrote:

Dear all,

Anyone who have had success using the mosquito for micromatrix seeding?
Which way is the optimal way of adding seed solution to sitting drops on an MRC 
plate?

Is it better to add 100 nl protein + 10 nl seed solution + 100 nl reservoir 
solution or
to add concentrated seed solution (1 microliter) directly to the reservoir 
solution and then pipett
100 nl protein + 100 nl reservoir solution.

Best regards and thanks in advance,

Maria Håkansson



__
Maria Håkansson, Ph.D.
Senior Scientist, Max-lab, Lund University
Phone: +46 (0) 76 8585 706
Fax: +46 (0) 46 222 47 10
Ole Römers väg 1 (P.O. Box 188)
SE-221 00 Lund, Sweden

Web address: http://www.maxlab.lu.se www.maxlab.lu.sehttp://www.maxlab.lu.se
Email: mailto:maria.hakans...@maxlab.lu.se 
maria.hakans...@maxlab.lu.semailto:maria.hakans...@maxlab.lu.se
__

Re: [ccp4bb] Phenix version 1.6.1 released

[Steiner, Roberto]

Dear Dirk

  For REFMAC, I
 haven't seen anything similar, yet.

The external restraints in Refmac should allow you to do this.

http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html


Best
Roberto