Re: [ccp4bb] EDR (Sophos) and CCP4 compatibility

[Andrew Purkiss]

Hi Mark and Dave (who just beat me to it),

Generally Sophos has been fine. However, I did get the following a  
couple of weeks ago which Sophos cleared up for me by deleting the  
relevant files.


"Generic ML PUA detected at C:\CCP4-7-1\7.1\bin\check_cell_sg.exe"
"Generic ML PUA detected at C:\CCP4-7-1\7.1\bin\alt_sg_list.exe"

As a PUA is a Potentially Unwanted Application, I fed back that  
deletion was a bit extreme. Our IT Team have now hopefully disabled  
the autodelete for PUAs.


Sophos did also find a (real) issue in one of the CCP4cloud libraries  
a while back, which the developers solved with an update.


Andy

Quoting David Briggs :


Hi Mark,


Our IT admin has mandated various AntiVirus software on OSX,  
including Sophos, and I have never encountered a problem installing  
and downloading CCP4, Phenix, Coot, Chimera , etc etc


HTH,

Dave



Dr David C. Briggs CSci MRSB

Principal Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

==

about.me/david_briggs


From: CCP4 bulletin board  on behalf of Mark  
J. van Raaij 

Sent: Tuesday, 4 October 2022, 10:31
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] EDR (Sophos) and CCP4 compatibility


External Sender: Use caution.


Dear CCP4-ers,

After a hacking scare, in our institution all computers connected to  
the internet will have to have EDR software installed for safety  
against hackers. We will get Sophos here, at least on OSX, to be  
installed directly by IT services, not by ourselves, from an admin  
account on all our computers controlled by them.
Is this compatible with CCP4 installation or should I be resigned to  
having an off-line computer for CCP4?
The other point is that IT services will update the operating  
systems of those computers from now on, and I worry about major OSX  
or Linux updates breaking CCP4 and other necessary programs.
Any comments and experience with EDR software in general and Sophos  
in particular is appreciated, both for OSX and Linux.


Saludos cordiales,

Mark


Mark J van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)
Section Editor Acta Crystallographica F
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Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Andrew Purkiss]

Is the data anisotropic? This would explain the strange processing
statistics beyond 3.0 Angstrom. If using Dials directly it is worth
looking for abnormalities with the reciprocal lattice viewer.

I've seen similar issues with the completeness being low, when data is
weak in one direction, despite reflections being reported in the
scaling output.

It may also be worth running some analysis of the data with Staraniso
(https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi) to try to
help.

Andy




Quoting Martin Malý :


Dear Matt,

thank you for asking. I am bit confused how you set up the PAIREF
run. In paired refinement, data are added step by step - going to
higher resolution, i.e. lower d_hkl. So the merged data in the
PAIREF input should not be cut to much. The data statistics look
from DIALS quite strange, there is very good completeness and CC1/2
for high resolution shells, but very poor  and Rmeas.

I would suggest to refine the model at 3 A to be safe. Then, run
PAIREF with the initial resolution 3 A and using the cutoffs 2.8,
2.6, 2.4 and 2.2 A. Diffraction data must be up to 2.2 A in that
case, no truncation to 2.4 A as you mentioned previously.

I hope it will help. Please feel free to ask and let me know if it
was successful.

Best regards,
Martin


On 30. 09. 22 17:29, Matt McLeod wrote:

Hi all,

I am having a bit of trouble with PAIREF.  I am trying to determine
the resolution cutoff of a dataset which has a high Rwork
(0.223)/free (0.275)value for the resolution (2.24A).  I have
truncated this data further to 2.4A and the R values get better but
the electron density maps do not improve whatsoever.  When I put
this data into PAIREF I get this message.

WARNING: There are only 40 < 50 free reflections in the resolution
shell 2.75-2.70 A. Values of statistics Rfree and CCfree in this
shell could be misleading. Consider setting thicker resolution
shells.

This error occurs for all resolution bins.  Looking at the pdb log
of the refined structure (where the data looks quite reasonable,
maybe not a 2.3 dataset but not much worse).

REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK
RFREE  CCWORK CCFREE
REMARK   3 1   60.08 -4.281.00 4135   213  0.1646
0.2213   0.940  0.901
REMARK   3 24.28 -3.401.00 4095   201  0.1951
0.2672   0.928  0.857
REMARK   3 33.40 -2.971.00 4099   204  0.2736
0.3303   0.861  0.739
REMARK   3 42.97 -2.701.00 4026   212  0.3486
0.3508   0.726  0.551
REMARK   3 52.70 -2.510.78 3178   154  0.4027
0.4062   0.637  0.594
REMARK   3 62.50 -2.360.29 115460  0.4118
0.3984   0.647  0.547
REMARK   3 72.36 -2.240.01   29 1  0.3366
0.4089   0.343  0.000

Where I assume NFree is the issue, but doesn't suggest that there
arent enough reflections.  There needs to be a higher cutoff as the
completeness goes to pot, but the scaling log from DIALS suggested
it was at least a good starting point.

 Statistics by resolution bin:
 d_max  d_min   #obs  #uniq   mult.  %comp   
r_mrg   r_measr_pim   cc1/2   cc_ano
118.81   5.97  10436   15776.62  99.94 797.6
22.80.1100.1200.046   0.992*  -0.397
  5.97   4.74   9602   15496.20 100.00 491.7
10.00.1720.1880.075   0.979*  -0.240
  4.74   4.14  10410   15286.81 100.00 513.5
10.30.1910.2070.079   0.978*  -0.281
  4.14   3.76  10833   15516.98 100.00 324.7
6.90.2380.2570.098   0.969*  -0.419
  3.76   3.49  10956   15267.18 100.00 207.5
4.60.2590.2800.105   0.975*  -0.271
  3.49   3.29  10899   15467.05 100.00 133.4
3.10.2720.2940.111   0.966*  -0.258
  3.29   3.12   9565   15286.26  99.93  86.9
2.00.3140.3430.136   0.935*  -0.346
  3.12   2.99   9256   15196.09 100.00  57.1
1.30.3540.3870.154   0.932*  -0.354
  2.99   2.87   9317   15246.11 100.00  43.6
1.00.4030.4410.177   0.934*  -0.198
  2.87   2.77  10087   15496.51 100.00  30.9
0.70.4550.4940.192   0.923*  -0.116
  2.77   2.69  10157   15246.66 100.00  26.4
0.60.5030.5460.210   0.927*  -0.132
  2.69   2.61  10351   15416.72 100.00  19.3
0.40.6130.6650.255   0.925*  -0.155
  2.61   2.54  10121   15046.73 100.00  15.5
0.40.7350.7970.306   0.906*  -0.088
  2.54   2.48  10510   15396.83 100.00  12.4
0.30.9321.0090.385   0.857*   0.006
  2.48   2.42  10432   15196.87 100.00  11.2
0.20.9721.0520.399   0.829*  -0.111
  2.42   2.37  10596   15326.92 100.00  10.2
0.21.0951.1840.447   0.844*  -0.083
  2.37   2.32  10577   

Re: [ccp4bb] AW: Strange cysteines

[Andrew Purkiss]

As you say, the Cys are too far apart for it to be a disulphide and it
looks like oxidation of the Cys. This could be due to radiation
damage, but other causes are possible.

A former colleague had one in betaB1-crystallin, which is visible in
pdbcode 1OKI at position 38. The difference density was quite clear
before it was modeled as Cysteine sulfinic acid (CSD). Of course, it
was easy to see at 1.4 Angstrom resolution.

Andy

Quoting "Hochberg, Georg" :


Hi oliver,


Thanks! Real space refinment was done in phenix with default
settings. The position of these cysteines is quite constrained by
where the main chain goes and the Phe you can see just next to the
cysteine. To me it seems it would require very odd geometry to pull
them into these centroids.


All the best,

Georg


Von: Weiergräber, Oliver H. 
Gesendet: Mittwoch, 22. Dezember 2021 10:51:59
An: Hochberg, Georg; CCP4BB@JISCMAIL.AC.UK
Betreff: RE: Strange cysteines

Hmm, this may indeed be a disulfide bond, but the sulfur atoms do
not seem to occupy their density centroids.
They could be either _pushed_ apart by the refinement algorithm
(which one are you using?) or _pulled_ apart due to incorrect
geometry in their neighbourhood.

Cheers
Oliver

==
  PD Dr. Oliver H. Weiergräber
  Institut für Biologische Informationsprozesse
  IBI-7: Strukturbiochemie
  Tel.: +49 2461 61-2028
  Fax: +49 2461 61-9540
==



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Hochberg, Georg [georg.hochb...@mpi-marburg.mpg.de]
Sent: 22 December 2021 10:06
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Strange cysteines

Dear CCP4ers,


We have recently solved the structure of an enzyme by cryoEM, which
has two cysteines at its dimer interface, one in each monomer. The
density around these two cysteines is very odd (see picture). They
are too far apart for a disulphide bond, and there is nothing around
these two cysteines that could help coordinate a metal. This density
is also not a result of symmetry constraints in the density
refinement either.  We'd be very grateful for any ideas.

[cid:b92417da-97f2-4dc3-9b5c-92278a5318fd]


All the best and happy holidays,

Georg Hochberg



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Re: [ccp4bb] Micro/Macro crystal seeding experience

[Andrew Purkiss]

We recently had a projects where removing the HIS-tag changed an
unsolvable crystal form into one where Molecular Replacement worked
immediately (and with an NMR ensemble as the search model to boot). In
this case the HIS-tag was about 5% of the total domain mass and the
tags were probably tangled up in the centre of the unit cell.

Along with all the other suggestions, I would also put a word in for
crystallisation at a lower/different temperature. We've had several
projects where this has improved diffraction from worse than 4 Ang. to
better than 2 Ang. or where different forms have grown. You can try all
the other suggestions in the cold room as well as well as your normal
condition.

I've been trying to get all our users to screen new crystal forms (both
new projects and new conditions in existing projects) in-situ, before
trying cryo-cooled data collection. This gives a baseline before
opening the drops for cryo-protection and cryo-cooling and may also
give some guidelines for dehydration etc.

Good luck.

Andy Purkiss

On Thu, 2020-12-17 at 21:30 +, Rafael Marques wrote:
> Hello all, how are you doing?
>  
> I have been working with two different proteins for 3 years. I was
> able to purify them by IMAC and SEC, no problems at all, and I have
> got some crystals of both. However, the best data I have got until
> now is around 4A. The diffraction experiment was carried out several
> times at DLS.
>  
> The crystals for each protein are different. One is really small
> whereas the other one is a regular size (Images below). Some people
> have told me to try microseeding and I did this, but with no success
> at all.
>  
> So I am asking here if there is someone experienced in this kind of
> witchcraft that could give me a hand and also answer me these two
> things:
>  
> Have you ever had good size crystals that didn’t diffract beyond 4A
> and after trying seeding you have got very good diffraction data (in
> these case with no change concerning the crystal size)?
>  
> What is the best protocol that you have tried to increase the size of
> your crystals and make them diffract better?
>  
> Many thanks in advance.
>  
> Best
>  
> 
>  
> 
> Rafael Marques da Silva
> Mestrando em Física Biomolecular
> Universidade de São Paulo
>  
> Bacharel em Ciências Biológicas
> Universidade Federal de São Carlos
>  
> phone: +55 16 99766-0021
>  
>"A sorte acompanha uma mente bem treinada"
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
-- 
Andrew Purkiss
Structural Biology STP
The Francis Crick Institute



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Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts

[Andrew Purkiss]

Hi Everyone,

Just to put a word in favour of the re-usable bases. We've been using
them for many years with little issue. The advantage of being able to
make up "emergency" loops when needed during a freezing session being
a big advantage.

I have occasionally noticed the slipping pin issue (and when it occurs
that base is withdrawn from use), but I've not noticed a general
problem with smaller movement upon rotation. However, we do see the
ice on the base issue (mainly due to impatient users freezing their
samples). Here, samples can be seen to shift, even without rotation,
for a few moments after mounting. Once the ice on the base/goniometer
inteface has melted, the position stabilises.

Of course, one advantage of the Diamond Light Source microfocus
beamline, I24, is that the pin is vertical in the beam, so the mount
isn't fighting gravity during rotation.

Andy

Quoting Diana Tomchick :


We no longer use the reusable bases for the same reasons, but we do
re-use our bases. If you use superglue to glue the pins into the
bases, you can remove the pins from the bases by soaking them in
acetone. This works about 75% of the time, especially if you are
careful not to use too much superglue when you glue the pin into the
base.

It goes without saying that the use of acetone will dissolve the
loop, but then the main reason we remove the pin is due to
imperfections in the loop, so no big deal.

Whenever we see the motions that you describe, we postulate that
somehow the pins were damaged and they are loose in the base.
Occasionally this motion is ascribed to ice between the base of the
pin and the magnetic mount, but this happens very rarely in our
experience.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of
Tao-Hsin Chang 
Sent: Sunday, November 15, 2020 3:07 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Stabilizing Mitegen reusable bases/mounts


EXTERNAL MAIL

Hi Patrick,

I have met the same issue and that is very bad for any micro-focus
beam and small crystals. I have talked with Mitegen and they are
developing a new type of reusable base having an improvement for
this issue. You may get some update from them. But, I do not use the
reusable bases anymore.

Best wishes,
Tao-Hsin

On Nov 15, 2020, at 3:45 PM, Patrick Loll
mailto:pjl...@gmail.com>> wrote:

Hi everyone,

I’ve become very fond of the Mitegen reusable bases for mounting 
crystals, since the reusable aspect savse me from having to discard

the base every time I break a microloop. However, once the crystals
arrive at the synchroteon, I observe motions of the loops (some
gradual, some sporadic). The the amplitudes of these motions are
becoming significant as I take data from smaller and smaller
crystals. I don’t think I’m imagining this, since the good folks at
NSLS-2/AMX have warned me about this very issue.

I’m writing to ask if anyone has any clever ideas about stabilizing
these assemblies. Obviously, I can epoxy the pins in place, but then
I’ll probably need to discard the entire assembly when I break a 
loop, and I’d prefer not to waste more money than necessary. I’ve

considered putting a bead of wax at the point where the pin enters
the base (although I haven’t yet checked to see if that will survive
immersion in liquid nitrogen). Does anyone have any other (better)
ideas?

Much obliged in advance,

Pat
__

Patrick J.  Loll, PhD
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St.
Philadelphia, PA 19102-1192 USA

(215) 762-7706
pj...@drexel.edu



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Re: [ccp4bb] Tyr pushed out during refinement

[Andrew Purkiss]

I've seen a similar behavior when, for the Phenix.refine refinement  
strategy, I accidentally selected both XYZ (reciprocal-space) and XYZ  
(real-space) at the same time. As well as a Phe jumping out of density  
in one NCS copy, planarity was very poor for several sidechains (but  
no obvious pattern as to which ended up with poor geometry).


Hope this helps,

Andy Purkiss.

Quoting "Philip D. Jeffrey" :

As Paul observes, there's a bona fide email list for phenix, but in  
fact comparing REFMAC to phenix.refine might be useful to see if  
this really is a program bug or if it's a bug in the model.
Sometimes one is better than the other.


For phenix.refine:
Put the Tyr in the "right" place and scour the .geo file created at  
the start of refinement for bad angles or bonds or bumps etc.  This  
will tell you what the offending energy term is, if there is one.   
If not, try turning off the rotamer fixing aspect of phenix.refine.   
I've had aspects of the algorithm "anti-refine" a structure  
(geometry, Rwork, Rfree all got worse at once) so I tend to  
streamline the process and run it as:
  strategy=individual_sites+individual_adp+occupancies   (+tls if  
you're using it)
from the command line (since I'm a Luddite and mostly eschew the  
GUI).  For example if it's enforcing rotamers during NCS refinement  
it could pull your s/chain out of density.


But also try REFMAC if the problem persists.

Cheers
Phil Jeffrey
Princeton


From: CCP4 bulletin board  on behalf of Paul  
Emsley 

Sent: Monday, October 19, 2020 2:58 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Tyr pushed out during refinement



On 19/10/2020 19:52, Boniecki, Michal wrote:

I have a problem during refining with one of the Tyr residues. It is  
constantly pushed out of the position during refinement in all 4  
chains in ASU.
I have tried to exclude it from refinement in phenix but it is  
refined anyway out of the position with wrong geometry. Is there a  
possibility to fix it during refinement?



If this is a question about refinement in phenix, then this may not  
be the most useful mailing list. If this is a question about how to  
pin down atoms and tweak bonds and contacts in Coot or Refmac, then  
we can proceed.



Regards,

Paul.




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Re: [ccp4bb] {Disarmed} Re: [ccp4bb] CCP4 7.1 problems

[Andrew Purkiss-Trew]

I had a similar problem with the beta. Do the different systems have  
different processor manufacturers? At that point, a couple of weeks  
ago, the relevant code then ran fine on Intel processors, but crashed  
on AMD. However, this was part of the CCP4Cloud software, I2 seemed to  
work fine after some limited testing.


Andy


Quoting Edward Lowe :

I have also experienced the exact problem below on trying to launch  
ccp4i2 - but only on one of the four Ubuntu systems I have installed  
ccp4-7.1 on.



Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction

Then, back to the prompt.




Dr. E.D. Lowe
edward.l...@bioch.ox.ac.uk

Department of BiochemistryTel: ++44 (0)1865 275392
University of Oxford
Oxford UK, OX1 3QU

From: CCP4 bulletin board  On Behalf Of  
Robert S Phillips

Sent: 24 April 2020 14:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4 7.1 problems

I installed CCP4 7.1 yesterday, and I have problems.  On an Ubuntu  
18.04 LTS system, I get the following:


rob@rob-SA76R4:~$ ccp4i2
Running CCP4i2 browser from: /home/rob/CCP4/ccp4-7.1/share/ccp4i2
Python 2.7.16 (default, Apr 22 2020, 09:15:14)
[GCC 4.9.1 20140922 (Red Hat 4.9.1-10)]
Qt version 4.8.7
Illegal instruction

Then, back to the prompt.

Similarly, with COOT:

rob@rob-SA76R4:~$ coot
INFO:: Reading coordinate file:  
/home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb
INFO:: file /home/rob/CCP4/ccp4-7.1/share/coot/standard-residues.pdb  
has been read.

Spacegroup: P 1
/home/rob/CCP4/ccp4-7.1/bin/coot: line 333: 13382 Illegal  
instruction $coot_bin "$@"
;;; note: source file  
/home/rob/CCP4/ccp4-7.1/share/guile/1.8/ice-9/boot-9.scm
;;;   newer than compiled  
/usr/lib/x86_64-linux-gnu/guile/2.2/ccache/ice-9/boot-9.go

Uncaught exception:
Throw to key syntax-error with args ("memoization" "In file ~S, line  
~S: ~A ~S." ("/home/rob/CCP4/cc
p4-7.1/share/guile/1.8/ice-9/boot-9.scm" 103 "Bad define placement"  
(define (syntax) (error "syntax

error in eval-case"))) #f)

I upgraded the system to Ubuntu 20.04 LTS (also released yesterday),  
and have the same problems.


However, ccp4i starts normally.

Rob

Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu
Web:   
http://tryptophan.net




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Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

[Andrew Purkiss]

t; Joāo Muniz (Instituto de Fisica de São Carlos, Brazil)
> > > > Garib Murshudov (Laboratory of Molecular Biology
> > > > MRC, Cambridge, UK)
> > > > Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot,
> > > > UK)
> > > > James Parkhurst (Diamond Light Source, Didcot, UK)
> > > > Randy Read (University of Cambridge, UK)
> > > > Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot,
> > > > UK)
> > > > Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK)
> > > > 
> > > > Please find the application form and further contact
> > > > information at http://pasteur.uy/novedades/mx2020/ 
> > > > (this www site will be updated regularly, so stay tuned!)
> > > > 
> > > > This Workshop is supported by the Collaborative Computational
> > > > Project Nº4 (CCP4, UK) & Science and Technology Facilities
> > > > Council (UK); the Centro de Biologia Estructural del Mercosur
> > > > (CeBEM); and the Programa Iberoamericano de Ciencia y
> > > > Tecnologia para el Desarrollo (CYTED) through de MICROBES
> > > > consortium.
> > > > 
> > > > Organizers:
> > > > Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo,
> > > > Uruguay
> > > > Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton
> > > > Laboratory, United Kingdom
> > > > Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP,
> > > > Brazil
> > > > 
> > > > Applicants:
> > > > 25 students will be selected, prioritizing advanced PhD,
> > > > postdocs and young researchers. The Course will provide
> > > > financial support covering registration fees, and for the case
> > > > of those students coming from abroad, all local expenses
> > > > (lodging, per diem and local transportation). Look in the www
> > > > site for details on application procedures.
> > > > 
> > > > The application deadline is July 9, 2020.
> > > > 
> > > > Please address further inquiries to: mx2...@pasteur.edu.uy
> > > > 
> > > > Looking forward to hosting you in Montevideo!
> > > > 
> > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> > > > 
> > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> > > 
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
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> 
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
Andrew Purkiss
Structural Biology STP
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Re: [ccp4bb] 3D stereo and pymol

[Andrew Purkiss]

Just to add that for the Dual-Link DP-DVI to work, you need an active
adaptor which includes a supplementary USB power connection.Some years
ago, we purchased some from Dell, with new machines. They are
considerably more expensive than simple passive adaptors, but we have
had no problems with a stable 3D display on older screens.
An example is available here: https://www.amazon.co.uk/Dell-BizLink-Dis
playPort-Adapter-Powered/dp/B003XYBA72
Regards,
Andrew
> > On Wed, Jan 3, 2018 at 1:42 AM, Wim
> >   Burmeister 
> >   wrote:
> > 
> >   
> > >  I answer a bit late,
> > >   but I repost a message on 3D graphics from Mai 2017
> > > : 
> > > 
> > >   
> > > 
> > >   Hello,
> > >    
> > >   we just
> > > wanted to share our experience in finding a
> > > configuration which allows to use 3D graphics
> > > under
> > > linux using Nvidia GeForce 3D glasses.
> > >    
> > >   We had quite
> > > a hard time to find a configurations which
> > > works
> > > correctly.
> > >    
> > >   We finally
> > > used Debian linux with a xfce desktop. Other
> > > recent
> > > desktops use a tiling which is not compatible
> > > with
> > > 3D graphics.
> > >    
> > >   The hardware
> > > consists of
> > >   
> > > a DELL Precision
> > > T5810  desktop computer with an Nvidia Quadro
> > > M4000
> > > (8 Gbyte memory, 4 DP) graphics card
> > > Nvidia GeForce 3D Vision 2
> > > (NVIDIA GEF 3D VISION 2 GLASSES KIT) active
> > > stereo
> > > glasses
> > > a stereo connector PNY Quadro
> > > 4000 3D for the synchronization of graphics
> > > card and
> > > glasses
> > > an ASUS 24" LED 3D - VG248QE
> > > display
> > > a DisplayPort-DisplayPort cable
> > >   
> > >   
> > >   The Nvidia
> > > linux drivers from version 367.57 can handle
> > > the
> > > current version of the Nvidia glasses.
> > >    
> > >   For an
> > > obscure reason a direct DP-DP connection
> > > between
> > > graphics card and display is absolutely
> > > required in
> > > order to obtain fully working stereo. If a
> > > DP-DVI
> > > dual link adapter is used, the stereo does
> > > not work
> > > on the top and the bottom part of the screen.
> > > This
> > > is true for a native DELL active adaptor or
> > > generic
> > > models. The exact reason remains unresolved,
> > > but the
> > > solution is to use a direct DP-DP connection.
> > > This
> > > limits the available choice of displays which
> > > require 120 Hz for 1080*1980 screen
> > > resolution and a
> > > DP input. We have been choosing a “Nvidia 3D
> > > ready”
> > > model.
> > >    
> > >   There has
> > > been a considerate about of exchange about
> > > this
> > > problem on
> > >    
> > >   

Re: [ccp4bb] Model parts rearrangement

[Andrew Purkiss-Trew]

Having just faced this problem, I used the coot 'symm shift reference  
chain here' command (in Extensions / Modelling menu) to assemble the  
model from the scattered fragments.


This should be scriptable, but I didn't think it was worth the effort  
for the 20 odd fragments I had.


Hope this helps,

Andy Purkiss.

Quoting Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com:


Hi Fellows,

I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a  reference model, where
the parts form a correct ASU.

Is the a program/script that can accomplish this assembly of parts onto the
correct model given the
reference model?

This is probably a common nuisance with a tool already available.

Best regards,  BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-






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[ccp4bb] Postdoctoral Position at Cancer Research UK, London Research Institute.

[Andrew Purkiss]

To all who may be interested. 

Neil McDonald has asked me to forward this message to the bulletin
board. Please reply to him at neil.mcdon...@cancer.org.uk and NOT to me.

Thanks

Andrew
=

Postdoctoral Position (4 years), Structural Biology Laboratory 
London Research Institute (LRI), Cancer Research UK 

Structural Biology of Growth Factor Signalling 

A postdoctoral position is available in the Structural Biology
Laboratory headed by Neil McDonald to work on molecular mechanisms
underlying the assembly and activation of growth factor signalling
complexes. The successful candidate will join a multidisciplinary group
using structural biology, biochemistry, biophysics and cell biology. We
are interested in how signals are initiated at the plasma membrane and
are propagated into the cell nucleus. This project will focus on the RET
receptor tyrosine kinase activation (see Plaza-Menacho et al. Mol. Cell
2014, Kjær et al. Nat. Struc. Mol. Biol. 2010 and Knowles et al. J.
Biol. Chem. 2006). More information on our research activities is
available at the lab website:
http://www.london-research-institute.org.uk/research/neil-mcdonald.

The postdoctoral fellow will join the lab at an exciting phase prior to
the London Research Institute becoming part of the Francis Crick
Institute (www.crick.ac.uk). The fellow will benefit from both the
multidisciplinary environment in the lab and a highly collaborative
LRI/Crick community. The lab has extensive crystallographic and robotics
equipment with local access to electron microscopy, TIRF and confocal
microscopes. We have regular access to synchrotron beamlines at Diamond
and ESRF as part of a Cancer Block Allocation Group. 

The successful candidate will have a relevant PhD or be in the final
stages of completing their PhD and have a strong interest in structural
biology or cell signalling. Previous experience in protein purification,
tissue culture, electron microscopy or crystallography would be an
advantage.

Informal enquires from interested individuals should be made by email to
Professor Neil McDonald at neil.mcdon...@cancer.org.uk.

Closing date for applications is sometime over the summer, 2014.

-- 
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK

Re: [ccp4bb] repulsive effects of arginine

[Andrew Purkiss]

An example of pi-pi stacking of the guanidinium groups, can be seen on a
structure which I worked on; pdb-code: 2x2u. Look at the interactions
between Arg 77 and its symmetry mate, with Arg 144 (and symmetry copy)
flanking, giving rise to a stack of 4 Arginine guanidinium groups, with
a sulphate ion neutralising the environment.

Such pi-pi stacking is also commonly seen with Tyrosine and
Phenylalanine, with cation-pi interactions also common (e.g. Lys NZ to
the planar side of Phe). Resonance is not really a correct description
of these delocalised pi-orbitals; as there are no single and double
bonds, but all the bonds are an average of both types.

Additionally, remember that the Arginine(s) may not actually be charged,
as the local environment of ionic sidechains can move the pKa value(s) a
long way from the expected value for an isolated sidechain, with the pH
of the crystallisation condition also potentially affecting what is
charged.

Andrew Purkiss.

On Tue, 2013-10-08 at 18:34 +0200, Nadir T. Mrabet wrote:
 Yes, indeed Andrey.
 And this results from resonance (tautomerization) of the guanidinium group.
 
 Regards,
 
 Nadir Mrabet
 
 Pr. Nadir T. Mrabet
 Structural  Molecular Biochemistry
 N-gere - INSERM U-954
 University of Lorraine, Nancy
 School of Sciences and Technologies
  School of Medicine
 9, Avenue de la Foret de Haye, BP 184
 54505 Vandoeuvre-les-Nancy Cedex
 France
 Phone: +33 (0)3.83.68.32.73
 Fax:   +33 (0)3.83.68.32.79
 E-mail: Nadir.Mrabet at univ-lorraine.fr
 
 On 08/10/2013 18:01, Andrey Feklistov wrote:
  Hi Jan,
 
  please note, Arg-Arg proximity is not always repulsive: guanidinium groups 
  can associate bridged by H-bonds and interactions with water molecules or 
  neighboring amino acids. There are many examples of these unusual Arg 
  formations, see for reference:
 
  Neves, Yeager and Abagyan (2012) Unusual Arginine Formations in Protein 
  Function and Assembly: Rings, Strings and Stacks, J. Phys. Chem. B 116, 
  7006−7013
 
  Hope this is helpful,
 
  Andrey
 

-- 
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK

Re: [ccp4bb] mmCIF as working format?

[Andrew Purkiss-Trew]

Quoting Jeffrey, Philip D. pjeff...@princeton.edu:


 Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or  
pdbset or many other tools.  Writing code for
this should only be necessary if you're processing large numbers of  
models, or have a spectacularly

misformatted PDB file.


Problem.  Coot is bad at the chain label aspect.
Create a pdb file containing residues A1-A20 and X101-X120 -  
non-overlapping numbering.

Try to change the chain label of X to A.
I get WARNING:: CONFLICT: chain id already exists in this molecule



Having had to show this to a student today, it does work fine if you  
select the Use Residue Range option rather than changing the whole  
chain. Not quite so convenient, but at least it makes the user think.




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Re: [ccp4bb] stereo monitor for DELL T7600

[Andrew Purkiss]

On Fri, 2013-03-01 at 12:52 +0100, mesters wrote:
 Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than
 sufficient. Even the quadro 600 will do fine. 

Except for a linux installation, as the 3 pin bracket is only available
on the Quadro 4000 (and higher)

 I noticed that the Nvidia linux driver has options for USB port etc.
 which suggests that in the near future USB ports can be used under
 linux for an external USB IR emitter. Can somebody comment on this
 please?
 

The driver only seems to use the USB connection for power and for
identifying that the emitter is connected. I don't think that there are
any plans to use USB to drive the stereo synchronisation (the mention of
USB has been in the release notes for many years now).


-- 
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK
 

Re: [ccp4bb] stereo monitor for DELL T7600

[Andrew Purkiss]

And that is because the emitter is powered by the screen and its
presence is detected via the HDMI monitor cable (and the signal to the
emitter is sent the same way). Use of these screens is via different
driver option (stereo option of 12) and there is a more limited range
available.

I have no experience of running with this option, as being early(ish)
adopters, we have a mix of Alienware OptX AW2310 and Samsung SyncMaster
2233RZ screens. I would be interested in how stable the stereo is, when
a low powered graphics card is under heavy load.

Having a graphics card with more power is not a waste of money (the CUDA
drivers used by the molecular simulation groups show what can be done).
The extra cost is quite small compared to the costs of getting crystals
in the first place!!

On Fri, 2013-03-01 at 13:21 +0100, Joachim Reichelt wrote:
 On Linux here the ASUS Monitor with build in Emitter runs fine even on a
 FX 380 Quadro without 3pin connection!
 
 Am 01.03.13 13:17, schrieb Andrew Purkiss:
  On Fri, 2013-03-01 at 12:52 +0100, mesters wrote:
  Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than
  sufficient. Even the quadro 600 will do fine.
  Except for a linux installation, as the 3 pin bracket is only available
  on the Quadro 4000 (and higher)
 
  I noticed that the Nvidia linux driver has options for USB port etc.
  which suggests that in the near future USB ports can be used under
  linux for an external USB IR emitter. Can somebody comment on this
  please?
 
  The driver only seems to use the USB connection for power and for
  identifying that the emitter is connected. I don't think that there are
  any plans to use USB to drive the stereo synchronisation (the mention of
  USB has been in the release notes for many years now).
 
 
 
 --
 Joachim Reichelt
 
 
 
 Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
 Braunschweig | www.helmholtz-hzi.de
 Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
 
 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
 Bundesministerium für Bildung und Forschung
 Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
 Ministerium für Wissenschaft und Kultur
 Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA
 Gesellschaft mit beschränkter Haftung (GmbH)
 Sitz der Gesellschaft: Braunschweig
 Handelsregister: Amtsgericht Braunschweig, HRB 477

-- 
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK

Re: [ccp4bb] Chiral volume outliers SO4

[Andrew Purkiss]

Dear Robbie and ccp4bb,

Is 1N1 not a different type of problem though, where a chirality
restraint is valid and so the atom labelling is important? 

Are you saying that we should always use the cif dictionary, even when
there are errors? Surely in the SO4 case, as Ian said, it is better to
remove the unnecessary restraint altogether. The sulphate cif file seems
to have had this bug introduced in the current CCP4 version.

Andrew

On Fri, 2012-07-13 at 12:54 +0200, Robbie Joosten wrote:
 Dear All,
 
 I'm with Dale on this one. It's better to have a standard and roll with it,
 than allow for ambiguity. The discussion just happened to start with a
 rather silly example as Tim pointed out. The ligand 1N1
 (http://ligand-expo.rcsb.org/reports/1/1N1/1N1_D3L1.gif) is a better
 example:
 The atoms N5 and N6 can have inverted chirality. If it is just one of the
 two, then the molecule is distorted (IFF the restraint file is correct!). If
 both have inverted chirality than the problem can be fixed by label
 swapping. Hacking the restraint file to allow both positive and negative
 chirality would allow you to distort the molecule. 
 
 Cheers,
 Robbie
 

-- 
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK

Re: [ccp4bb] harvesting in cold room (was: cryo for high salt crystal)

[Andrew Purkiss-Trew]

Quoting Jacob Keller j-kell...@fsm.northwestern.edu:



The expansion ratio of liquid to gaseous nitrogen is approximately 1:700,
that is, 1 liter of liquid becomes 700 liters of gas (at room temperature).
When you are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide
and 10 (~30ft) meters long and you assume that it is poorly ventilated
(i.e. no gas replacement at all), then you will have 3x6x10 = 180m3 volume
of gas, which is 180,000 liters. Air consists of 21% oxygen and is
considered deficient if it goes down to 19.5%. OSHA recommends having
monitors present in the case you might, in worst case scenario, reach
19.5%. Note: I don't know, but it seems unlikely that you are critically
injured at 19.5%



How can this OSHA number be right? At fairly high altitude, say 2500 m, the
partial pressure of O2 will be about 75% of that at sea level, and most are
okay with it--so how can a drop from 21% to 19.5% have any importance? Is
N2 competing with O2, perhaps? Never heard of that. Can N2 really be a
poison, such that we are constantly poised at the cusp of suffocation?



Not N2 poisoning, but lack of Oxygen in the blood. At altitude, the  
body adjusts by breathing deeper and faster and people can become  
acclimatised (so giving rise to altitude training for athletes). The  
really dangerous levels, for a healthy adult, are a fair way below the  
19.5%. The UK generally seems to have O2 alarms set at 19% and maybe a  
second alarm at 17%.


More details are given on the OHSA website  
(http://www.osha.gov/pls/oshaweb/owadisp.show_document?p_id=25743p_table=INTERPRETATIONS  found with a quick google) and on one of the UK Liquid Nitrogen supplier's websites  
(http://www.cryoservice.co.uk/oxygen_depletion.aspx)


Hope this helps,

Andrew Purkiss



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Re: [ccp4bb] Linux stereo set-up

[Andrew Purkiss]

On Thu, 2011-12-01 at 16:33 +0100, Michael Hothorn wrote:
 Dear all,
 
 sorry for the off topic question (that has been asked many times before, 
 but the hardware keeps changing): I want to buy a linux workstation with 
 Nvidia 3D vision and an Alienware OptX AW2310 23-inch 3D TFT monitor. 
 This set-up suggested by the CCP4 wiki for TFT stereo. Has anyone a 
 similar set-up running under linux and can suggest a matching graphics 
 card? It would be perfect if it could handle twinview with a second, non 
 3D/stereo TFT monitor. Does the Nvidia Quadro 4000 do this, and is the 
 Nvidia driver running stable under linux?
 

Dear Michael,

We have exactly that set up running here. A dual screen linux machine
with one Alienware OptV AW2310 screen running in stereo using the NVIDIA
Quadro 4000 card and the second screen in 'normal' mode. As far as I can
remember, the only restriction is that the second screen can only
display the same resolution as the first. Just remember that you need
the optional stereo out connector as well (make sure it is the Quadro
4000 model). This uses an additional slot, separate from the graphic
card, on the back of the machine. The current NVIDIA driver works fine
and the quality of the stereo is very good. 

Additionally, if you are going to have a lot of machines with this
setup, then you may want to consider the 3D Vision Pro, which uses radio
transmission to talk to the glasses and allows pairing of glasses to
individual computers. The standard 3D Vision systems uses Infra-Red and
the glasses can get confused with if two people are using stereo next to
each other. The 3D Vision Pro is considerably more expensive though.

Hope this helps,

Andrew

-- 
Andrew Purkiss
X-ray Laboratory Manager,
London Research Institute,
Cancer Research UK.

Re: [ccp4bb] adxv

[Andrew Purkiss]

Hi Rajesh,

That is a very old version (1.9.4) of ADXV.

Try the current version from here

http://www.scripps.edu/~arvai/adxv/

version 1.9.8 works fine for us and opens Pilatus data without modifying
the files. 

Hope this helps.

Andrew Purkiss

-- 
X-ray Laboratory Manager,
London Research Institute,
Cancer Research UK. 

On Tue, 2011-11-22 at 09:30 -0500, Rajesh kumar wrote:
 Hi Andrzej,
 
 
 I used exactly what you have suggested.
 Downloaded file adxv.i686FC2.tgz from some place.
 untar Gunzip  so I get a folder adxv.1686FC2 which has adxv and
   adxv.1686FC2_static files.
 I made both executable using chmod.
 I put the PATH in .bashrc
 If I run this command in the folder where images are then
 it opens with Windows open but the file selection dialogue is locked
 and the selection  pattern is 0.*.
 
 
 But not functional  and get  the error I posted recently
 
 
 pin8]$ adxv pin8_1_144.img
 (standard_in) 1: parse error
 (standard_in) 1: parse error
 (standard_in) 1: parse error
 beam_center x = pixels , mm
 beam_center y = pixels , mm
 distance = mm
 overload = counts
 pixelsize = 0.172 mm
 wavelength = Angstroem
 
 
 Adxv Version 1.9.4-beta
 Copyright (C) 1994-2007 by Andrew Arvai, Area Detector Systems
 Corporation
 Using 24-bit TrueColor visual
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  ManagerParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfBeginLine
 Warning: ... found while parsing ':KeyosfBeginLine:
 ManagerGadgetTraverseHome()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:  osfHelp
 Warning: ... found while parsing ':KeyosfHelp:
ManagerGadgetHelp()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  ManagerParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  PrimitiveParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:  osfHelp
 Warning: ... found while parsing ':KeyosfHelp:
  Help()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  PrimitiveParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfCancel
 Warning: ... found while parsing ':KeyosfCancel:  MenuEscape()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfSelect
 Warning: ... found while parsing ':KeyosfSelect:
  ArmAndActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  PrimitiveParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: Locale not supported for XmbTextListToTextProperty
 Warning: Cannot convert XmString to compound text
 Warning: translation table syntax error: Unknown keysym name:
  osfPrimaryPaste
 Warning: ... found while parsing ':m
 KeyosfPrimaryPaste:cut-primary()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  PrimitiveParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfActivate
 Warning: ... found while parsing ':KeyosfActivate:
  PrimitiveParentActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfSelect
 Warning: ... found while parsing ':KeyosfSelect:
  ArmAndActivate()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfPrimaryPaste
 Warning: ... found while parsing ':m
 KeyosfPrimaryPaste:cut-primary()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfSelect
 Warning: ... found while parsing ':KeyosfSelect:
  ManagerGadgetSelect()'
 Warning: String to TranslationTable conversion encountered errors
 Warning: translation table syntax error: Unknown keysym name:
  osfSelect
 Warning: ... found while parsing

Re: [ccp4bb] cryo protection

[Andrew Purkiss-Trew]

Another possibility (other than those already mentioned) is to try  
freezing without a cryoprotectant, by fishing the crystals out onto a  
mesh and removing all the mother liquor.


The following paper has some details:
Direct cryocooling of naked crystals: are cryoprotection agents  
always necessary?


Erika Pellegrini, Dario Pianoa, and Matthew W. Bowlera

Acta Cryst. (2011). D67, 902–906

--
Andrew Purkiss
X-ray Laboratory Manager
Cancer Research UK
London Research Institute.


Quoting Leonard Thomas lmtho...@ou.edu:


Hi All,

I have run into a very sensitive crystals system when it comes to  
cryo protecting them.  I have run through the usual suspects and  
trays are going to be setup with a cryo protectant as part of  
crystallization cocktail.  The one problem that  seems to be  
occurring is that the crystals crack as soon as they are transfered  
out of the original drop.  I am running out of ideas and really  
would love some new ones.


Thanks in advance.

Len

Leonard Thomas Ph.D.
Macromolecular Crystallography Laboratory Manager
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251

lmtho...@ou.edu
http://barlywine.chem.ou.edu
Office: (405)325-1126
Lab: (405)325-7571






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Re: [ccp4bb] UV imaging of crystals

[Andrew Purkiss-Trew]

Quoting Harman, Christine christine.har...@fda.hhs.gov:


Hi All,
I was curious if any of you have tried or even know if it is  
possible to adapt a stereoscope (in my case an Olympus SZX10 model)  
so as to view protein crystals with UV illumination. Basically, I  
want a cheap manual version of what a Rock UV Imager does.  I know  
this is probably a crazy dream.  However, I would greatly appreciate  
any comments, advice or experience any of you may have.




Molecular Dimension do such an adaptor which fits to existing microscopes.

See  
http://www.moleculardimensions.com/shopdisplayproducts.asp?id=121cat=X%2DtaLight%3Csup%3E%99%3C%2Fsup%3E+100+%2D+UV+for+Microscope+




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Re: [ccp4bb] UV imaging of crystals

[Andrew Purkiss-Trew]

Quoting Ed Pozharski epozh...@umaryland.edu:


On Thu, 2011-09-15 at 20:50 +0100, Andrew Purkiss-Trew wrote:

Molecular Dimension do such an adaptor which fits to existing
microscopes.


Do you by any chance know the price?  I can seemingly order it through
the website for the hefty price of $0.00, which is too good to be true.



Sorry, I don't know, I think that a new PI at our institute has  
ordered one from his new equipment budget. But I don't have a price to  
hand, I can ask though.


--
Andrew Purkiss-Trew
X-ray Laboratory Manager
London Research Institute
Cancer Research UK




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Re: [ccp4bb] I compressed my images by ~ a factor of two, and they load and process in mosflm faster

[Andrew Purkiss-Trew]

The current bottleneck with file systems is the speed of getting data  
on or off the magnetic surface. So filesystem compression helps, as  
less data needs to be physically written or read per image. The CPU  
time spent compressing the data is less than the time saved in writing  
less data to the surface.


I would be interested to see if the speed up is the same with a solid  
state drive, as there is near 'random access' here, unlike with a  
magnetic drive where the seek time is one of the bottlenecks. For  
example, mechanical hard drives are limited to about 130MB/s, whereas  
SSDs can already manage 200MB/s (faster than a first generation SATA  
interface at 150MB/s can cope with and one of the drivers behind the  
2nd (300MB/s) and 3rd generation (600MB/s) SATA intefaces). The large  
size of our image files should make them ideal for use with SSDs.



Quoting James Holton jmhol...@lbl.gov:

I think it important to point out that despite the subject line, Dr.  
Scott's statement was:

I think they process a bit faster too
Strangely enough, this has not convinced me to re-format my RAID  
array with an new file system nor re-write all my software to  
support yet another new file format.  I guess I am just lazy that  
way.  Has anyone measured the speed increase?  Have macs become  
I/O-bound again? In any case, I think it is important to remember  
that there are good reasons for leaving image file formats  
uncompressed.  Probably the most important is the activation barrier  
to new authors writing new programs that read them.  fread() is  
one thing, but finding the third-party code for a particular  
compression algorithm, navigating a CVS repository and linking to a  
library are quite another!  This is actually quite a leap for those  
of us who never had any formal training in computer science.   
Personally, I still haven't figured out how to read pck images, as  
it is much easier to write jiffy programs for uncompressed data.   
For example, if all you want to do is extract a group of pixels  
(such as a spot), then you have to decompress the whole image!  In  
computer speak: fseek() is rendered useless by compression.  This  
could be why Mar opted not to use the pck compression for their  
newer CCD-based detectors?


That said, compressed file systems do appear particularly attractive  
if space is limiting.  Apparently HFS can do it, but what about  
other operating systems?  Does anyone have experience with a Linux  
file system that both supports compression and doesn't get corrupted  
easily?


-James Holton
MAD Scientist


Graeme Winter wrote:

Hi David,

If the data compression is carefully chosen you are right: lossless
jpeg2000 compression on diffraction images works very well, but is a
spot slow. The CBF compression using the byte offset method is a
little less good at compression put massively faster... as you point
out, this is the one used in the pilatus images. I recall that the
.pck format used for the MAR image plates had the same property - it
was quicker to read in a compressed image that the raw equivalent.

So... once everyone is using the CBF standard for their images, with
native lossless compression, it'll save a fair amount in disk space
(=£/$), make life easier for people and - perhaps most importantly -
save a lot of data transfer time.

Now the funny thing with this is that if we compress the images before
we store them, the compression implemented in the file system will be
less effective... oh well, can't win em all...

Cheers,

Graeme



2009/9/18 Waterman, David (DLSLtd,RAL,DIA) david.water...@diamond.ac.uk:


Just to comment on this, my friend in the computer game industry insists
that compression begets speed in almost all data handling situations.
This will be worth bearing in mind as we start to have more fine-sliced
Pilatus 6M (or similar) datasets to deal with.

Cheers,
David.

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
William G. Scott
Sent: 17 September 2009 22:48
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] I compressed my images by ~ a factor of two, and they
load and process in mosflm faster

If you have OS X 10.6, this will impress your friends and save you some
disk space:

% du -h -d 1 mydata
3.5Gmydata

mv mydata mydata.1

sudo ditto --hfsCompression mydata.1  mydata rm -rf mydata.1

% du -h -d 1 mydata
1.8Gmydata

This does hfs filesystem compression, so the images are still recognized
by mosflm, et al.  I think they process a bit faster too, because half
the information is packed into the resource fork.
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Re: [ccp4bb] weak magnet of goniometer of MAR345dtb

[Andrew Purkiss-Trew]

Quoting aidong a...@xmu.edu.cn:


Hi,

We have recently installed a new home source diffraction system  
using MAR 345 dtb. It works much better than the rigaku because this  
new device has automatic motor control system.  However, we have a  
lot of trouble to mount crystals.  The magnet of MAR goniometer is  
significantly weak so the pins do not stick on.  The old pins we  
used nicely in old rigaku are not working most of time.  The new  
pins from hampton research particularly designed for ALS  
high-through put data collection are not easily working either.   I  
wonder whether anyone has similar experience and it could be fixed  
by replacing with a stronger magnet base.   Thanks for your  
suggestions in advance.




Have you made sure that the electro-magnet for the goniometer is  
switched on and working. You can switch the magnet on and off on the  
control panel and a pin will not 'stick' without a green light here.




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Re: [ccp4bb] images

[Andrew Purkiss-Trew]

On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote:
 Maybe, but images without experimental context (sequence? ligands? 
 purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! 
 relationship to the other 15 similar datasets) are as good as no 
 images.  And as far as I know, there's no good discussion on the table 
 for that.  At least, no-one on the thread mentioned it, so they're 
 probably not thinking about it either.
 
 I suppose efforts like PIMS or are a start, and maybe they can even have 
 enough information (my feeling is they currently don't).  But that's 
 where the discussion should start:  how to index (in sense of annotate) 
 the datasets.  The technicalities are just that: technicalities.
 
 Or even closer to home: does ANY detector/beamline write even timestamps 
 into the image header...?  Never mind ring current, intensity of the 
 beam, size of beam, size of crystal, length of direct beam path, etc 
 etc... 
 

As far as I know, most detectors write the current time into the image
header. Certainly our in house MAR image plate systems do, as do the
detectors at Diamond and ESRF (for those that I've looked at this
morning).

Re: [ccp4bb] Google marks CCP4 web site as a potential security threat

[Andrew Purkiss-Trew]

Quoting Pedro J. B. Pereira ppere...@ibmc.up.pt:


Miguel Ortiz Lombardia wrote:

Dear all,

While searching for some definition of rotations angles I have  
bumped into this very disagreeable indeed discovery: google adds  
now a step if you want to go to places _they_ consider as  
potentially dangerous. You can proceed that have to copy and paste  
the address yourself or tell the relevant webmasters to do whatever  
Google wants them to do so their pages don't appear as risky. One  
such place happens to be the full ccp4 web site.


In my opinion, the real danger is Google.
Time to switch to another search engine?

In any case, I wanted CCP4 developers and users to know.
( the search was done from a home adsl connection in France )

Best regards,


Miguel

The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and  
ScienceDirect websites, among many others... including google.com!


Hope it's a (short-lived) bug.



Looks like the bug has been fixed now. I was getting all searches  
showing the same symptoms, except for 'News Result'. All are back to  
normal now.




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Re: [ccp4bb] Google marks CCP4 web site as a potential security threat

[Andrew Purkiss-Trew]

Quoting Miguel Ortiz Lombardia miguel.ortiz-lombar...@afmb.univ-mrs.fr:



The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and  
ScienceDirect websites, among many others... including google.com!


Hope it's a (short-lived) bug.

Pedro



The bug is for them to decide what we have or have not to consider  
as a threat and to force us to change our websites as they please.  
They may change their filters in one hour or so and we won't notice  
this behaviour for our favourite, neutral and usually so compliant  
'science' sites. I'm wary of the principle itself of Google shaping  
the internet as they want it to be.


It seems they are free to do all that, but so we are to stop using Google.

Best,



Personally I am in favour of such extra filtering. At least it might  
give some warning for the less careful home users before they download  
yet another worm that recruits their machine into a bot-net. If it  
means an extra click to follow a link, then so be it. As you say, no  
one is forced to use Google, but I imagine that if Google do it, so  
will most of the other search engines.




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Re: [ccp4bb] structure (factor) amplitude

[Andrew Purkiss-Trew]

On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:
 I was taught 'structure amplitude' - makes perfect sense to me!  Why
 does 'structure amplitude' make any less sense than 'structure factor'?
 
 It also clearly made sense to Phil Coppens, a crystallographer of
 considerable repute, see ITC Vol. B (2nd Ed.), sect 1.2., p.10: 'The
 Structure Factor'.  To quote the introduction to the section: The
 'structure factor' is the central concept in structure analysis by
 diffraction methods.  Its modulus is called the 'structure amplitude'.
 
 Also I did a 'Google vote' for the two terms.  'Structure amplitude' has
 11300 hits.  'Structure factor amplitude' has only 4750.  So all round I
 would say that 'structure amplitude' wins by a considerable margin.
 

Having had a quick look at the google results myself, I think that there
is a problem is the methodology. Google doesn't take into account
punctuation when searching. So the first search includes results such as
'structure. Amplitude', where the two words are in different sentences,
or 'structure, amplitude' where the words are part of a list. Given this
case, the winning margin is likely to be less.

My preference would also be for the full 'Structure factor amplitude'.
'Structure amplitude' leaves me with visions of comparing the pdb files
of a small single domain protein and a ribosome. Two structures having
different sizes (or amplitudes).

 Cheers
 
 -- Ian
 
  -Original Message-
  From: owner-ccp...@jiscmail.ac.uk 
  [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Pavel Afonine
  Sent: 11 January 2009 03:01
  To: Ethan A Merritt
  Cc: CCP4BB@jiscmail.ac.uk
  Subject: Re: [ccp4bb] structure (factor) amplitude
  
  
  
  On 1/10/2009 5:14 PM, Ethan A Merritt wrote: 
  
  On Saturday 10 January 2009, Bernhard Rupp wrote:

  
  Dear All,
  
  I am getting conflicting comments on the use of 
  'structure factor amplitude'
  vs. just
  'structure amplitude'
  for |F|.
  
  
  
  ???
  That's just... odd.
  
  |F| is the amplitude of F.
  But no way F is a structure.

  
  
  I agree. If F is a structure factor then |F| is a structure 
  factor amplitude. structure amplitude doesn't make much sense...
  Pavel.
 
 
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Re: [ccp4bb] Molecular Dynamics for dummies.

[Andrew Purkiss-Trew]

Just a word of warning regarding metals in macromolecular simulation.
There is no 'good' way of modeling protein-metal interactions in many
cases. Some metal ions are very polarizable (Ca 2+ being one example)
and the simple mechanics used in protein simulation don't allow for
this. Even using a polarizable forcefield is unlikely to give accurate
answers due to the complex nature of the atomic orbitals in many metal
ions when compared to protein atoms (mainly due to the addition of
d-orbitals to the mix). So, Na+, Mg2+ are generally OK, Ca2+, Fe, Mn,
etc. are much more tricky, especially in a quick and dirty simulation.

On Thu, 2008-07-03 at 12:20 +0100, Martyn Winn wrote:
 Gromacs   www.gromacs.org
 
 It is GPL. It can certainly handle metals, although as is always the
 case, you have to be careful in the choice of force field. It is fairly
 user friendly (by the standards of that field ;-). Not sure what the
 situation is for Macs but certainly runs well on Linux.
 
 Alternatives: charmm, amber, namd, etc etc
 
 Your suggested project is perfectly reasonable, but don't expect it to
 be a day's work 
 
 HTH
 Martyn
 
 
 On Thu, 2008-07-03 at 11:30 +0100, David Briggs wrote:
  Hi everyone.
  
  I have a slightly off topic question I hope someone can help with.
  
  I have a structure of a wild type domain, which binds metal ions.
  Certain mutations in chelating residues cause changes in the apparent
  affinity for said metal ions.
  
  As I have (so far) failed to crystallise the mutant, I would like to
  do some molecular dynamics in a water box, (with afore mentioned
  mutations) to get  a handle on the origin of the change in metal ion
  affinity.
  
  Does anyone know of a suitable package which:
  
  a) is open source, or basically free to academics
  b) allows inclusion of metal ions
  c) gives an understandable and interpretable output, in terms of
  changes in energy, etc.
  d) Preferably runs on mac, (although I do have access to linux as well.)
  
  Am I asking for the moon on a stick?
  
  Looking forward to your responses.
  
  Regards,
  
  Dave

[ccp4bb] Pointless 1.2.15 and ccp4i

[Andrew Purkiss-Trew]

Dear List,

I am having a problem with running the latest version of pointless
(1.2.15) via ccp4i. This is with the new GUI task.

The logfile has the following, rather unhelpful information:
SNIP

***
* Information from CCP4Interface script
***
The program run with command: pointless 
has failed with error message
child killed: segmentation violation
***


#CCP4I TERMINATION STATUS 0 child killed: segmentation violation
#CCP4I TERMINATION TIME 27 Mar 2008  14:16:02
#CCP4I MESSAGE Task failed



The program runs fine with the equivalent command line:

pointless HKLIN Plate2_B6_001.mtz


This is happening on both 32 and 64 bit linux machines, running either
Fedora Core or SuSE.

I have not, yet, recompiled the program from source, but that is next on
the list. Has anyone else had this problem?

Many thanks

Andrew Purkiss-Trew

Re: [ccp4bb] Pointless 1.2.15 and ccp4i

[Andrew Purkiss-Trew]

Installation of pointless-1.2.16 appears to have solved the problem.

On Thu, 2008-03-27 at 14:55 +, Phil Evans wrote:
 I've had some problems getting recent versions of Pointless to link in a
 portable way, due to a new call into the CCP4 library,  this can cause
 segfaults on some systems. I keep hoping someone will tel me how to get
 round this (a ccp4 routine calls getpwid which apparently cannot be
 static)
 
 You could try
 
 ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.16.linux
 
 to see if that behaves better 
 
 If it's going to crash, it will crash immediately on starting from the
 command line
 
 Phil
 
 On Thu, 2008-03-27 at 14:39 +, Andrew Purkiss-Trew wrote:
  Dear List,
  
  I am having a problem with running the latest version of pointless
  (1.2.15) via ccp4i. This is with the new GUI task.
  
  The logfile has the following, rather unhelpful information:
  SNIP
  
  ***
  * Information from CCP4Interface script
  ***
  The program run with command: pointless 
  has failed with error message
  child killed: segmentation violation
  ***
  
  
  #CCP4I TERMINATION STATUS 0 child killed: segmentation violation
  #CCP4I TERMINATION TIME 27 Mar 2008  14:16:02
  #CCP4I MESSAGE Task failed
  
  
  
  The program runs fine with the equivalent command line:
  
  pointless HKLIN Plate2_B6_001.mtz
  
  
  This is happening on both 32 and 64 bit linux machines, running either
  Fedora Core or SuSE.
  
  I have not, yet, recompiled the program from source, but that is next on
  the list. Has anyone else had this problem?
  
  Many thanks
  
  Andrew Purkiss-Trew