Re: [ccp4bb] Reprocessing images collected on an Eiger2 detector using Xia2Dials on CCP4i2's GUI

[Andreas Förster]

Dear Graeme, all,

to make it easier for Rigaku Oxford Diffraction's CrysAlisPro to process
EIGER and EIGER2 data collected at the synchrotron, Herbert Bernstein
created a Windows installer for Takanori Nakane's eiger2cbf converter.  You
can find it here:  https://github.com/nsls-ii-mx/eiger2cbf.  Documentation
is at the very bottom.  It works for CAP.  I haven't tried to see how
useful it is in other contexts.  It's a converter, not a plugin, but it
lets you work with HDF5 data under Windows.

All best.

Andreas



On Mon, Jan 4, 2021 at 10:22 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
graeme.win...@diamond.ac.uk> wrote:

> Hi All,
>
> Sorry for the slow response - holiday season & all (I am sure many of us
> needed a break at the end of 2020)
>
> Windows is currently not super well supported for xia2 / DIALS work and
> won’t work at all for xia2 / XDS for the simple reason that XDS is not
> available for the platform (hence absence of durin plugin for Windows
> mentioned elsewhere in this thread)
>
> Your data are from 2019 I would guess from the log text
>
> In this case I would honestly suggest that the best method to process this
> data is to either -
>  - work on a UNIX based system
> or
>  - restage the data to Diamond and process there
>
> I’m happy to help (off list) with the details of this if it would help
>
> We probably should invest some effort in properly supporting Windows for
> xia2 / DIALS - however there are a bunch of rather nasty jobs to do in
> making this possible and it’s never “the most important thing” sorry :-(
>
> Happy new year & best wishes Graeme
>
> On 22 Dec 2020, at 16:53, Irwin Selvam <
> irwin.sel...@postgrad.manchester.ac.uk> wrote:
>
> Hi,
>
> I'd like to reprocess some data that were collected on an Eiger2 detector
> at Diamond with Xia2Dials using CCP4i2's GUI. I'm running CCP4i2 on a
> 64-bit Windows 10 machine. The data were processed successfully at Diamond
> with no obvious pathologies, the high resolution limit was just a little
> generous. The folder in question contains a Diamond specific file (.nsx
> extension), two image files (.h5), a header (.cbf), a master (.h5) and meta
> file (.h5). I've tried pointing Xia2 to the folder itself (which works
> when processing data collected on PILATUS detectors) and each of the files
> contained therein (except the Diamond specific file). Each time this
> results in the error " -ERROR- None:56 Error in wrapper xia2_dials 0.0::
> External process exited with exit code != 0 Process:
> C:\CCP4-7\7.1\bin\xia2.bat -ERROR- None:47 Error in wrapper xia2_dials
> 0.0:: Error in checking external process after completion exit status and
> code: 0 1". I've attached the error, debug etc files for a representative
> 'run' to this email. Which files do I need to point xia2 towards to get it
> to run? Any help would be appreciated.
>
> All the best,
>
> Irwin
>
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[ccp4bb] Satellite meeting on MX raw image data formats, metadata and validation

[Andreas Förster]

Dear all,

how many times do you have to refer back to information in the most obscure
places to prepare a PDB submission?  With the right metadata associated
with your dataset, the process could be much simpler.  This is one of the
points that will be addressed during a virtual meeting on MX raw image data
formats, metadata and validation this Saturday, 22 Aug 2020, from 9 am
until 3 pm, Prague Time (GMT+2, you do the math for your time zone).

Organized and put together by Herbert Bernstein for the most part, the
meeting will put the recently published Gold standard (
https://doi.org/10.1107/S2052252520008672) before a discerning audience of
beamline scientists and crystallographers and ask how
- we can assure that all relevant experimental information is save with the
diffraction data,
- crystallographic data should be recorded to be findable, accessible,
interoperable and reusable,
- correctly recorded metadata makes automatic processing simpler,
- PDB submission can be made more automatic with the right metadata,
- chemical crystallography can benefit from the work put into the Gold
standard.

Please register for the meeting by replying to this email (include your
name and affiliation).  It's free and fun.  More information can be found
at http://www.medsbio.org/meetings/HDRMX_22Aug20.html.

In my humble opinion, everyone with responsibility for a crystallographic
beamline anywhere in the world should be interested in this topic, though I
understand that the timing of the meeting will only let the most dedicated
scientists from the US attend.

I hope to see many of you on Saturday.


Andreas



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Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email:
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Re: [ccp4bb] number of frames to get a full dataset?

[Andreas Förster]

I like to think that the reflections I carefully measured at high
multiplicity are not redundant, which the dictionary on my computer defines
as "not or no longer needed or useful; superfluous" and the American
Heritage Dictionary as "exceeding what is necessary or natural;
superfluous" and "needlessly repetitive; verbose".

Please don't use the term Needless repetitivity in your Table 1.  It sends
the wrong message.  Multiplicity is good.

All best.


Andreas



On Tue, Jun 30, 2020 at 12:03 AM James Holton  wrote:

> I have found that the use of "redundancy" vs "multiplicity" correlates
> very well with the speaker's favorite processing software.  The Denzo/HKL
> program scalepack outputs "redundancy", whereas scala/aimless and other
> more Europe-centric programs output "multiplicity".
>
> At least it is not as bad as "intensity", which is so ambiguous as to be
> almost useless as a word on its own.
>
> -James Holton
> MAD Scientist
>
> On 6/24/2020 10:27 AM, Bernhard Rupp wrote:
>
> > Oh, and some of us prefer the word 'multiplicity' ;-0
>
> Hmmm…maybe not. ‘Multiplicity’ in crystallography is context sensitive,
> and not uniquely defined. It can refer to
>
>1. the position multiplicity (number of equivalent sites per unit
>cell, aka Wyckoff-Multiplicity), the only (!) cif use of multiplicity
>2. the multiplicity of the reflection, which means the superposition
>of reflections with the same *d*  (mostly powder diffraction)
>3. the multiplicity of observations, aka redundancy.
>
> While (a) and (b) are clearly defined, (c) is an arbitrary experimental
> number.
>
> How from (a) real space symmetry follows (b) in reciprocal space
> (including the epsilon zones, another ‘multiplicity’) is explained here
>
> https://scripts.iucr.org/cgi-bin/paper?a14080
>
> and also on page 306 in BMC.
>
> Too much multiplicity might create duplicity…
>
> Cheers, BR
>
>
>
> Jon Cooper
>
>
>
> On 23 Jun 2020 22:04, "Peat, Tom (Manufacturing, Parkville)" <
> tom.p...@csiro.au> wrote:
>
> I would just like to point out that for those of us who have worked too
> many times with P1 or P21 that even 360 degrees will not give you 'super'
> anomalous differences.
>
> I'm not a minimalist when it comes to data- redundancy is a good thing to
> have.
>
> cheers, tom
>
>
>
> Tom Peat
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
>
>
> --
>
> *From:* CCP4 bulletin board  on behalf of
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk <
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Wednesday, June 24, 2020 1:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* Re: [ccp4bb] number of frames to get a full dataset?
>
>
>
> Someone told me there is a cubic space group where you can get away with
> something like 11 degrees of data. It would be interesting if that's
> correct. These minimum ranges for data collection rely on the crystal being
> pre-oriented, which is unheard-of these days, although they can help if
> someone is nagging you to get off the beam line or if your diffraction
> fades quickly. Going for 180 degrees always makes sense for a well-behaved
> crystal, or 360 degrees if you want super anomalous differences. Hope this
> helps a bit.
>
> Jon Cooper
>
>
>
> On 23 Jun 2020 07:29, Andreas Förster 
> wrote:
>
> Hi Murpholino,
>
>
>
> in my opinion (*), the question is neither number of frames nor degrees.
> The only thing that matters to your crystal is dose.  How many photons does
> your crystal take before it dies?  Consequently, the question to ask is How
> best to use photons.  Some people have done exactly that.
>
> https://doi.org/10.1107/S2059798319003528
>
>
> All best.
>
>
>
>
>
> Andreas
>
>
>
>
>
> (*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you
> to use them to your advantage.
>
>
>
>
>
>
>
> On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
> wrote:
>
> Hi.
> Quick question...
>
> I have seen *somewhere* that to get a 'full dataset we need to collect n
> frames':
>
> at least 180 frames if symmetry is X
>
> at least 90 frames if symmetry is Y
>
> at least 45 frames if symmetry is Z
>
> Can somebody point where is *somewhere*?
>
>
>
> ...also...
>
> what other factors can change n... besides symmetry and radiation damage?
>
>
>
> Thanks
>
>
> -

Re: [ccp4bb] number of frames to get a full dataset?

[Andreas Förster]

Hi Murpholino,

in my opinion (*), the question is neither number of frames nor degrees.
The only thing that matters to your crystal is dose.  How many photons does
your crystal take before it dies?  Consequently, the question to ask is How
best to use photons.  Some people have done exactly that.
https://doi.org/10.1107/S2059798319003528

All best.


Andreas


(*) Disclaimer:  I benefit when you use PILATUS or EIGER - but I want you
to use them to your advantage.



On Tue, Jun 23, 2020 at 12:04 AM Murpholino Peligro 
wrote:

> Hi.
> Quick question...
> I have seen *somewhere* that to get a 'full dataset we need to collect n
> frames':
> at least 180 frames if symmetry is X
> at least 90 frames if symmetry is Y
> at least 45 frames if symmetry is Z
> Can somebody point where is *somewhere*?
>
> ...also...
> what other factors can change n... besides symmetry and radiation damage?
>
> Thanks
>
> --
>
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Re: [ccp4bb] Dose in diffraction patterns?

[Andreas Förster]

Dear Murpholino,

all diffraction patterns contain information on absorbed dose in the form
of radiation damage.

You might be more interested in a quantitative description of dose.  For
this, you need information on the size and shape of your crystal; the
sequence of your protein + cofactors, ligands, metals and crystallization
buffer; the size, shape and flux of your beam; and the position of the
rotation axis relative to the beam (does the crystal rotate or wobble in
the beam?).  In a perfect world, all this information would be part of the
metadata that's saved with your diffraction data.  Currently, none of this
is.  (Correct me if I'm wrong.  I'd like to know.)  With it, you can
estimate dose with the current or future versions of Raddose 3D.

All best.


Andreas



On Tue, May 5, 2020 at 8:49 PM Murpholino Peligro 
wrote:

> Do diffraction patterns publicly accessible contain information about the
> x-ray absorbed dose?
>
>
>
> Thanks
>
> --
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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

mat to be used for integration ?
> >
> > While those text files would be heavy, they'd be still lighter than raw
> images and the whole useless white space they carry with them between
> reflections.
> >
> > If not possible, could we imagine to eliminate all the unused space on
> these ? Like a super raw image diet-plan for the incoming summer !
> >
> > Best regards,
> >
> > Julien CAPPELE
> > Université de Lorraine, Nancy, France
> > PhD student - 2nd Year
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

Hi Clemens,

this is curious.  You are right that there's a direct link to the raw data
on 6vs4, but there isn't one on http://www.rcsb.org/structure/6H56.  I'll
contact RCSB to see where the problem lies.

All best.


Andreas



On Thu, Mar 19, 2020 at 8:34 AM Clemens Vonrhein 
wrote:

> Hi Andreas,
>
> On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote:
> > - The link to the raw data can be found inside the mmCIF file under
> > _pdbx_related_exp_data_set.data_reference.  Whether it's also shown on
> one
> > of the PDB sites is up to the designers of these sides.  I cannot find a
> > link to the experimental data on rcsb.org.
>
> They are available near the bottom of a rcsb.org page ("Experimental
> Data & Validation" section) - see e.g. 6VS4 page
>
>   http://www.rcsb.org/structure/6VS4
>
> (the newest deposited PDB structure with deposited data recorded).
>
> Cheers
>
> Clemens
>
> PS: if anyone is in need of a simple script for finding and
> downloading such PDB entries, please let me know.
>
>



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Andreas Förster]

As someone who's done this (for one structure of minor significance), I
would like to make a few comments:

- I highly encourage deposition of raw data.  Why would you not?  Now that
many labs are shut is the time to do it for all these datasets hiding
somewhere on abandoned hard disk.  These disks will break.  One hopes
Zenodo will not.

- The link to the raw data can be found inside the mmCIF file under
_pdbx_related_exp_data_set.data_reference.  Whether it's also shown on one
of the PDB sites is up to the designers of these sides.  I cannot find a
link to the experimental data on rcsb.org.  PDBe, in contrast, has a
clearly visible box linking to "Experimental raw data" on the start page of
the structure.

Deposit your raw data!


Andreas



On Wed, Mar 18, 2020 at 11:31 PM Gerard Bricogne 
wrote:

> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to improve these if refinements could be repeated after some reprocessing
> and further analysis of the raw diffraction images, rather than against the
> deposited merged data. This statement should in no way be construed as a
> criticism of the remarkable achievements of the research groups concerned,
> who have been operating under tremendous time pressure, but as an exciting
> opportunity to push methods to their limits on a uniquely significant class
> of structures.
>
> Another consideration is that the various logistical problems created by
> COVID-19 may soon make it increasingly difficult to collect new diffraction
> data on potential drug targets relevant to the fight against SARS-CoV-2,
> underlining the importance of ensuring that the best results be obtained
> from every dataset actually collected, and that the most useful conclusions
> be drawn from the analysis of those datasets towards improving the quality
> of subsequent data collections.
>
> On this basis we would like to propose that special efforts be made to
> grant
> public access to the raw image data associated with any SARS-CoV-2 related
> structure that is deposited into the PDB. This can be done by (1) archiving
> these raw image data using resources such as data.sbgrid.org, zenodo.org,
> proteindiffraction.org or any other cloud-based data-sharing service, and
> (2) communicating the corresponding DOIs to the wwPDB centres. This idea
> could be extended to datasets that investigators would like to offer to
> interested methods developers or expert users at the pre-deposition stage.
>
> Experts making use of those raw data would be encouraged to document, in as
> much detail as possible, how particular programs or workflows could be used
> on those structures/datasets to obtain the best results. This would be a
> kind of "virtual workshop", a particularly valuable collective activity at
> the present time when several in-person workshops (e.g. RapiData) have been
> cancelled and many meetings are in limbo for several months.
>
> The latter activity would benefit from having a centralised facility set up
> for the experts to post their results and annotations: we could create such
> a facility, but other, larger groups might want to consider doing so.
>
>
> With best wishes,
>
> Clemens & Gerard.
>
> 
>
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Re: [ccp4bb] [3dem] Which resolution?

[Andreas Förster]

A very good point, Gerard, but maybe too late.  It seems to me that a 
lot of microscopists have already given up this abundantly discussed 
question.  They just call everything atomic resolution irrespective of 
whatever numerical value they arrive at by whatever means.


All best.


Andreas



On 23/02/2020 8:41, Gerard Bricogne wrote:

Gentlemen,

  Please consider for a moment that by such intemperate language and
tone, you are making a topic of fundamental importance to both the MX and
the EM communities into a no-go area. This cannot be good for anyone's
reputation nor for the two fields in general. It has to be possible to
discuss the topic of "resolution" in a dispassionate way, so as to jointly
gain an improved and shared understanding of the matter, without feeling
implicitly under pressure to support one side or the other. An acrimonious
dispute like this one can only be putting people off getting involved in the
discussion, which is exactly the opposite of what a thread on a scientific
bulletin board should be doing.


  With best wishes,

   Gerard.

--
On Sun, Feb 23, 2020 at 08:15:34AM -0300, Marin van Heel wrote:

Hi Carlos Oscar and Jose-Maria,

I choose to answer you guys first, because it will take little of my time
to counter your criticism and because I have long since been less than
amused by your published, ill-conceived criticism:

“*Marin, I always suffer with your reference to sloppy statistics. If we
take your paper of 2005 where the 1/2 bit criterion was proposed, Eqs. 4 to
15 have completely ignored the fact that you are dealing with Fourier
components, that are complex numbers, and consequently you have to deal
with random variables that have TWO components, which moreover the real and
imaginary part are not independent and, in their turn, they are not
independent of the nearby Fourier coefficients so that for computing radial
averages you would need to account for the correlation among coefficients*”

I had seen this argumentation against our (2005) paper in your
manuscript/paper years back. I was so stunned by the level of
misunderstanding expressed in your manuscript that I chose not to spend any
time reacting to those statements. Now that you choose to so openly display
your thoughts on the matter, I have no other choice than to spell out your
errors in public.



All complex arrays in our 2005 paper are Hermitian (since they are the FTs
of real data), and so are all their inner products. In all the integrals
over rings one always averages a complex Fourier-space voxel with its
Hermitian conjugate yielding *ONE* real value (times two)!  Without that
Hermitian property, FRCs and FSCs, which are real normalised correlation
functions would not even have been possible. I was - and still am - stunned
by this level of misunderstanding!



This is a blatant blunder that you are propagating over years, a blunder
that does not do any good to your reputation, yet also a blunder that has
probably damaged to our research income. The fact that you can divulgate
such rubbish and leave it out there for years for referees to read (who are
possibly not as well educated in physics and mathematics) will do – and may
already have done – damage to our research.  An apology is appropriate but
an apology is not enough.



Maybe you should ask your granting agencies how to transfer 25% of your
grant income to our research, in compensation of damages created by your
blunder!



Success with your request!



Marin



PS. You have also missed that our 2005 paper explicitly includes the
influence of the size of the object within the sampling box (your: “*they
are not independent of the nearby Fourier coefficients*”). I remain
flabbergasted.

On Fri, Feb 21, 2020 at 3:15 PM Carlos Oscar Sorzano 
wrote:


Dear all,

I always try to refrain myself from getting into these discussions, but I
cannot resist more the temptation. Here are some more ideas that I hope
bring more light than confusion:

- There must be some functional relationship between the FSC and the SNR,
but the exact analytical form of this relationship is unknown (I suspect
that it must be at least monotonic, the worse the SNR, the worse FSC; but
even this is difficult to prove). The relationship we normally use
FSC=SNR/(1+SNR) was derived in a context that does not apply to CryoEM (1D
stationary signals in real space; our molecules are not stationary), and
consequently any reasoning of any threshold based on this relationship is
incorrect (see our review).

- Still, as long as we all use the same threshold, the reported
resolutions are comparable to each other. In that regard, I am happy that
we have set 0.143 (although any other number would have served the purpose)
as the standard.

- I totally agree with Steve that the full FSC is much more informative
than its crossing with the threshold. Specially, because we should be much
more worried about its behavior when it has high values than when it has
low values. Before 

Re: [ccp4bb] SeMet data

[Andreas Förster]

Dear Lindsey,

I'm all with Nukri on this one.  12 Se atoms (whose incorporation you've
shown) should be plenty to give you enough anomalous signal to phase the
data and solve the structure.  That's why I would do the simplest
experiment first.  Collect 360° of data at the peak energy, maybe a bit
finer sliced than you have now (0.1° per image) and with fewer X-rays.
Reduce exposure fivefold (just a guess, but most people tend to overexpose
- see Winter et al., Acta D 75:242, 2019) and see what you can get from
this one dataset after processing with FRIEDEL'S_LAW= FALSE.

Look at the table "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS
FUNCTION OF RESOLUTION" in CORRECT.LP and see how far the anomalous signal
extends (Anomal Corr values above 15 to 20, highlighted by XDS with an
asterisk) and how strong it is (SigAno values, above 3 gives you
confidence, though I have solved structures with much less signal).

If the anomalous signal isn't enough for structure solution, collect more
data from the same crystal.  This is one reason why you reduced the
exposure in the first place.  Move the detector in or out depending on the
processing of the first 360° (How far does diffraction extend?) and collect
another 360°.  Or change chi/kappa.  (See Basu et al., Acta D 75:262, 2019
for inspiration.)  Or - and this is the best but unlikely to be necessary
with your crystals - do two-wavelength MAD.  This shouldn't be an
afterthought to the SAD experiment, though, but properly planned as one
comprehensive experiment.  Using the inflection and remote energies might
be a good idea because it maximizes the differences between the two
datasets.

Inverse beam can be powerful but also poses challenges.  I use this
technique only if I fail otherwise.

All best.


Andreas





On Tue, Aug 27, 2019 at 3:55 AM Nukri Sanishvili  wrote:

> Hi Lindsey,
> Obviously, one would need a lot more information to properly diagnose the
> problem and I am sure much smarter people them me will ask you for that.
> But just to move the task by couple of steps, I want to point out couple of
> things.
> 1. Trivial question: did you have the anomalous option turned on during
> data processing? (Just like from the IT help - is your computer turned on?)
> 2. How much data did you collect for each half of the inverse beam
> geometry? If you have enough, try phasing with only one half. When done
> properly, inverse beam experiment is great but it can easily get tricky
> introducing systematic errors and thus swamping anomalous signal.  If you
> redo the inverse beam, use little wider wedges, say, 5-10 degrees.
> 3. I thought an example of diffraction image would not give any useful
> information but... Judging by how smooth the background is on your Pilatus
> image, I am guessing you have used a lot of exposure. Can you calculate how
> much dose did you put in your crystal? If you are going to re-do the
> experiment, I would suggest reducing the exposure level and collecting more
> data.
> 4. Because you are not showing f' and f" plots, I am guessing that you are
> doing SAD. If it fails and you end up redoing your experiment and you have
> crystals for it, you might want to try 2-wavelength MAD but for that you
> would need to know exactly where is inflection point and collect one of the
> datasets there.
>
> Good luck!
> Nukri
>
> On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:
>
>> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
>> acids, incorporation verified by Mass Spec). I've already collected several
>> datasets (ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of
>> anomalous signal during data processing. I'm most familiar with HKL2000,
>> but I have tried XDS and DIALS auto-processing. Here is a scan:
>> https://ibb.co/LZqm33p and here is an example of a frame:
>> https://ibb.co/gR3ZR47. Each frame is 0.25° and I'm using inverse beam
>> with wedge size 1°. Maybe I need to adjust my collection strategy? All
>> previous datasets have been in space group P 21 with dimensions of approx.
>> 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional things I
>> can be doing in HKL but I've run out of ideas. Any advice or
>> recommendations would be appreciated. Please let me know if you need
>> additional information.
>>
>> Thank you,
>> Lindsey
>>
>> 
>>
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>>
>
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Re: [ccp4bb] Better Beamline suggestion!

[Andreas Förster]

Dear Chandra,

where at APS did you collect?  NE-CAT (and in particular beamline 24-ID-E)
is well set-up for long unit cells.  You could ask Yury Polikanov (
https://bios.uic.edu/profiles/polikanov-yury/) for advice.  He crystallizes
ribosomes with unit cell that are not quite as big as what you have, but
quite big nevertheless.

An alternative would be P14 at EMBL.  They have measured crystals with unit
cell dimensions beyond 1 kÅ.

All best.


Andreas



On Mon, Aug 19, 2019 at 5:08 PM Chandramohan Kattamuri <
1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk> wrote:

>
> Dear All
>
> We recently collected a data set at APS, Chicago with unit cell dimensions
> of 68.4; 68.4 and 991.6 A. Our diffraction data extends to 3A with the APS
> set up, however, the long axis has been problematic, resulting in streaking
> of the diffraction data and requires a very specific orientation of the
> crystal for usable diffraction. Can anyone recommend beamlines that can
> give us higher resolution, or a source with a better goniometer allowing
> for more angle manipulation after looping?
>
> Thank a lot
> Chandra K
>
>
>
>
> --
>
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Re: [ccp4bb] cbf to sfrm

[Andreas Förster]

Dear Tim and all,

if anyone is interested in converting EIGER HDF5 files directly to Bruker
format (SFRM), please contact me.  There's no need to go via CBF or similar
intermediaries.

All best.


Andreas



On Sun, Jul 28, 2019 at 12:25 PM Tim Gruene  wrote:

> Dear all,
>
> recently the conversion from CBF to SFRM frame format with APEX was
> discussed
> on the Bruker mailing list ("Synchrotron data with Bruker Software"),
> including a potential bug that parameters in the frames other than the
> first
> frame are not set correctly. The workaround to re-convert from SFRM to
> SFRM a
> second time did not help in my case.
>
> I therefore updated my program sfrmtools, available at https://
> homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/
>
> With the option '-u',you can provide the first frame of the run, and via
> '-p'
> a parameter file that contains the critical parameters (see documentation
> at
> above URL) to update the header for all frames in this run. In case you
> have
> twinned data and want to benefit from SAINT, this should be possible with
> this
> feature.
>
> Both 64bit Linux binary and the source code are available. The program has
> no
> dependencies and should compile under any platform.
>
> I did not debug this new feature very thoroughly, but it worked for me so
> far.
> Any bug reports are welcome to this address tim.gru...@univie.ac.at
>
> I hope this is helpful for one or two users.
>
> I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM
> header format.
>
> Kind regards,
> Tim
>
> cc Bruker mailing list, CCP4BB, phenixBB
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
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Re: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets deadline 18th June!

[Andreas Förster]

Would it be fair to call it CCP40 now?


Andreas



On Mon, Jun 3, 2019 at 4:37 PM Paula Salgado 
wrote:

>
>
> This year, CCP4 turns 40 and is celebrating in style with an event in
> London. CCP4 has a strong focus on training the new generation of
> crystallographers and developers so, as part of the celebrations, we are
> inviting 10 PhD students and Post-doctoral researchers to showcase their
> work using CCP4.
>
>
>
> If you are a PhD student or Postdoc protein crystallographer and have
> published work featureing CCP4 as a strong component, or have made a
> recognised contribution to CCP4 software, you could be joining the
> celebrations at the Royal Society, London, on *Tuesday 9 July, from
> 13:00-17:00*.
>
>
>
> To win, just submit a piece of published work highlighting CCP4, where you
> are the first author. If selected, you will be asked to create a poster to
> present to a wide range of audiences at the event.  Small travel
> bursaries are available to help with costs (details
> http://www.ccp4.ac.uk/40thccp4golden.htm).
>
>
> Deadline to apply is *June 18th,* so hurry! Please share with your
> students, postdocs, colleagues and friends! We want to hear about your
> great work and want you to join the party on July 9th!
>
>
> Attached is a flyer you can use to help advertise the competition.
>
>
> Hope to see you at the Royal Society!
>
>
> Competition details :
>
> http://www.ccp4.ac.uk/40thccp4golden.htm
>
>
>
> On behalf of the CCP4 Executive
>
> Paula Salgado
>
>
> ===
>
> Dr Paula S. Salgado
> Senior Lecturer in Macromolecular Crystallography
> Institute for Cell and Molecular Biosciences
> Faculty of Medical Sciences
> 3rd Floor Cookson Building
> Newcastle University
> Newcastle upon Tyne, NE2 4HH, UK
>
> Tel: +44 (0)191 208 7432
> Fax: +44 (0)191 208 7424
> Email: paula.salg...@ncl.ac.uk
>
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Re: [ccp4bb] beryllium chloride

[Andreas Förster]

##
>
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>
> --
>
> UT Southwestern
>
> Medical Center
>
> The future of medicine, today.
>
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Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Refinement

[Andreas Förster]

Yeah, good stuff:

http://www.auspex.de/

All best.


Andreas



On Mon, Mar 25, 2019 at 10:45 AM CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Even if you can't see them, it may be worthwhile investigating with Auspex
> (Parkhurst, Thorn, Winter & Waterman - sorry, I can't remember the
> reference off-hand). There's an easy to use webserver somewhere that runs
> it...
>
> Harry
> --
> Dr Harry Powell
>
> On 25 Mar 2019, at 09:03, herman.schreu...@sanofi.com wrote:
>
> Dear ???,
>
> Do you have any ice rings (even hardly visible ones) in your diffraction
> data?
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *Im Auftrag von *StrBio
> *Gesendet:* Sonntag, 24. März 2019 05:17
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] Refinement
>
>
>
> ALL.
>
>
>
> I have data at 2.4 A in P21 sp gr, helical protein.
>
> Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics
> oither Rfactor (by Phenix). Refmac quit same.
>
> Should I deposit it or look better data?
>
> Any suggestion?
>
>
>
>
>
>
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Re: [ccp4bb] Open Access Repositories for Big Data?

[Andreas Förster]

Hi Aaron,

can you slice your data and then link to the bits?

We're currently trying to find out what "unlimited Google Drive storage"
means by uploading pi in chunks of 70 GB or so.

All best.


Andreas



On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke  wrote:

> Dear CCP4ites,
>
> Is anyone aware of online repositories that will store huge sets of raw
> data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is
> typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to
> respond to my emails.
>
> I could host them myself, but the involuntary dry heaving response I got
> when I brought up the idea to our IT department implied they were less
> enthused with the idea than I was. So a cloud service would be far more
> preferable as a long term solution.
>
> Thanks,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>
> --
>
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Re: [ccp4bb] suggestions for cryoprotectant

[Andreas Förster]

Dear Firdous,

get some Mitegen sleeves and test your crystals at RT. Before you establish
 diffraction, there’s no need to agonize about cryo-conditions.

Good luck!


Andreas

On Fri, 19 Oct 2018 at 23:57, Firdous Tarique 
wrote:

> Dear members
>
> I have got beautiful crystal hits in SaltRx screens which are not
> diffracting to a good resoultion. All of them are salt based condition and
> I am not able to formulate a good cryoprotectant for these crystals. I also
> think that in my case the poor resolution is due to a poor cryoprotectant
> selection.
>
> The conditions are as follows:
>
> 1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
> 2>0.5M KCN 100mM Tris pH8.5
> 3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
> 4>4M Sodium Nitrate 100mM Tris pH8.5
> 5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6
>
> There are few more conditions but so far not able to see good diffraction
> with using lower peg and glycerol based cryoprotectants.
>
> Can anybody suggest me good cryos conditions for salt based
> crystallization conditions or anything good for SaltRx crystallization hits.
>
> Thanks
>
> Firdous
>
> --
>
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Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

[Andreas Förster]

Hi James,

you’re probably aware of this but you can edit CBF headers in place with
sed. That’s what I do when I make the detector on my diffractometer go
closer than the hardware limit.

All best - Andreas
On Sat, 22 Sep 2018 at 00:51, James Holton 
wrote:

> For teaching purposes I have found that controlled pairs of data sets
> are most instructive.  You are right that an easy one-button-push
> processing run tells you nothing, but so does a bang-it-crashed-now-what
> data set.  Most useful are two data sets that are identical in every
> respect but one, and that one thing is the point you are trying to get
> across.  It's hard to collect such perfectly paired data sets, so I
> ended up just simulating them. I deliberately chose a high-symmetry
> space group to keep the download size small. You can download them from
> here:
>
> http://bl831.als.lbl.gov/~jamesh/workshop/
>
> These five datasets represent the four biggest problems I see users have
> when trying to solve structures: 1) poor anomalous signal, 2) overlaps
> from a bad crystal orientation, 3) hidden radiation damage to sites, and
> 4) ice rings.  The 5th "goodsignal" dataset is the positive control.
>
> The web page contains everything from images to processed MTZ files,
> maps and the "right answer" in pdb and mtz format.  A slightly more
> "realistic" version with a bigger download size is here:
>
> http://bl831.als.lbl.gov/~jamesh/workshop2/
>
> This is the one I used for my "weak anomalous challenge" a few years
> back. The teaching advantage is that you can use the image-mixer script
> to modulate the severity of problems like ice rings and anomalous
> signal.  If you make a competition of it, people tend to get more
> interested.
>
> When it comes to beam centers, it is not all that hard to take a data
> set with a "correct" beam center and just edit the headers. How you do
> this depends on the file format, but I have some instructions for
> editing images in general here:
>
> http://bl831.als.lbl.gov/~jamesh/bin_stuff/
>
> In general, you can usually separate the header from the data with the
> unix command "head" or "dd", edit the header with your favorite text
> editor, and then put the two parts back together with "cat". As for
> which beam center is "correct", it is important to tell your students
> that that depends on which software you are using.  I wrote all this
> down in the last paragraph on page 7 of this doc:
>
> https://submit.biorxiv.org/submission/pdf?msid=BIORXIV/2018/394965
>
> This doc also describes another simulated data set that demonstrates the
> challenges of combining lots of short wedges together.  May or may not
> be too advanced a topic for your students?  Or maybe not. As you can
> guess I'm experimenting with biorxiv.  So far, no comments.
>
> Good luck with your class!
>
> -James Holton
> MAD Scientist
>
>
> On 9/19/2018 5:15 PM, Whitley, Matthew J wrote:
> > Dear colleagues,
> >
> > For teaching purposes, I am looking for a small number (< 5) of
> > macromolecular diffraction datasets (raw images) that might be
> > considered 'difficult' for a beginning crystallography student to
> > process.  By 'difficult' I generally mean not able to be processed
> > automatically by a common processing package (XDS, Mosflm, DIALS, etc)
> > using default settings, i.e., no black box "click and done" processing.
> > The datasets I am looking for would have some stumbling block such as
> > incorrect experimental parameters recorded in the image headers,
> > multiple lattices that cause indexing to fail, datasets for which
> > determining the correct space group is tricky, datasets for experiments
> > in which the crystal slipped or moved in the beam, or anything else you
> > can think of.  The idea is for these beginning students to examine
> > several datasets that highlight various phenomena that can lead one
> > astray during processing.
> >
> > A good candidate dataset would also ideally comprise a modest number of
> > images so as to keep integration time to a minimum.  Factors that are
> > mostly irrelevant for my purpose: resolution (as long as better than
> > ~3.5 Å), source (home vs synchrotron), presence/absence of anomalous
> > scattering,  presence/absence of ligands, monomeric vs oligomeric
> > structures, etc.  Also, to be clear, I am not looking for datasets that
> > have so many pathologies that they would require many long hours of work
> > for an expert to process correctly.
> >
> > I have checked public repositories such as proteindiffraction.org and
> > SBGrid databank, but all of the datasets I acquired from these sources
> > process satisfactorily with little effort, and in any event I know of no
> > way to search for 'challenging' datasets.  (I also wonder whether
> > anybody is in the habit of depositing, shall we say, less-than-pristine
> > images to public repositories?)
> >
> > If you know of such a dataset that is already publicly available, or if
> > you have such a dataset that you are 

Re: [ccp4bb] data processing with split/bad crystals

[Andreas Förster]

Dear Tommi,

DIALS is good with multiple lattices.  It might not have given you best 
results as part of the Diamond pipeline, but give it a try with the 
max_lattices=2 parameter during dials.index and see where it takes you.


That said, you'll end up with worse statistics if you have two lattices. 
 Don't expect magic from your processing programs.


All best.


Andreas



On 16/07/2018 10:55, Kajander, Tommi A wrote:

Dear All,

I was wondering what would be the best software nowadays to try to process data 
from crystal that clearly is split or
has a secondary set of lattice points (close, poor data) in the raw data - data 
can be processed with XDS (2.9-2.8 Å) but Rmerge tends to be
bit high at low resolution (close to 7-8% depending on processing) - using 
XSCALE helps with the radiation damage correction some what.

Data looks like primitive orthorombic but not quite sure (also seems like it 
has one screw axis e.g. P2212 - but oddly phaser finds
solutions in P22121 also or even preferably…..). I am wondering a bit if it 
isn’t actually monoclinic.

Based on automated processing by Diamond pipeline XDS seems most robust - but 
any hints on such cases would
be welcome. Of course we will try to get better crystal but so far no luck.

Thanks for comments,

Best
Tommi



---

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Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
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Re: [ccp4bb] processing hd5 files from Dectris detector

[Andreas Förster]

Dear Laurent,

sorry for getting into this discussion a bit late, but I was traveling.
Many good points have been raised in response to your question.  I'd like
to summarize and add to them.

1.  Your beamline scientist WILL know how to process the data, and if the
software she recommends is not what you're familiar with, she will also be
able to help you with your favorite software.  This should always be your
first port of call.

2.  HDF5 in itself doesn't pose problems to XDS.  If the HDF read library
Neggia that was mentioned in a few of the responses doesn't help XDS read
HDF5 files, let me and Kay Diederichs know.  We'll try to figure out the
problem.

3.  XDS pipelines (autoProc, xdsme, xdsgui, xds-app, etc) should be able to
process HDF5 data as long as they know where Neggia is located.

4.  HDF5 files written by the detector should all look the same (files
written when the detector was introduced looked slightly different).  Many
beamlines are now streaming the data off the detector and write the files
themselves.  Here, considerable variety in the metadata is possible.  We
are working on a validator for HDF5 metadata, but that's still work in
progress.

5.  Besides XDS, DIALS and HKL-2000 should process HDF5 files without
complaints.

6.  Conversion of HDF5 files into CBF is still required for processing with
iMosflm, but that's likely to change before too long.

7.  Our tool H5ToXds is technically not a converter but an extractor.  It
writes the images in headerless CBF, which is not a standard.  H5ToXds was
written with the singular purpose of helping XDS process HDF5 data by
presenting individual images as temporary CBFs upon request.  Since the
introduction of the plugin mechanism and Neggia, H5ToXds is obsolete.  If
you do need to create CBFs, eiger2cbf or hdf2mini-cbf should be used.  They
write miniCBF headers.  Best is to work with HDF5, though.

8.  The source code for eiger2cbf (https://github.com/biochem-fan/eiger2cbf)
doesn't just contain a CBF converter but also a plugin for XDS.  This
plugin does the same thing as Neggia but works even better under extreme
load (data from NSLS-II).

I'm happy to answer any questions that might remain.  Thanks to everyone
for answering.

All best.


Andreas




On Thu, May 31, 2018 at 8:58 AM, maveyrau  wrote:

> Hi CCP4ers
>
> we recently collected many datasets on dectris detectors producing hd5
> files. I would like to use some auto processing tools to process them
> (xdsapp, xdsme…). As far as I can say, xdsapp or xdsme cannot process hd5
> natively. I tried to convert them to cbf format (eiger2cbf,
> hdf2mini-cbf,...), but then it seams that the header of the caf files are
> lacking some required informations…
>
> Any idea how to convert hd5 files to complete caf files ? Are there any
> plans for xdsapp to be able to work on hd5 files ?
>
> thanks for your help
>
> Laurent
> --
> Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
> P I C T   ---  Plateforme Intégrée de Criblage de Toulouse
> Université  Paul  Sabatier /  CNRS  /  I.P.B.S.  UMR  5089
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Re: [ccp4bb] Sulphur SAD at home source

[Andreas Förster]

Dear Manoj,

I'm happy to answer your questions and have a look at your data.  Maybe we
can take this off-list and you report back if and when you solve your
structure.

By the way, I'm processing native data collected with a MetalJet at the
moment.  The anomalous signal is even weaker at 1.35 Å but can be useful.

All best.


Andreas



On Tue, Apr 3, 2018 at 5:36 PM, Manoj Saxena <manoj.sax...@upr.edu> wrote:

> Thank you!, Andreas and all others who replied.
>  I have seen your tutorial and that's what I was referring to.
> Maybe I can consult you later when I screen some samples and have an idea
> of signal strength?
>
> Regards
> Manoj
>
>
> 2018-04-03 10:55 GMT-04:00 Andreas Förster <andreas.foers...@dectris.com>:
>
>> Dear Manoj,
>>
>> providing your crystals diffract to at least 2.5 Å and the sulfurs are
>> ordered, you should be able to solve your structure without too many
>> problems.  As a first experiment, I would recommend collecting 360 degrees
>> of data.  Process these with XDS and the FRIEDEL'S_LAW= FALSE option and
>> see how much anomalous signal CORRECT.LP reports, if you've got stars in
>> the values of the Anomal Corr column, you're on the right track.  Try to
>> phase with SHELXD, following the advice on http://shelx.uni-goettingen
>> .de/tutorials.php.
>>
>> If you don't succeed, you might need higher multiplicity.  If you have a
>> kappa or chi goniometer, you can reorient the crystal and collect another
>> 360 degrees and another 360 degrees, and so on.  Merge all data in XSCALE
>> until you can solve the structure.
>>
>> I once wrote a little tutorial for doing S-SAD on the home source that
>> you might want to follow.  http://www.imperial.ac.uk/x-ra
>> y-crystallography/learning-more/sulphur-sad/  With an HPC detector (or
>> even an image plate) you'd getter better data than with a CCD detector
>> and be able to solve your structure quicker.  (Disclaimer: I work for a
>> company that makes HPC detectors.)  I consider the home source a great
>> place to solve structures by native SAD.
>>
>> All best.
>>
>>
>> Andreas
>>
>>
>>
>> On Tue, Apr 3, 2018 at 4:26 PM, Manoj Saxena <
>> 1d16aa30e8a1-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Hi All,
>>>
>>> I am writing to seek advice on doing  sulphur SAD data collection
>>> at Cu based home source for a protein that is 12 KDa and has 6 S atoms.
>>> I have seen some links online and some references but would be grateful
>>> if
>>> you can share your know-how for success with this.
>>> Like what multiplicity of data would be good to aim for and
>>> data processing tips.
>>> Inputs from people who have tried and failed would also be highly
>>> appreciated.
>>>
>>> Thank you
>>> Manoj Saxena
>>> University of Puerto Rico
>>>
>>>
>>>
>>
>>
>> --
>> <https://www.dectris.com>
>> Andreas Förster, Ph.D.
>> MX Application Scientist, Scientific Sales
>> Phone: +41 56 500 21 00 <+41%2056%20500%2021%2000> | Direct: +41 56 500
>> 21 76 <+41%2056%20500%2021%2076> | Email: andreas.foers...@dectris.com
>> DECTRIS Ltd. | Taefernweg 1
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz+erland=gmail=g>
>>
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz+erland=gmail=g>|
>> 5405 Baden-Daettwil
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz+erland=gmail=g>
>>
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>> | Switz
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz+erland=gmail=g>
>> erland
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz+erland=gmail=g>
>>
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz=gmail=g>
>> |
>> <https://maps.google.com/?q=Taefernweg+1+%C2%A0+%7C+5405+Baden-Daettwil+%C2%A0+%7C%C2%A0Switz=gmail=g>
>> www.dectris.com
>>
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>>  [image: facebook]
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Re: [ccp4bb] Sulphur SAD at home source

[Andreas Förster]

Dear Manoj,

providing your crystals diffract to at least 2.5 Å and the sulfurs are
ordered, you should be able to solve your structure without too many
problems.  As a first experiment, I would recommend collecting 360 degrees
of data.  Process these with XDS and the FRIEDEL'S_LAW= FALSE option and
see how much anomalous signal CORRECT.LP reports, if you've got stars in
the values of the Anomal Corr column, you're on the right track.  Try to
phase with SHELXD, following the advice on http://shelx.uni-goettingen
.de/tutorials.php.

If you don't succeed, you might need higher multiplicity.  If you have a
kappa or chi goniometer, you can reorient the crystal and collect another
360 degrees and another 360 degrees, and so on.  Merge all data in XSCALE
until you can solve the structure.

I once wrote a little tutorial for doing S-SAD on the home source that you
might want to follow.  http://www.imperial.ac.uk/x-
ray-crystallography/learning-more/sulphur-sad/  With an HPC detector (or
even an image plate) you'd getter better data than with a CCD detector and
be able to solve your structure quicker.  (Disclaimer: I work for a company
that makes HPC detectors.)  I consider the home source a great place to
solve structures by native SAD.

All best.


Andreas



On Tue, Apr 3, 2018 at 4:26 PM, Manoj Saxena <1d16aa30e8a1-dmarc-reques
t...@jiscmail.ac.uk> wrote:

> Hi All,
>
> I am writing to seek advice on doing  sulphur SAD data collection
> at Cu based home source for a protein that is 12 KDa and has 6 S atoms.
> I have seen some links online and some references but would be grateful if
> you can share your know-how for success with this.
> Like what multiplicity of data would be good to aim for and
> data processing tips.
> Inputs from people who have tried and failed would also be highly
> appreciated.
>
> Thank you
> Manoj Saxena
> University of Puerto Rico
>
>
>


-- 
<https://www.dectris.com>
Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 21 00 <+41%2056%20500%2021%2000> | Direct: +41 56 500 21
76 <+41%2056%20500%2021%2076> | Email: andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

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Re: [ccp4bb] Eiger 16M detector in HKL2000

[Andreas Förster]

Dear Aidong,

as I don't have access to HKL2000 myself, I can't tell you what might need
to be done to have the software display EIGER X 16M images.  Wladek showed
me that it was possible.  It might just be a question of getting the latest
version.

There are alternatives to HKL-2000.

DIALS can process EIGER data with no questions asked (
https://dials.github.io/).  It is free, open-source software.  DIALS exists
as a powerful command line tool but can also be run through the xia2
pipeline (https://xia2.github.io/).  Both are part of CCP4, but I'd
recommend installing the latest DIALS nightly because development is
rapid.  The developers respond quickly to questions.

XDS can process EIGER data (
http://xds.mpimf-heidelberg.mpg.de/html_doc/XDS.html).  It is free to
academic users.  To process data in HDF5 format (*.h5), make sure to
download the neggia plugin (
https://www.dectris.com/support/downloads/software/neggia, free, but
registration required) and adjust the LIB= parameter to point to where the
plugin is saved.  XDS is a command line tool, but several GUIs exist.

Please give DIALS or XDS a try and tell me how you get along.  If you
continue to encounter problems, let me and the beamline staff at SSRF know.

All best.



Andreas



On Tue, Dec 19, 2017 at 6:48 AM, Aidong Han <a...@xmu.edu.cn> wrote:

> Hi All,
>
> We have recently collected several data sets in the Shanghai synchrotron
> facility with a newly installed Eiger 16M. However, we are not able to
> process these data using our home HKL2000 package. Even though we can
> easily add this detector in, we can not display images. I believe ours has
> not been properly set up. While we are still waiting for a response from
> HKL2000 administration managers (it has been a few days), I wonder whether
> someone can provide me your solution since this detector has been in market
> for more than a year. Thank you for your help.
>
> Sincerely,
>
> Aidong
>
>




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Re: [ccp4bb] Pilatus Issues

[Andreas Förster]

Dear John,

I can't answer your questions with the limited information you supply, but
I would recommend contacting the company that sold you the detector.  Most
probably that's the maker of your diffractometer.  They'll be able to help
you out.  If it's something that requires repair, they might even send you
a loan instrument while taking care of yours.  If you bought the detector
directly from Dectris, please send an email to our support team with
details.

All best.


Andreas



On Fri, Jul 14, 2017 at 6:14 PM, John Hardin <jwhcambri...@gmail.com> wrote:

> Hi,
>
> We have recently noticed an issue with our Pilatus (biased pixels/vertical
> lines).
> I was curious as to whether anyone else has seen this or might know what
> could have caused it?
>
> Best,
> John
>
>
>


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[ccp4bb] SHELXE: peptide occupancy refined to negative value

[Andreas Förster]

Dear all,

since SHELX is now part of CCP4, this question is not entirely off-topic.

I'm trying to solve structures by S-SAD.  Substructure looks weak but ok if
the right resolution cutoff is picked in SHELXD.

SHELXE is happy to do its thing for a while but then gives up with a
"Peptide occupancy has refined to negative value" error in one hand.  The
other hand is quite obviously (CC for partial structure, number of residues
built) wrong, but the PDB obtained with the antimatter peptides looks like
protein, is 80% complete and quite obviously the right solution.

Because of the error, SHELXE doesn't write phases.  How do I get these?  (I
could do MR, but there must be a more elegant way...)  Better yet, what
might cause the "negative occupancy" error and how do I avoid it?

Thanks and all best.


Andreas



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Re: [ccp4bb] High Rfree: Phasing issue or partial crystal disorder

[Andreas Förster]

Dear Pravin,

this brings me to re-emphasize a point I've just made at RapiData.  If
you're working with PILATUS or EIGER detectors, there is no good reason not
to spread your dose over at least 360° of data.  You will get better
statistics than if you collect 57.2° or whatever your strategy software
recommends - and you can laugh P1 in the face if it comes your way.  Just
make sure to adjust expose time or attenuation accordingly when expanding
your data collection to 360°.

This is of no help after data collection, but since you collected data for
SeMet SAD, you probably already have 360° or more and can thus work in P1
(as James suggested) without much pain.

All best.


Andreas



On Thu, Apr 20, 2017 at 12:11 AM, James Holton <jmhol...@slac.stanford.edu>
wrote:

>
> In situations like this I always try dropping to P1.  Even if the data are
> highly incomplete in P1 you can still refine it.  Difference maps are
> degraded by poor completeness, but you still might see something.  But
> either way, the R-factors will tell you something.  if dropping to P1
> solves your R-factor problems then you know you were in the wrong space
> group.
>
> The biggest caveat to dropping symmetry operators (and essentially
> replacing them with NCS operators) is that you want to be VERY careful not
> to mix your working and free sets.  The best way to do this is pick your
> free set with the highest-possible symmetry given your lattice, and then
> expand that to P1 using the CCP4 program "CAD".  Then you change the space
> group in "CAD" and it will chunk out the right asymmetric unit.  Oh, and
> then use PDBSET to expand your model to P1 as well.
> All this is done automatically by the program Zanuda, but even Zanuda
> cannot un-merge data.  You need to provide the P1 structure factors and
> then see what it tells you.
>
> Does that help?
>
> -James Holton
> MAD Scientist
>
> On 4/18/2017 5:56 PM, gnufreebsd wrote:
>
> Dear Pravin
> for a kinase, n lobe is quite flexible ,  especially beta1 and beta2, and
> residues beyond theses two strands.
>
>
> best regards
> tiger
>
> 发自 WPS邮箱客戶端 <http://mo.wps.cn/wps-mail/mail.html>
> 在 Pravinkumar Jagtap <pravinja...@gmail.com> <pravinja...@gmail.com>
> ，2017年4月12日 上午2:55写道：
>
> Dear All,
> I am stuck with this problem for 2 months and hope you could help.
>
> We have a 2.1 A dataset for a 380 amino acid long protein. The space group
> is I4 (single molecule in asymmetric unit, 48% solvent content) and the
> dataset is quite perfect (no obvious pathologies). The protein itself is
> organised in 2 lobes (N and C terminal lobes). The sequence identity to
> nearest homologue structure is 17%.
>
> We could  get the phases by SeMet SAD phasing (3A resolution dataset, 5
> SeMet (excluding N-terminal Met), 3 full occupancy SeMet in C-terminal lobe
> and 2 partial occupancy (~0.5 each; present on surface) SeMet in N-terminal
> lobe). Automated  model building (at 2.1 A) yielded nice model for the
> C-terminal lobe (215 residues)  and manually I could build parts (around 80
> residues) of N-terminal lobe with high confidence. In addition we could
> also build a ligand which is sandwiched between C and N terminal lobe.
>
> However the Rfree is stuck at 0.39 (Rwork 0.33). There is indeed some
> patchy density left at the N terminal lobe but as it is discontinuous, I
> cannot build anything in it (except lots of water molecules). In total I am
> missing around 85 residues. These residues are predicted to be present in
> secondary structure (and not flexible).
>
> As I have around 75-80% model built, I would expect that I would have all
> the phases and  should get nice density for the remaining part. But as I
> dont see it, could the rest part be flexible? But again, this is not
> reflected in the R factors (I would then expect low Rfree).
>
> Could it be that I still lack phases (due to partial occupancy of SeMeth
> in N-terminal lobe ) and have to try to get them by heavy metal soaking, or
> there is disorder in the N-terminal lobe? I have also tried solving
> different datasets for same crystal but this has not been useful.
>
> Regards,
> Pravin.
>
>
>


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[ccp4bb] Further information on the HDF5 read plugin for XDS

[Andreas Förster]

Dear all,


after the announcement of the plugin a few minutes ago, I would like to
give some more detail for those who are interested.


1) The point of the plugin architecture is the logical separation between
data and program.  With plugins written for input data, program developers
can focus on improving their algorithms instead of dealing with data
formats.  There is no reason the ideas behind the plugin couldn't be used
by HKL-2000, Mosflm, DIALS or any other program that processes EIGER images
from HDF5 data.


2) The source code of Neggia has been released under MIT license (open
source) at https://github.com/dectris/neggia.  Feel free to identify
shortcomings and improve the code.


3) Neggia doesn't rely on the official HDF5 library.  As it makes
assumptions about the inner structure of HDF5 files, modifications might
throw it off.  Data written with the EIGER Filewriter can be read.  HDF5
data written from the Stream or where the master file has been modified
after data collection might pose problems.  We are working with beamlines
to make sure all EIGER data can be read by Neggia.  If you encounter
problems, please let me (and your beamline) know.  You can still process
the data with whatever approach you used before adopting the library.


4) The plugin mechanism of XDS is generic.  Anyone can write a plugin to
take advantage of it.  This might be useful to manufacturers of future
detectors with unsupported data formats.  The plugin communicates with XDS
through four function calls:
- subroutine generic_get_header (nx, ny, nbyte, qx, qy, number_of_frames,
info_array, error_flag)

- subroutine generic_open (library, template_name, info_array, error_flag)

- subroutine generic_get_data (frame_number, nx, ny, data_array,
info_array, error_flag)

- subroutine generic_close (error_flag)

If you think you can write more efficient read routines for already
supported formats, please contact Kay Diederichs.


All best.



Andreas



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MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
andreas.foers...@dectris.com
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[ccp4bb] XDS plugin for efficient reading of HDF5 data

[Andreas Förster]

Dear all,

DECTRIS is proud to announce the release of an HDF5 read plugin to take
advantage of the recently added XDS plugin support (thanks to Wolfgang
Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files.

EIGER detectors produce data in the large-data format HDF5. Despite
substantial advantages (few files to handle, excellent compression), HDF5
data pose some difficulties.  While DIALS and HKL-2000 process HDF5 data
natively, they are limited in their performance by the lack of parallel
reading of the HDF library.  Processing of HDF5 data by XDS has thus far
relied on extraction of temporary CBF images, which adds to the processing
time.

Neggia, our read plugin for XDS, presents HDF5 data to XDS in a fully
parallelized way, directly and without interconversion.  Processing of HDF5
data is now as fast as processing of CBFs.  Refer to the plugin with LIB=
/path/to/plugin.so in XDS.INP.  The parameter DETECTOR= EIGER should remain.

You can download the plugin from www.dectris.com/neggia.html (registration
required).  To run it you need a reasonably recent OSX or linux system with
gcc 4.8 or higher.  We have tested macOS Sierra, CentOS 6, CentOS 7, Mint
17.3.  Alternatively, you can compile the plugin from the source available
at https://github.com/dectris/neggia.

The plugin was written to work with recent EIGER data and has been tested
in house and at a few adventurous beamlines.  If you encounter issues,
please let me now.  Your problem reports will help make the plugin better,
to the benefit of the entire community.

All best and happy data processing


Andreas



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Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
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Re: [ccp4bb] merge weak anomalous signal from multiple datasets

[Andreas Förster]

Hi Charles,

I don't know what multiscale does.  Probably the right thing.  If the 
anomalous signal is weaker after scaling of multiple datasets, 
non-isomorphism might be at fault.  Try Blend to scale your datasets. 
Blend is part of ccp4 and gives good graphical diagnostic feedback.



Andreas



On 01/03/2015 4:20, CPMAS Chen wrote:

Dear CCP4 users,

Recently, I got some datasets with weak anomalous Br signal. I tried to
merge them according to  Q. Liu et al Science 336, p1033 (2012). I am
using the script multiscale@SSRL. The merged dataset has WEAKER
anomalous signals.

Liu et al used SCALA for scaling and merging while multiscale@SSRL using
AIMLESS. Should this cause such a difference? The SCALA@SSRL has a
limitation on the number of frames it can process. So I cannot directly
check if this caused the difference.

Any suggestions?

Thanks!

Charles

--

***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**

Re: [ccp4bb] Ramachandran maps

[Andreas Förster]

I thought Procheck was pre-war, and we should all be using Molprobity 
these day?



Andreas



On 11/12/2014 9:19, Evgeny Osipov wrote:

Dear Patrick,
Try to use procheck from ccp4:
Correct usage is:

   procheck  filename  [chain]  resolution


where  filename= the coordinates file in Brookhaven format
   [chain] = an optional one-letter chain-ID
   resolution  = a real number giving the resolution
 of the structure

For example:-

   procheck  /data/pdb/p1amt.pdb  A  1.5

It also generates a few other useful charts for your structure

On 09.12.2014 18:47, PC wrote:

Hi guys,

Sorry for the repost in COOT/CCP4/PHENIX.
It is possible on of the users in one of these communities might know
the answer

I was wondering if there is a small script I can use to generate the
outline of the allowed regions of Ramachandran map on to which I can
superimpose my coordinates phi and psi?

Something like what appears in COOT-Validate-Ramachandran Plot.

How does one generate such images for publications?

Thank you,
Patrick


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   X-ray Crystallography Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] CrystalClear tape rolls

[Andreas Förster]

Hi Mark,

last time I checked (few months back), Hampton still sold tape. 
Shipping to Europe is extortionate but if you combine with screens and 
other goodies, it's just about bearable.



Andreas



On 01/12/2014 10:24, Mark J van Raaij wrote:

Dear All,

Just wondering what the current situation on CrystalClear tray sealing tape is.
Molecular Dimensions, Hampton, Jena seem to be selling mainly sheets or strips 
precut for plates - I guess related with the fact that the consumer box sealing 
tape changed specifications and now clouds over with certain reservoir 
solutions. See:
https://www.mail-archive.com/ccp4bb@dl.ac.uk/msg00622.html
We are stilll using rolls which came with plates we bought years back, but now 
only have two rolls left - so I am wondering if there is a more economic 
solution than buying sheets or strips.

Greetings,

Mark

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



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   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] The phase problem

[Andreas Förster]

Hi Giuliana,

if your crystal diffracts to 3 Å or better and you have at least one 
Cys/Met per 25 residues, put it on the home source and collect until the 
sulfur signal rises above the noise.  Then solve by SAD.


http://www3.imperial.ac.uk/xraycrystallography/learning/sulfur_sad


Andreas



On 05/11/2014 7:20, Giulliana Rangel wrote:

Dear all,


I would like to known if someone could help me with some idea about the
phase problem.

I am a beginner in crystallography and the first time I tryed to solve
the structure by Molrep, amore, mr. Bump and I didnt find anything for
molecular replacement.

Thus, currently I've tried to soak heavy-atom ( Hg, Pt, I, Pb) and the
diffraction was good, the results in XDS didnt show so good. I didnt
look the heavy atom in density.

I appreciate any suggestion and ideas what I could do.

Best regards,



--
Giulliana Rangel
Mestranda PPG-Biotecnologia UNIFESP
Laboratório de Biologia Estrutural
Tel.: (12) 3309-9698
Rua Talim 330, Vila Nair
CEP 12231-280
São José dos Campos - SP



--
  Andreas Förster
   X-ray Crystallograhpy Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] 3 letter code

[Andreas Förster]

I took the liberty of googling this for you.  I trust that other search 
engines will give the same answer.  Try your favorite next time.


http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/complete/4NP


Andreas



On 02/10/2014 11:50, Faisal Tarique wrote:


Hello everyone

I request you to please tell me the 3 letter code for p nitrophenyl
phosphate..
--
Regards

Faisal
School of Life Sciences
JNU



--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] XDS

[Andreas Förster]

Hi Almudena,

if you run XDS through xia2, you can define multiple wedges in your info:

BEGIN SWEEP SWEEP1
IMAGE image_0001.cbf
DIRECTORY /path/to/files/
START_END 1 900
END SWEEP

BEGIN SWEEP SWEEP2
IMAGE image_0001.cbf
DIRECTORY /path/to/files/
START_END 1001 1200
END SWEEP



Andreas



On 29/09/2014 10:56, Almudena Ponce Salvatierra wrote:

Dear all,

I would like to ask something regarding XDS. Is it possible, without
changing the Name of the Frames, to leave some out while processing?

i.e. something like defining twice the data range
DATA_RANGE= 1 900
!DATA_RANGE= 901 1000
DATA_RANGE= 1001 1200

Is there a way to do so? to leave out wedges like this? I have tried
like so, but I have the Impression it only takes then the last number of
Frames, in this example it would only take 1001 to 1200.

Thanks a lot.

Best wishes,

Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany



--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] frozen pellet insoluble protein

[Andreas Förster]

Dear all,

I've encountered people who refuse to freeze cells and always lyse fresh 
pellets.  Better protein, they say.  I've never had reason to do so 
myself, or even to believe in their voodoo.  Up until now, maybe.


My protein expresses well and is almost all in the soluble fraction in 
an expression test from a fresh pellet.  The large-scale expression from 
the same pellet, now frozen and thawed, yielded 90% insoluble protein.


If it's the freezing that dooms the protein, I'm happy to redo the 
fermentor run.  Are there other examples out there of this?


Thanks.


Andreas




--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] is small dialysis tubes reusable??

[Andreas Förster]

If cost is an issue, I recommend preparing your own MINI Dialysis 
Devices at 99.74% savings.


Cut a hole in the lid of an Eppendorf tube, put your sample in the tube, 
then close the lid over a small piece of dialysis tubing, trapping it as 
a cover.  Float inverted in dialysis buffer and Bob's your uncles for 
pennies.



Andreas



On 26/09/2014 4:51, Manjula Ramu wrote:

Hi all,

I use Slide-A-Lyzer MINI Dialysis Devices from Thermo for dialysis of
small protein volumes. Are they reusable? if so how can we store them??

Thanks and Regards,
Manjula R
Research Scholar
Department of Biophysics
National Institute of Mental Health and Neurosciences
Bengaluru-29, Karnataka
INDIA
E-mail: manjula@gmail.com mailto:manjula@gmail.com
Mobile no:+91-9538553356
http://www.nimhans.kar.nic.in/
https://www.nimhans.kar.nic.in/


--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Lattice Translocation Disorder Correction

[Andreas Förster]

Dear Arko,

my first port of call would be the man himself:

jimin.wang AT yale.edu


Andreas



On 27/08/2014 7:12, Arka Chakraborty wrote:

Dear CCPers,

Is there an existing script or program for implementing the intensity
corrections for  trans-located lattices  in macromolecular crystals as
described in Wang et al (2004)?. Any input or sharing will be immensely
helpful.

Thanks a lot,

Arko

--
*Arka Chakraborty*
*ibmb (Institut de Biologia Molecular de Barcelona)*/
/*BARCELONA, SPAIN*/
/


--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] dynapro DLS cuvettes

[Andreas Förster]

Here's another one, catalog number 105-250-15-40:

http://www.hellma-analytics.com/kuevetten/136/en/pg_id,41$g_id,24$item_id,63/fluorescence-cells.html#63

We use that for light scattering on a Zetasizer Nano.


Andreas



On 14/08/2014 10:35, Gloria Borgstahl wrote:

Does any one know of a source of these cuvettes?
Protein Solution doesn't exist anymore
and Wyatt no longer has these.


--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Heavy Atom Phasing

[Andreas Förster]

Dear Rhys,

the humidity control device at Diamond and ESRF (HC1) is apparently 
especially recommended for crystals that show large variability.  You 
might want to give this a try, collect a few wedges at RT off many 
crystals and then Blend them.  This approach might increase resolution 
and, a la W. Hendrickson as mentioned already, signal.



Andreas



On 27/07/2014 10:48, RHYS GRINTER wrote:

Hi All,

I thought I might put a question to the community, with the hope of getting 
some tips of the best way to proceed with my heavy atom phasing problem.
I'm working on solving the structure of an integral beta-barrel membrane 
protein of approximately 100 kDa. I've crystallised protein, growing some very 
flimsy needle like crystals, and collected datasets to around 3.1 A.
I then produced selenomet derivative protein and repeated crystallisation 
trials in the same conditions and also repeated broad screens, however the 
derivative protein failed to produce crystals that diffracted beyond 10 A (in 
fact it barely crystallises at all).
So I've moved on to heavy atom soaks and have had some success with 
tetrachloroplatinate and tetranitroplatinate compounds, in that the crystals 
didn't dissolve (as they did with gold and samarium compounds) and diffracted 
to some degree. I collected SAD data to around 6.5 A from these crystals and 
there seems to be anomolous signal. However, while I get a good CC of 0.4 from 
HYSS in phenix with this dataset and the phaser EP FOM is 0.56, the maps before 
and after DM are uninterpretable. I'm guessing the quality and resolution of 
the data I collected just aren't good enough (the data is reasonably 
anisotropic).
I performed the metal soaking, by taking a small amount of the platinate salt 
and adding it to the crystallisation drop as the crystals are extremely fragile 
and don't stand up well to handling through a soaking or cryo solution. Leaving 
the crystals to soak for 48 hours and then, freezing them directly. The 
solution is on the border of cryoprotection (the conditions has PEG2000MME and 
PVP and the precipitants), but with native crystals this doesn't seem to be a 
parameter which affects diffraction. The crystals are very variable in 
performance, so while I feel that the heavy atom soaking has compromised their 
diffractability to a degree, inherent variation may play a part.

What I was wondering is if some one with more experience than me found 
themselves in this position, how would they proceed? Questions which spring to 
mind are, how much heavy atom compound do people add and how long do they soak 
for? Is there anyway I can squeeze something out of the anomalous data I have, 
given I have 'reasonable' native data, or will poor quality data give 
spuriously positive statistics for heavy atom phasing? And are there any tricks 
people have experienced to improve performance of crystals like these (aside 
from the usual seeding, additives, different detergents etc which I have spend 
a fair bit of time on optimization already).

Thanks in advance,

Rhys



--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] rigaku micromax 007 cooling

[Andreas Förster]

Thanks to all who replied.  I was a bit unclear.  We don't have house 
water cool the anode directly.  A Haskris WW1 water/water exchanger 
mediates that.  Problem is that this overheats, presumably when the 
house water supply is cut because of a pump failure in the building.


Things seem clean overall, but I'll have closer look at that and 
consider adding filters.  A pump to pull water through the chiller was 
also mentioned by some.  Lastly the building side itself.  Maybe the 
pump is programmed to switch off under low overall load.  I'll look into 
this.


I've emailed Haskris, but would anyone have a manual for the WW1 by chance?

Best.


Andreas



On 24/07/2014 10:32, Ed Hoeffner wrote:

Hi

Ours is cooled by a Haskris R250, which is sized for an XStream also. While
our heat exchangers have had a couple of issues, overall the Haskris heat
exchangers have performed quite well. They redesigned ours when they found
out about our building chilled water. I'm not affiliated with and heartily
recommend them.

As for the water itself, I would ***NEVER*** allow building chilled water
into the generator. Our water is extremely dirty and the supply is slightly
below spec, so we have a pump downstream of the heat exchanger. There are
also 2 filters upstream to pull some of the junk out. Lately, startup has
required the use of the pump, which I interpret as buildup in the condenser,
so that's eventually going to need a cleanout. That was what the redesign
was all about.

I imagine ours is an extreme case, but the heat exchanger makes up for a
variety of ills. Rigaku also recommends a DI filter to keep conductivity low
in the water going into the generator, which improves anode lifetime.
Building chilled water will never be able to be as low as desired. Besides,
facilities people can change things and you'd never know until it's too
late...

Ed

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Andreas Förster
Sent: Thursday, July 24, 2014 10:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] rigaku micromax 007 cooling

Dear all,

I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by chilled
water supplied rather unreliably through the building infrastructure.  I was
wondering what alternatives exist.

Could other MicroMax 007 users share their experiences with alternative
cooling solutions with me?

Thank you.


Andreas






--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] rigaku micromax 007 cooling

[Andreas Förster]

Dear all,

I have a Rigaku MicroMax 007 HF X-ray generator that is cooled by 
chilled water supplied rather unreliably through the building 
infrastructure.  I was wondering what alternatives exist.


Could other MicroMax 007 users share their experiences with alternative 
cooling solutions with me?


Thank you.


Andreas




--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] m_range_check error in aimless

[Andreas Förster]

Dear all,

I'm trying to scale/merge mtz files in ccp4 
(Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an


UNHANDLED EXCEPTION: vector::_M_range_check

at the end of the aimless step, right after the standard deviation v. 
intensity tables.  The output mtz file is not written and consequently 
ctruncate craps out because of no input file.


This occurs with the temporary directory on NSF and local, and with one 
or two mtz files as input.


How can I go beyond this?


Andreas


--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] NEW! Try depositing X-ray data using the wwPDB deposition system

[Andreas Förster]

I was getting very excited here for a second.  Deposition of X-ray data? 
 Is this finally possible?  Raw diffraction data, in other words? 
Image files?


Sadly, the text of the email doesn't support that conclusion.


Andreas



On 25/04/2014 8:16, Rachel Kramer Green wrote:

Depositing a new X-ray crystal structure to the PDB archive?Try the new
and improved wwPDB Deposition system at
http://deposit.wwpdb.org/deposition/.

Since the new system went live on January 27^th , 2014, ~700 structures
have been deposited and promptly annotated.Detailed information on the
system can be found at http://www.wwpdb.org/system_info.html.The new
system was developed to allow the wwPDB partners to meet the evolving
needs of the scientific community over the next decade, including
support for very large systems, complex chemistry, and joint use of
multiple experimental methods. The system replaces all current
deposition and annotation systems in use at the wwPDB deposition
centers, and will lead to improved efficiency and consistency.

New or enhanced features of the deposition system include the generation
of X-ray validation reports (following the recommendations of the wwPDB
X-ray Validation Task Force), improved capture and review of ligand
information, the ability to replace coordinate and/or experimental data
files pre- and post-submission, improved communication process between
depositors and wwPDB curators, and the ability to preview and download
the PDBx/mmCIF entry file prior to submission.

Depositors will have the option to use the new system or one of the
legacy deposition tools (ADIT, AutoDep) for most of 2014. After the
transition to the new system, the legacy tools will be available for a
limited period of time to complete any unfinished deposition sessions.

The wwPDB continues to improve the deposition interface and supporting
functionality as it receives more submissions and input.Questions,
comments, and suggestions should be sent to:
http://deposit-feedback.wwpdb.org_._

--



Rachel Kramer Green, Ph.D.

RCSB PDB

kra...@rcsb.rutgers.edu

*New!*Deposit X-ray data with the wwPDB at:

http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon).

___

Twitter: https://twitter.com/#!/buildmodels

Facebook: http://www.facebook.com/RCSBPDB



--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] PyMol and Schrodinger

[Andreas Förster]

No one is keeping you from downloading the source code and compiling. 
It's straightforward and free.



Andreas



On 23/04/2014 4:43, Cygler, Miroslaw wrote:

Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was
surprised by their answer. The access to PyMol is only through a yearly
licence. They do not offer the option of purchasing the software and
using the obtained version without time limitation. This policy is very
different from many other software packages, which one can use without
continuing licensing fees and additional fees are only when an upgrade
is needed. At least I believe that Office, EndNote, Photoshop and others
are distributed this way.
I also remember very vividly the Warren’s reason for developing PyMol,
and that was the free access to the source code. He later implemented
fees for downloading binary code specific for one’s operating system but
there were no time restrictions on its use.
As far as I recollect, Schrodinger took over PyMol distribution and
development promising to continue in the same spirit. Please correct me
if I am wrong.
I find the constant yearly licensing policy disturbing and will be
looking for alternatives. I would like to hear if you have had the same
experience and what you think about the Schrodinger policy.
Best wishes,

Mirek





--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Merging Data from Multiple Crystals

[Andreas Förster]

Contact James Foadi.

http://diamond.ac.uk/Beamlines/Mx/I24/Staff/Foadi.html


Andreas



On 29/03/2014 1:21, Alexander Batyuk wrote:

Dear Tassos,

Do you know by chance whether BLEND is available?

Best wishes,

Alex

[ccp4bb] summary - small molecule crystallography

[Andreas Förster]

Thanks again for all the responses to my question about small-molecule 
crystallography.  I almost regret having sent the student to the 
chemist.  Trying this at home sounds like a fun afternoon.


On the ccp4 wiki, there was already a section describing how to solve a 
small-molecule structure.  I have now added a few points on data 
collection based on the discussion here.


strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Solve_a_small-molecule_structure


Andreas



On 24/03/2014 7:15, esse...@helix.nih.gov wrote:

Hi,

   this depends on your equipment. You can mount a 0.1-0.2 mm xtal as if it was
a protein crystal onto a regular litho loop or better yet on a steel pin
that has a glass fibre glued into it. Use superglue to glue the crystal at
one end carefully to the glass fibre.
Then it is easy to mount the crystal as if it was a protein crystal.
Expect to move your detector as close as it is possible without bumping into
things. Hopefully you can get to about 1.4 A (or better but 1.4 is probably
the least resolution you need to get). Try different exposure times and or
x-ray generator currents so that you don't get overloads. Still use 1 deg
oscillation range. Not useful to go higher in my experience.
HKL2000 will work with the small molecule license but even the macro license
should work (but requires a bit more fiddling with some of the parameters).
Use direct methods in shelxs or shelxd(?). Keep in mind that the space group
may be centric or has mirror planes: P21/c is quite common but I would not go
so far as to suggest a space group without having seen some data.
Then use shelxs (or h) to refine the structure. You may find it useful to get
a copy of platon (Prof. Spek). http://www.cryst.chem.uu.nl/spek/platon/

Or wingx: http://www.chem.gla.ac.uk/~louis/software/wingx/

It's doable but takes a bit of time if you have no small molecule
crystallography background.

Ah and before you start, ask the student for elemental analysis results. If
the compound contains very heavy atoms, your CuKa radiation may not be useful.
In that case or perhaps in all cases if you need to switch to Mo radiation
(then resolution is not a problem as in the case of CuKa radiation).


Good luck.

Lothar

[ccp4bb] small molecule crystallography

[Andreas Förster]

Dear all,

I've been approached by a materials student with a petri dish full of 
big, sturdy, salty, yellow crystals.  He claims I have the best kit for 
single-crystal diffraction on campus.


I would very much appreciate advice on how to deal with this, anything 
in the range from won't work to use software X to analyze data in 
space group P-43N would be welcome.


Thanks.


Andreas




--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

[Andreas Förster]

Hi Matic,

I'm using a Quadro 600 on an Asus VG278HR screen on RHEL 6.3.  All is 
golden.  I created xorg.conf (below) by running nvidia-xconfig after 
installation of the Nvidia driver.  (Recent Nvidia drivers are buggy and 
you'll have to wear your stereo glasses upside down from time to time 
because the stereo pairs are flipped, but I guess you'd be happy to get 
to that point.)


After creation of the xorg.conf file, I added two options

Option Stereo 10

and

Option Composite Disable

in sections Screen and Extensions, respectively.


Hope that helps.


Andreas


# nvidia-xconfig: X configuration file generated by nvidia-xconfig
# nvidia-xconfig:  version 331.20 
(buildmeister@swio-display-x86-rhel47-05)  Wed Oct 30 18:20:53 PDT 2013



Section ServerLayout
Identifier Layout0
Screen  0  Screen0 0 0
InputDeviceKeyboard0 CoreKeyboard
InputDeviceMouse0 CorePointer
EndSection

Section Files
FontPath/usr/share/fonts/default/Type1
EndSection

Section InputDevice

# generated from default
Identifier Mouse0
Driver mouse
Option Protocol auto
Option Device /dev/input/mice
Option Emulate3Buttons no
Option ZAxisMapping 4 5
EndSection

Section InputDevice

# generated from data in /etc/sysconfig/keyboard
Identifier Keyboard0
Driver kbd
Option XkbLayout gb
Option XkbModel pc105
EndSection

Section Monitor
Identifier Monitor0
VendorName Unknown
ModelName  Unknown
HorizSync   28.0 - 33.0
VertRefresh 43.0 - 72.0
Option DPMS
EndSection

Section Device
Identifier Device0
Driver nvidia
VendorName NVIDIA Corporation
EndSection

Section Screen
Identifier Screen0
Device Device0
MonitorMonitor0
DefaultDepth24
Option Stereo 10
SubSection Display
Depth   24
Modes  1920x1080 1920x1080_120
EndSubSection
EndSection

Section Extensions
Option Composite Disable
EndSection



On 10/03/2014 9:23, Matic Kisovec wrote:

Dear everybody,

to my recent experience not everything is good in the stereo world.
Since I see that others don't have these problems (and I am happy/sad to
see that the same exact combinations work without problems) I would just
like to add my experience.

For the past 4 months I have been struggling to configure a stereo setup
for viewing structures in Pymol.
I got the VG278HR and PNY Quadro K600 connected over the original DVI-D
cable. Since then I was unable to get anything in stereo on Linux (tried
Ubuntu, OpenSUSE, Fedora). Unfortunately I get a blank/black screen
whenever I use the stereo option in xorg.conf. Also tried changing the
motherboard and CPU but got the same result.

In Windows the demo stuff from Nvidia works just fine but again I have
problems with Pymol. So far the only way to see anything connected to
molecular structures in Windows was via DVI-to-HDMI cable but due to
HDMI restrictions the quality isn't as good as it would be over DVI-D.
If I use DVI-D that was shipped with the monitor the quadro card is
detected in Pymol but the monitor doesn't switch to stereo.

I have been in contact with the company that makes Quadro cards (PNY)
but they were unable to help me. I also contacted some very kind users
of CCP4BB and they kindly answered a bunch of question regarding
specific setup options. Thanks again! Still there was no success so far.

I am slowly giving up on the stereo so if anybody has any ideas/thoughts
what could be wrong/done I would greatly appreciate any insight.

Kind regards,
Matic




--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

[Andreas Förster]

On 22/02/2014 10:15, Mark van Raaij wrote:

As the excellent tips that you got indicate, lower R-factors can be
obtained by getting better data (better crystals, better data
collection, better data processing) or better fitting, i.e. refinement.
In this respect, I am impressed by the automatic data processing
protocols now being implemented. Also, the automatic local NCS
refinement in REFMAC seems very good for our recent structures.
But I would really want to make a general comment - not ALL structures
can be better than the average!


Except structures from the Lake Wobegon Center for Structural Biology, 
of course.


There will always be structures with 5%

higher R/Rfree than the average in the same resolution range. Sometimes
this will be due to suboptimal refinement, but sometimes it may simply
not be possible to get better crystals and better data. Better not
necessarily in term of resolution, but in terms of disorders like you
describe for your plate-shaped crystals.
What I mean is that one should make all efforts to get better crystals
and data and refine structures as well as possible, but sometimes it may
not be possible to beat the average of the pdb and one should not get
too hung up by that. These structures should also be deposited and
published.
On the other hand, these rules that R-factor should be a certain value
at a certain resolution, may lead to suboptimal refinement. For example
the thought my R-factor is already better than the average could be
counterproductive and lead people to stop refinement prematurely.
Sometimes a structure will have Rs better than the average for the
resolution, but still better refinement could lower it further and this
should then be done. I can think of an MR solution using a very
homologous model that was refined at higher resolution, structures with
high NCS, or simply certain rock-solid proteins...
Another popular one is (was?) that Rfree should always be below 30%,
while several important structures justifiably have Rfrees quite a bit
higher (others perhaps have not been refined enough).
So while comparing R/Rfree to the average of existing structures is
useful, it may not necessarily be a sign that a structure is bad if
your Rs are 5 % higher, not should your Rs being at or below the average
be an excuse for stopping refinement too early.
Fear that ones Rs are not low enough may even lead to certain forms of
cheating, for example not keeping the Rfree reflections truly free.

On 22 Feb 2014, at 01:41, Chris Fage wrote:


Dear CCP4BB Users,

I recently collected a number of datasets from plate-shaped crystals
that diffracted to 1.9-2.0 angstroms and yielded very nice electron
density maps. There is no major density unaccounted for by the model;
however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
~0.30, respectively. Probably due to the more 2-dimensional nature of
my crystals, there is a range of phi angles in which the reflections
are smeared, and I am wondering if the problem lies therein.

I would be grateful if anyone could provide advice for improving my
refinement statistics, as I was under the impression that the
R-factors should be ~5% lower for the given resolution.

A few more pieces of information:
-Space group = P21, with 2 monomers per asymmetric unit;
-Chi square = 1.0-1.5;
-Rmerge = 0.10-0.15;
-Data were processed in HKL2000 and refined in Refmac5 and/or
phenix.refine;
-PHENIX Xtriage does not detect twinning, but hints at possible weak
translational pseudosymmetry;
-I was previously able to grow one atypically thick crystal which
diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22.
Unfortunately, the completeness of the dataset was only ~90%.

Regards,
Chris


Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Stereo monitor

[Andreas Förster]

I second everything Jeroen said except the need for a €450 graphics 
card.  We have a Quadro 600, which was only £105 or something like that. 
 The slightly cheaper Quadro 400 would have worked as well.  There are 
now successors to these cards.  Unless something has changed in their 
specification, they should work with the monitor with built-in emitter. 
 Others can comment on that.


Best regards.


Andreas



On 21/11/2013 10:49, Tobias Beck wrote:

Dear all,

We are looking into ordering a stereo monitor. I am aware that this
question comes up every so often on this BB (and I read the post by
Alice), but maybe someone has any comments or recent experience with
passive vs. active monitors?

And: Which graphics card can you recommended? The monitor will be used
with Linux and Windows, so support of the correspoding graphics card
with both systems is required.

Thanks and best wishes,

Tobias.

--
___

Dr. Tobias Beck
ETH Zurich
Laboratory of Organic Chemistry
Wolfgang-Pauli-Str. 10, HCI F 322
8093 Zurich, Switzerland
phone:   +41 44 632 68 65
fax:+41 44 632 14 86
web: http://www.protein.ethz.ch/people/tobias
___


--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] diffraction image repository

[Andreas Förster]

Dear all,

there has been ample discussion on this bulletin board regarding the 
benefits of making diffraction images available for published X-ray 
structures.


I'm considering implementing a repository at Imperial College, but I 
don't want to reinvent the wheel or create something out of synch with 
the consensus.  Are there any established solutions out there that I 
could modify?  I know of Tardis.  Are there alternatives?


I have the following workflow in mind.  After logging on and selecting 
create new, the user will be asked to:


- give PDB code
- enter mandatory metadata through well-thought out mask
- upload any number of datasets (native, SeMet, etc)
- make existence of datasets or datasets themselves public


Any suggestions would be appreciated.


Andreas




--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Andreas Förster]

Dear all,

this water discussion is flowing increasingly towards a place where I 
feel a bit out of my depth.


What is the convention for numbering water molecules?  Is there 
preference for:


- putting waters into a separate chain (W for water or S for solvent)?
- splitting waters according to the peptide chains in the structure?
- appending all waters to chain A?


Thanks.


Andreas




On 30/10/2013 11:57, MARTYN SYMMONS wrote:

At deposition the PDB runs a script that renumbers authors'  waters
according to a scheme based on the residue they are nearest from N to C
terminus along each chain. This renumbering started  when waters were
assigned to macromolecular chains rather than getting a chain id of
their own.  I have failed to find the rationale explained in any PDB
documents - but it could be motivated by this sort of consideration when
waters from different chains or entries are to be compared. Having said
that I do not know if there are any cases where this approach has
successfully matched waters. ..

However an associated step which is certainly a help is that, in the
case of multiple chains, the crystal symmetry is applied to replace
waters with their symmetry equivalent position if it is closer to a
different chain.

I believe a freely available program implementing a similar approach is
WATERTIDY in CCP4 which might be a good place to start.  It gives a
pretty complete output, detailing residues actually H-bonded to the
waters, and you could parse that for further analysis and comparisons.

Best wishes.
   Martyn


--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

[Andreas Förster]

Hi David,

I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then 
defined


MOSFLM_EXEC as /path/to/ccp4-6.3.0/bin/ipmosflm.

CCP4 6.3 needs to be installed for this to work.


Andreas



On 23/10/2013 5:39, David Schuller wrote:

iMosflm developers:

I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and ipmosflm
7.0.9.
This is on Scientific Linux 6.x, 64 bit distribution.

When I run iMosflm either from the command shell or from the ccp4i
interface, I get an error just like this:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html

iMosflm claims it cannot run without mosflm 7.0.9, followed by output
indicating that mosflm 7.0.9 runs. (See attached screen capture of error
message)
Note the linked description is for the previous versions of imosflm amd
mosflm, so this error seems to be a repeat.

I downloaded the iMosflm and ipmosflm executables from the iMosflm web
site, put ipmosflm in my executable directory, and this seems to fix the
problem.

You should get the CCP4 folks to investigate this and propagate a fix.

Cheers,



--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] weekend puzzle

[Andreas Förster]

Thanks to all who engaged with my little puzzle.  The weekend is over 
and I'm not exactly closer to fitting the right pieces into the density. 
 Benzamidine was a good suggestion for the first bit of density. 
However, I didn't use that inhibitor during purification.  The second 
set of blobs doesn't sit on a twofold.  It might just remain undefined.


Thanks anyway for all replies.



Andreas




On 13/09/13 17:50, Andreas Förster wrote:

Dear all,

a structure I'm refining is enjoying a free R factor of 18 but still
suffers from mystery density that nothing in the crystallization
condition could explain.  I can't explain it either.  Maybe you like
to venture some guesses?

The missing ligand is derivatized benzoic acid, nitrobenzene or
benzamide.  I didn't find anything obvious in the PDB.  Any suggestions?
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png

The second ligand is a longer shot, two blobs connected by a
substantial bridge.  The two views are slightly rotated, and a bit of
peptide is shown to give an idea of the size.
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png

Happy guessing!




--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

[ccp4bb] weekend puzzle

[Andreas Förster]

Dear all,

a structure I'm refining is enjoying a free R factor of 18 but still 
suffers from mystery density that nothing in the crystallization 
condition could explain.  I can't explain it either.  Maybe you like to 
venture some guesses?


The missing ligand is derivatized benzoic acid, nitrobenzene or 
benzamide.  I didn't find anything obvious in the PDB.  Any suggestions?

http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png

The second ligand is a longer shot, two blobs connected by a substantial 
bridge.  The two views are slightly rotated, and a bit of peptide is 
shown to give an idea of the size.

http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png
http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png

Happy guessing!


Andreas




--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] reversed stereo issue in coot and pymol

[Andreas Förster]

Same here.  I noticed this is very much dependent on which version of 
the graphics driver you use.  The very latest one (319.17) inverts the 
stereo (which can sometimes be fixed by repeatedly switching between 
mono and stereo).  An older one (310.32) works fine (with a Quadro 600).



Andreas


On 19/06/2013 6:44, jlliu liu wrote:

I am sure if others have the similiar experience as me, sometimes when I
launch pymol and coot, I got the reversed stereo view which is pretty
annoying.  I am using the ASUS VG278H LCD monitor... Thanks in advance
for your advice.


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Why the name aimless

[Andreas Förster]

Occasionally given to losing extremities.

is that a good thing?


Andreas


On 02/05/2013 11:10, Phil Evans wrote:

Reference:
Gibbons, S. (1932) Cold Comfort Farm, Longmans, London

On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it 
wrote:


Hi everyone,
just a curiosity, why the name aimless for the recent data reduction and 
analysis program in CCP4? You know, my students are curious ...
Thank you,
Roberto.

Re: [ccp4bb] COOT running slow after upgrading to CENTOS 6.4 from 6.3

[Andreas Förster]

Hi Zhijie,

our system administrator has warned me sternly against touching RHEL 
6.4.  The same might hold true for CentOS.


I would be interested to hear from anyone running 6.4 successfully.


Andreas



On 20/03/2013 2:42, Zhijie Li wrote:

Hello,
We have a curious situation here: after upgrading CentOS 6.3 to 6.4,
COOT runs slowly every time after the go to atom command is executed
- every rotation of the molecules takes nearly 1 second to finish. But
if the go to atom command is never sent then the speed is normal. A
COOT running in a virtual machine windows XP on the same computer
behaves OK though. It doesn't seem to be a conflict with the CentOS 6.4
either, because COOT on another computer with newly installed CentOS 6.4
runs perfectly fine. So I guess it might has to do with some libraries
that COOT might use. The computer with trouble have python upgraded to
2.7 from the python source code when it was running CentOS 6.3, could
this be a problem?
Zhijie


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] correction to: Post Doctoral Position at Imperial College London in Structural Biology

[Andreas Förster]

Dear all,

the recent advertisement for a postdoc position in the Freemont/Zhang 
labs at Imperial had a small error in the job code needed to find it 
online.  The correct code is


NS 2013 047 IL

Use it at http://www3.imperial.ac.uk/employment (Job search) to apply 
for the position.  Closing date is 25 Mar midnight GMT.


The entire advertisement is repeated below.  Sorry about the confusion.


Andreas




Post Doctoral Position at Imperial College London in Structural Biology


Imperial College London

Department of Life Sciences

Faculty of Natural Sciences

Research Associate

Salary: £32,100 - £35,620 per annum

We wish to recruit a Research Associate for up to 24 months in the first 
instance with possible extension to up to five years to work in the 
research group of Professor Paul Freemont and Professor Xiaodong Zhang 
(http://www.msf.bio.ic.ac.uk/index.php)  in the Centre for Structural 
Biology, Department of Life Sciences at the South Kensington Campus of 
Imperial College London.


Our research group comprise research fellows, research associates and 
PhD students from a diverse range of background including molecular 
biology, biochemistry, X-ray crystallography, electron microscopy, 
physics and engineering. We employ a multi-disciplinary approach to 
study the structures and mechanisms of large macromolecular complexes.


Funded by a CRUK programme grant to Professor Paul Freemont and 
Professor Xiaodong Zhang, you will join a multi-disciplinary group to 
investigate the structure and mechanism of the AAA ATPase p97.  p97 is a 
versatile participant of the ubiquitin proteasome system, interacting 
with a larger network of adaptor proteins to mediate a variety of 
cellular processes including ER associated degradation, autophagy and 
DNA damage repair.


Successful candidates must hold a PhD in a structural biology or 
biochemistry discipline or an equivalent level of research, industrial 
or commercial experience and have demonstrated capacity for innovative 
high quality structural biological research.  Previous research 
experience in a structural biological laboratory environment covering 
X-ray crystallography or electron microscopy single particle analysis is 
essential.  The successful candidate must also have an advanced 
knowledge of protein biochemistry and structural biology.  Experience in 
supervision and training of junior research staff and students and in 
writing scientific research papers would be advantageous.


The successful candidate must be able to work effectively within a team, 
have the ability to develop and apply new concepts, and have a creative 
approach to problem-solving.  They will also be expected to demonstrate 
excellent verbal and written communication skills, and be able to write 
clearly and succinctly for publication.


For informal enquiries please contact Professor Paul Freemont
(p.freem...@imperial.ac.uk) or Professor Xiaodong Zhang
(xiaodong.zh...@imperial.ac.uk)

Our preferred method of application is online via our website
http://www3.imperial.ac.uk/employment (please select “Job Search” then 
enter the job title or vacancy reference number – NS 2013 047 IL - 
including spaces into “Keywords”).  Please complete and upload an 
application form as directed.




***
Professor Paul Freemont

Co-director of Macromolecular Structure and Function Group
Department of Life Sciences
Sir Ernst Chain Building - Wolfson Laboratories
South Kensington Campus
London SW7 2AZ, UK
www.msf.bio.ic.ac.uk

Tel: 02075945327
Email: p.freem...@imperial.ac.uk

Re: [ccp4bb] ccp4 update

[Andreas Förster]

Ah, I see.  This was part of update 10.  Thank you.


Andreas



On 16/01/2013 2:51, Qixu Cai wrote:

Dear Andreas Förster,

You can use ccp4um (ccp4 update manage) to update CCP4 from command line.

Best wishes,

Q. Cai



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] ccp4 update

[Andreas Förster]

Dear CCP4 maintainers,

I've come to appreciate the CCP4 update functionality, which, in our 
multiuser network (RHEL 6.2), I used to invoke by calling $CCP4/bin/update.


Update 012 removed that script with no immediately obvious replacement. 
 Was that on purpose?  Is there a way of updating CCP4 from the command 
line without calling CCP4i?


Thanks


Andreas


(from update.log:

[Thu Jan 3 2013 11:00:21]
Ready to make changes

 --- applying update 6.3.0-012
 --- update header read
 --- creating restore package, please wait ...
 --- done
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/bin/update' removed
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/update' removed
   ... file '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec/_update' removed
   ... directory '/csb/soft/Linux64/share/ccp4-6.3.0/lib_exec' removed


some more blah blah)


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] vitrification vs freezing

[Andreas Förster]

Hi Tim,

in the UK, you'd probably be rather surprised how many nuts your 
fruitcake contains, none of them strawberries (thus the saying as nutty 
as a fruitcake).



Andreas



On 15/11/2012 5:59, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear s,

I have heard this discussion before and reminds me of people claiming
strawberries were nuts - which botanically may be correct, but would
still not make me complain about strawberries in a fruit cake I
ordered at a restaurant.

My Pengiun English Dictionary states (amongst other explanations)
freeze: to make extremely cold, so as long as you think your article
is written in English, you did not say anything wrong, assuming your
readers are intelligent enough to understand what you are trying to
say - and in a crystallographic article, the process of 'freezing'
your crystal is most likely not your main point where you need to be
100% unambiguous.

Cheers,
Tim



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] map sharpening

[Andreas Förster]

Dear all,

a follow-up to yesterday's question about map sharpening.  The problem 
was that the sharpened maps aren't displayed in coot, but this is not 
coot's fault, as can be seen from the output:


regular map:

making conventional map from MTZ filename unsharp.mtz using FWT PHWT
Number of OBSERVED reflections: 34725
INFO:: finding ASU unique map points with sampling rate 1.5
INFO grid sampling...Nuvw = ( 128, 128, 384)
INFO:: 0.086 seconds to read MTZ file
INFO:: 0.002 seconds to initialize map
INFO:: 0.305 seconds for FFT
INFO:: 0.013 seconds for statistics
  Map mean:  -1.4987e-06
  Map sigma: ... 0.0957995
  Map maximum: . 0.629714
  Map minimum: . -0.606727
INFO:: 0.026 seconds for contour map
INFO:: 0.432 seconds in total

sharpened map:
(as above, except:)

  Map mean:  0
  Map sigma: ... 0
  Map maximum: . 0
  Map minimum: . 0


These mtz files are generated identically, zero rounds of refinement in 
Refmac 5.7 (from ccp4 6.3.0) with sharpening disabled or enabled (B 
value = 5, 20, 60, 200).  There are no features in the sharpened maps.  Why?


When I don't specify a B value for map sharpening, it is calculated to 
61 and the resulting map displays just fine.



Andreas




On 25/09/2012 11:52, Robert Nicholls wrote:

Hi Andreas,

In your case, it sounds like a reasonable strategy would be to use external 
restraints for a few rounds of refinement (as you have done), but then release 
them and instead use jelly-body restraints. This two-stage process will help to 
initially hold your model in a sensible conformation using external restraints, 
but then gently release the structure in order to reduce further bias in later 
rounds. The immediate subsequent use of jelly-body restraints after external 
restraints will ensure that the model won't deviate too far from that sensible 
conformation, unless the data suggests otherwise.

Of course, if certain regions lose their sensible conformations in subsequent 
rounds of refinement, you can continue to use external restraints just in these 
regions.


I substantially rebuilt a surface loop that I don't want to restrain by the 
model.



In this case, I would recommend re-generating the external restraints, this 
time telling ProSMART not to generate restraints for these particular 
residues/regions. This can be done using the -restrain and -restrain_rm 
keywords, as described in the documentation (let me know off-board if you want 
help with this).

If you enable map sharpening then the single output MTZ file should be the 
sharpened map… I'm not sure why you are finding that the map is not displayed… 
do you see any difference between enabling/disabling map sharpening?

Cheers,
Rob




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] low-resolution refinement

[Andreas Förster]

Dear all,

I'm making first steps in the desolate world of low-resolution 
refinement.  With dodgy 3.8A data, the magic of Phaser was able to solve 
the structure of a complex by MR with its components as MR models. 
Jelly-body refinement does wonders for R free.  There are three issues 
that I would like to get some advice on:


1)  Using external restraints calculated with ProSMART improved the 
structure further, but I'm worried that using restraints derived from 
the structures used for MR gets me into a sinkhole of model bias. 
Should it be either molecular replacement or homology restraints?


2)  Do I recalculate restraints at each round of refinement?  In 
particular, I substantially rebuilt a surface loop that I don't want to 
restrain by the model.


3)  Activating map sharpening results in mtz files that look just normal 
and open in coot after the typical map calculation break, but no maps 
are displayed.  This is independent of the sharpening factor I choose 
(between 5 and 60).


Thanks for your help.


Andreas


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] imosflm background definition

[Andreas Förster]

Hi all,

I'm integrating data from a crystal with a fairly long axis.  In iMosflm 
(1.0.7), the background definition is so generous that plenty of pixels 
from adjacent peaks are included (see attached).  Can someone tell me 
how I redefine the background to be tighter around the spots?


Thanks.


Andreas


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
attachment: backgroundSpots.png

Re: [ccp4bb] Various OSes and Crystallography

[Andreas Förster]

Mac OSX because of Time Machine, Illustrator and crystallographic 
software in one happy box.  XP on a Virtual Box for emergencies (SAXS, 
AUC and ITC programs).


Though with Microsoft and Apple both pushing towards gestures, fingertip 
interaction and tablets, Linux will be the only option for laptops in 
two/three years' time.


Mind that if you buy a MacBook, there's only one (hefty 15) model 
without a mirror-coated screen.



Andreas



On 09/08/2012 3:58, Nat Echols wrote:

On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:

one. Are there any really reasonable arguments for preferring Mac over
windows (or linux) with regard to crystallography? What can Mac/Linux do
that windows cannot (especially considering that there is Cygwin)? What
wonderful features am I missing?


Mac vs. Linux: mostly a matter of personal preference, but I agree
with Graeme.  Most programs run equally well on either - with Coot a
partial exception, apparently due to problems with the X11
implementation (but once you get used to these, it's not a big deal).

Windows, on the other hand, simply doesn't support the full range of
modern crystallography software.  And in my experience, it has
crippling flaws that mean some programs will always work better on
Mac/Linux.  I wouldn't ever endorse trying to use Windows for serious
scientific computing unless you need to run an application that won't
work on any other OS, and as far as I know there isn't a single
(macromolecular) crystallography program that falls into this
category.

-Nat

[ccp4bb] NCS on multiple conformations

[Andreas Förster]

Dear all,

ok, never mind.  I defined either peptide conformation as part of the 
protein it binds to and applied NCS to that.


Should have thought of that before sending out the question.


Andreas



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] NCS on multiple conformations

[Andreas Förster]

Dear all,

I have solved the structure of a protein with twofold NCS.  On the axis 
relating the protein molecules sits a peptide ligand in two (mutually 
exclusive, partially occupied) conformations, effectively interacting 
with either protein molecule half of the time.  Sorting out the side 
chain conformations of the ligand proves difficult.


I would like to impose twofold NCS on the two conformations of the 
ligand.  In Refmac, I can relate residue n of chain A to residue n of 
chain B.  Can I also relate residue An of chain C to residue Bn of chain 
C?  Or is there some other clever way of dealing with this situation?


Thanks.


Andreas




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Andreas Förster]

Dear Gerard,

inside Germany it's apparently called German Humour.  There's a 
Wikipedia entry for that as well.  Go figure:


http://en.wikipedia.org/wiki/German_humor


Andreas

(still living on Sunday time)


On 02/04/2012 4:03, Gerard DVD Kleywegt wrote:

Dear Manfred,

Outside Germany, such excursions are called humour. If you are
interested, here is the Wikipedia page for it:
http://en.wikipedia.org/wiki/Humour

--Gerard

PS: It was on a Sunday so all levity was perpetrated in people's own
time. Today we'll all be serious again and frown and tut-tut appropriately.

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Andreas Förster]

That's pretty funny, isn't it?


Andreas



On 02/04/2012 6:52, Jacob Keller wrote:

Sorry to beat a dead horse, but:


  * *Antiwitz* (/anti-joke/): A short, often absurd scene, which has the
recognizable structure of a joke, but is illogical or lacking a
punch-line.

Example: /Two thick feet are crossing the street. Says one thick
foot to the other thick foot: Hello!/

Other examples: Nachts ist es kälter als draußen (At night it's
colder than outside) or Zu Fuß ist es kürzer als über'n Berg
(Walking is faster than over the mountain).

Re: [ccp4bb] live streaming of ccp4 study weekend

[Andreas Förster]

For what it's worth, I get it on Firefox and Safari  using a Mac with OS 
10.6.8.  The sound is fine but the slides don't update automatically.  I 
have to hit reload at every slide.  Keeps me awake.



Andreas



On 05/01/2012 2:38, David Mueller wrote:

I can't get it to work on Firefox, Safari, or Chrome using a Mac with OS
10.6.8.


David Mueller




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Off topic: Kendrew Model

[Andreas Förster]

Is it like this one:

http://www.sciencemuseum.org.uk/images/I053/10321094.aspx

Not sure I would want to put it into the dining room...


Andreas



On 01/11/2011 2:34, Katherine Sippel wrote:

Hi all,

I'm going to interject into the middle of this rousing though protracted
debate to pick your brains. I am in possession of a rather large and
intact brass scale Kendrew model (sans mirrors). Due to facility
restructuring we no longer have room for it. I have approached the local
health science and natural science museums but have gotten nothing but
the run around. This amazing model is in need of a forever home and I'm
stumped as far as alternative ideas. I am seriously considering
suspending a Mars bars in the sugar binding cleft, calling it MBP, and
trying to spin it to the art museum as a modernist piece commenting on
the diets in Western civilization. Either that or putting it in my
dining room if I can get it in the door. Any suggestions would be
appreciated.

Cheers,

Katherine


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Mac OSX 10.7 Lion

[Andreas Förster]

I've bitched enough about all things Mac, but this one's just too good 
to pass on (from the article that Peter linked to):


The fundamental issue here is Lion's assumption that you don't know 
what you're doing, and it's going to ensure you're protected from 
cock-ups that, in your ignorance, you may make.


The first half of that sentence has always been my major gripe with Mac 
OS.  If there just were a Pro version for those that know what they're 
doing, but the iPadification of computing goes exactly the opposite way.



Andreas




On 19/09/2011 9:58, Peter Keller wrote:

On Fri, 2011-09-16 at 06:37 -0700, William G. Scott wrote:


If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts.  
There are all sorts of perverse changes, and (unlike the reversal in scrolling 
direction) not a lot of over-ride options.


I guess this is one of them:

How Apple's Lion won't let you trash documents
The operating system for the nanny state?

http://www.reghardware.com/2011/09/07/apple_mac_os_x_lion_the_nanny_os/

One of the reasons why I'm sticking with Snow Lepoard for now

Regards,
Peter.



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Trying to digest PISA results

[Andreas Förster]

AUC !


Andreas



On 05/09/2011 6:00, Jacob Keller wrote:

mea culpa! How about FRET?

JPK

On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergenjubo...@jhsph.edu  wrote:

Hi Jacob,
you forgot cross-linking to stabilize a weak complex and verify that it
exists.
Jürgen
On Sep 5, 2011, at 11:45 AM, Jacob Keller wrote:

Well, I guess I have always been curious what is the gold standard
here--perhaps SEC, ITC, SPR, pulldowns? What if SEC shows a
polydisperse sample with weak oligomerization, or SPR a very weak
binding constant? Do we then revert to a functional assay? Or what if
the functional assay does not show anything, but the binding constant
is really strong? Or vice versa, the binding is completely
undetectable, but the functional assay shows something?

JPK




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] more Computer encryption matters

[Andreas Förster]

Since we're on the subject...  I've been tempted on and off to encrypt 
my hard drive, but after getting burned once a hundred years ago when 
encrypted data turned into garbled bytes all of a sudden I've been 
hesitant.  I've gone so far as to install TrueCrypt (on a MacBook), but 
I haven't put it into action.  Before I do, the big question:


What software do people on the bb use for encryption?  What can be 
recommended without hesitation?


Thanks.


Andreas


On 18/08/2011 1:19, Eric Bennett wrote:

John,

Since so many people have said it's flawless, I'd like to point out this is not 
always the case.  The particular version of the particular package that we have 
installs some system libraries that caused a program I use on a moderately 
frequent basis to crash every time I tried to open a file on a network drive.  
It took me about 9 months to figure out what the cause was, during which time I 
had to manually copy things to the local drive before I could open them in that 
particular program.  The vendor of the encryption software has a newer version 
but our IT department is using an older version.  There is another workaround 
but it's kind of a hack.

So I'd say problems are very rare, but if you run into strange behavior, don't 
rule out encryption as a possible cause.

-Eric




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] BLT wish

[Andreas Förster]

Dear Phil,

for me (RHEL 6.1, 64-bit, ccp4 6.2), loggraph works with wish but 
requires bltwish.  The command is


exec $CCP4I_TCLTK/wish $0 -- ${1+$@}

but if I set

export CCP4I_TCLTK=/sharedSoftware/ActiveTcl-8.5/bin

I get the same error that you report because ActiveTcl-8.5 doesn't 
contain bltwish, which is required in loggraph.tcl.  When I set


export CCP4I_TCLTK=$CCP4_MASTER/tcltk++/bin

I don't get the error.


Andreas


On 17/08/2011 10:22, Phil Evans wrote:

In previous CCP4 releases CCP4/ccp4i/bin/loggraph used bltwish

exec $CCP4I_TCLTK/bltwish $0 -- ${1+$@}

In 6.2.0 this has mutated to

exec $CCP4I_TCLTK/wish $0 -- ${1+$@}

which doesn't work on our systems, see error below

I've fixed it by changing back to the previous exec bltwish, but does this new 
version work for other people? Should it work for me, and with what version of 
TCL?

(I look forward to replacing loggraph!)

Phil

Error in startup script: can't find package BLT
while executing
package require BLT
(file /public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl line 
47)
invoked from within
source [file join $env(CCP4I_TOP) bin loggraph.tcl]
(file /public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph line 5)



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] protein segments from pdb

[Andreas Förster]

Dear all,

how do you extract segments from a pdb file, so that from an input pdb 
file you get output like this:


10-103, 120-174, 200-240

or, better yet:

A: 10-103, 120-174, 200-240
B: 10-104, 120-174, 199-241

if the N terminus is missing and there are two gaps in the structure.

I tend to open the pdb file with PyMOL and click on the ends, but a 
script/command would be much quicker.


Thanks.


Andreas


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] protein segments from pdb

[Andreas Förster]

I see that my questions was highly ambiguous/unclear.  Martyn saw 
through it anyway.  pdbcur does what I want.



Andreas



On 10/08/2011 5:32, Martyn Winn wrote:


If you mean what I think you mean, then use the SUMMarise option of
pdbcur. That gives output like:

  Chain A has 505 residues
  in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730
  0 residues have alternative conformations
  Composition: ALA 23 ARG 23 ASN 36 ASP 24
   CYS 34 CYH 0 GLN 21 GLU 30
   GLY 38 HIS 11 ILE 29 LEU 44
   LYS 32 MET 8 PHE 17 PRO 21
   SER 36 THR 28 TRP 5 TYR 13
   VAL 26 HEM 0 WAT 0 SUL 0
   END 0 DUM 0 Other 6

HTH
Martyn

On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote:

Dear all,

how do you extract segments from a pdb file, so that from an input pdb
file you get output like this:

10-103, 120-174, 200-240

or, better yet:

A: 10-103, 120-174, 200-240
B: 10-104, 120-174, 199-241

if the N terminus is missing and there are two gaps in the structure.

I tend to open the pdb file with PyMOL and click on the ends, but a
script/command would be much quicker.

Thanks.


Andreas






--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Installation of ccp4 on 64bit fedora core 13

[Andreas Förster]

Somehow I missed Mark Del Campo's 
path-towards-a-working-tcltk/blt/wish-email.  But does it have to be 
that complicated?  On RHEL 6.1, 64-bit, CCP4 6.2 I do:


1. edit 1 line in ccp4.setup-bash (export 
CCP4I_TCLTK=$CCP4_MASTER/tcltk++/bin)


2. install Activestate's tcltk 8.5.9.1 from 
https://www.activestate.com/activetcl/downloads/


3. go to /path/to/ActiveTcl-8.5/bin and install one additional package: 
./teacup install --with-recommends Iwidgets


4. add 1 line to .bashrc (export 
MOSFLM_WISH=/path/to/ActiveTcl-8.5/bin/wish)


5. open a new terminal: imosflm and ccp4i work (as far as I have tested)


Andreas



On 09/08/2011 2:46, Edward A. Berry wrote:

Edward A. Berry wrote:



If you have trouble with TCL/TK read below-quoted message.
Mosflm site has more suggestions.
better yet:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/CCP4_on_Fedora_12



which says: Now Tcl/Tk tools are bundled with Fedora 12, and they work
well for CCP4i/imosflm. Install tcl, tk, blt, itcl, itk, tkimg,
tcl-tktreectrl, iwidgets, and tdom packages and set $CCP4I_TCLTK to
/usr/bin.

BUT the blt bundled with Fedora 14 does not include bltwish.
better use patched blt2.4 as described by del Campo below.

Apparently same is true of ubuntu and the developers do not consider
this a bug, according to the bug report filed by wgscott:
https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148
not a bug. It doesn't make sense to provide a separate shell for each Tcl
Extension. Also, the current blt version is 8.0.

just use wish for your scripts:

#!/usr/bin/wish
package require BLT
[...] 
I tend to agree with Bill, but if it would be this easy to remove a
dependency
that makes trouble for newbies like me, maybe CCP4 should do it.


Mark Del Campo wrote:


Okay, I got the problem resolved in the following way (thanks go to
Clint
Leysath):

1. removed the tcltk++ directory that came with my ccp4 download
2. installed Activestate's tcltk 8.4.19.2 from
https://www.activestate.com/activetcl/downloads/
3. downloaded blt2.4z.tar.gz and the blt2.4z-patch-2 from
http://sourceforge.net/projects/blt/files/
4. unpacked blt2.4z.tar.gz and moved the patch file into the blt2.4z
directory
5. patched the blt installation (patch -p1 -i blt2.4z-patch-2)
6. then reordered statements in blt2.4z/src/bltTree.c [this is
detailed at
http://www.ccp4.ac.uk/ccp4i/install_tcltkblt.html under the heading
Compilation failure in bltTree on 64-bit machines]
7. configured the blt install (./configure
--with-tcl=/path/to/ActiveTcl-8.4)
8. installed blt (make)
9. for some reason bltwish did not end up in
/path/to/ActiveTcl-8.4/bin even
though the configure script said that is where it would be put, so I
moved
it to /path/to/ActiveTcl-8.4/bin
10. edited 1 line in ccp4.setup-bash (setenv CCP4I_TCLTK
/path/to/ActiveTcl-8.4/bin/)
11. opened a new terminal window ccp4i works







--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] ARP/wARP install on 6.2.0 RHEL 6?

[Andreas Förster]

Dear all,

I had no problem with Arp/wARP, but I didn't reinstall.  Assume ccp4 
sits in /installation/directory/ccp4 and arp in 
/installation/directory/arp_warp_7.1.  The new ccp4 doesn't recognize 
the existing arp because the task interface is not installed.  I run 
./install.sh in /installation/directory/arp_warp_7.1, and five seconds 
later, all is good.


I hope this is of help for someone.


Andreas




On 28/07/2011 4:35, Ethan Merritt wrote:

On Wednesday, 27 July 2011, you wrote:

Hi Jonathan,
seems to be a UW centered day today on the BB (Eric, Jan, you, me).
Have the permissions changed ? I assume you are installing as root ?
Wouldn't be surprised if Ethan replies soon :-)


Sure.

I hit the same problem trying to install Arp/wARP on Mandriva.
The specific error message you quote comes because the install
script fails to create the temp directory before trying to unpack
into it.  You can fix that by creating the directory by hand first.
Unfortunately, that doesn't help very much.  The next thing that
happens is that the ccp4i installer complains that the tarball
is not recognized as a ccp4i install tarball.  I gave up at that
point.

Ethan





Jürgen

..
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/

On Jul 27, 2011, at 20:31, Jonathan Kayjp...@u.washington.edu  wrote:


Hi all,

I have a RHEL 6 x86_64 machine I recently installed CCP4-6.2.0 onto; the install 
went through fine, but when I went to install the ARP/wARP GUI (via System 
Administration -  Install/uninstall task), I received the following error in 
the shell window I started ccp4i from:

UnpackTaskArchive: uncompress failed to create 
/tmp/user/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar
ExamineTaskArchive: failed to unpack temporary copy of 
/usr/local/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz

/tmp is not at all full and has plenty of inodes left.
(running the install.sh from the arp_warp_7.1 directory doesn't install it 
either)

I have searched around for some solutions, but haven't found anything really 
relevant.
The odd thing I have another x86_64 machine running RHEL 5 that I can do the 
exact same install method and it works (and using the install.sh from 
arp_warp_7.1/ works too), so I wonder if something changed with RHEL6 that 
might be causing problems?

Anyone have any suggestions?

Thanks!
Jonathan






--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Fab:antigen complex crystallization!!!

[Andreas Förster]

Hi Ivan,

you might also want to find out what buffers your particular system likes.

Jancarik et al. Optimum solubility (OS) screening: an efficient method 
to optimize buffer conditions for homogeneity and crystallization of 
proteins. Acta Crystallogr D Biol Crystallogr (2004) vol. 60 (Pt 9) pp. 
1670-3



Andreas



On 28/07/2011 4:40, xaravich ivan wrote:

Hi everyone,
I have been trying to crystallize Fab:antigen complex( 50kda:90kDa)
complex and initially got needle clusters which after microseeding gave
me single crystals but they are very small and I could not repeat the
results. I have been using HEPES buffer at pH 6.8 to do the final SEC
purification step of the complex before setting trays.
I was wondering whether there are some other buffers (that one could
suggest eg tris-hcl etc) which have given decent positive results when
crystallizing Fab complexes.Though I have gone through individual papers
(case by case) to get some idea, It would be great if anyone could
direct me to a comprehensive literature towards studying the
crystatllization conditions of Fab complexes.
  Equally, people who have considerable experience could suggest a list
of must do steps for such problems which have routinely been practiced
in their lab


Also what is a good storage condition for the excess complex that you
want to use later?

I would really appreciate any suggestion,help, direction.

Thanks
ivan


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Lion kills moleman (and all other USF programs on the Mac)

[Andreas Förster]

As Lion seems to be, above all, an wonky iPad emulator, you're probably 
better off keeping the Snow Leopard alive until Apple obsolesces it in a 
few months.



Andreas



On 22/07/2011 11:59, Gerard DVD Kleywegt wrote:

Hi all,

Just a heads-up - if you upgrade to OSX Lion, your trusty old USF
executables will no longer work.

Help is on its way - in the near future the indefatigable and intrepid
Lion-taming heroes of the USF will release a distribution kit that
includes source code. However, for now you may want to postpone
upgrading to Lion if your will to live would be compromised by not being
able to run Moleman, Mapman, Lsqman, etc.

--Mr Anchovy (Proud owner of a lion taming hat. A hat with 'lion tamer'
written on it. And it lights up saying 'lion tamer' in big red neon
letters, so you can tame them after dark when they're less stroppy.)

PS: http://www.youtube.com/watch?v=XMOmB1q8W4Y

**
Gerard J. Kleywegt

http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
**
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
**



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0

[Andreas Förster]

Dear Oliver and others,

an alternative way of installing system-wide third party software is 
with a non-root account that is in the same group as all the users.  Use 
that account to install software centrally and initialize in each user's 
.bashrc.  (Root is used only for administrative tasks on the local 
machines and installation of RPMs.)  Users can use all the software but 
have no permission to tinker with it and potentially screw it up.


Still, with this setup, there's a problem with ccp4 6.2.
ccp4-6.2.0/src/phaser/bin/machine_type needs to be made executable for 
the group.



Andreas



On 19/07/2011 11:25, Weiergräber, Oliver H. wrote:

Hello,

version 6.2.0 of ccp4 has strange permissions set to several 
setup/configuration scripts which are read while sourcing ccp4.setup.

For a long time, ccp4 packages have been distributed with some arbitrary file 
and directory ownerships which users are obviously supposed to edit to meet 
their needs. On unix/linux workstations, we usually install under /usr/local 
and change all ownerships to root.root (default practice for third-party 
software).
Up to now, this has not caused any problems.
In version 6.2.0, however, ccp4.setup has permissions rwx r-- --- which makes 
it unreadable (and un-sourcable) for ordinary users! Strangely, 
ccp4-others.setup has the usual permissions rwx r-x r-x (although rw- r-- r-- 
should be sufficient for sourcing).
After rectifying the permissions of ccp4.setup, additional errors appear, 
concerning permissions of several scripts in the xia2 and phaser trees:
ccp4-6.2.0/share/xia2/setup.csh
ccp4-6.2.0/share/xia2/xia2core/setup.csh
ccp4-6.2.0/share/xia2/xia2/setup.csh
ccp4-6.2.0/src/phaser/bin/machine_type
ccp4-6.2.0/src/phaser/conf/version.csh
All these files have the same problematic permissions as ccp4.setup. After 
fixing them, ccp4.setup can be sourced without errors.
The bad thing is that there may be many more issues of this kind, which will 
only surface when trying to run a specific ccp4 program...

Maybe the developers or packagers could comment on this issue. It looks like 
this ccp4 version is supposed to be installed in a user's home directory, so 
that he/she can take ownership of all the files.
While in general there is nothing wrong with this type of installation, it 
should _NOT_ be considered the default on unix-type (i.e. multi-user) operating 
systems.

Best regards,
Oliver



   PD Dr. Oliver H. Weiergräber
   Institute of Complex Systems
   ICS-6: Structural Biochemistry
   Tel.: +49 2461 61-2028
   Fax: +49 2461 61-1448




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt





--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] mutation and minimization - SUMMARY

[Andreas Förster]

First off, thanks to all those who sent me their suggestions, a great 
variety indeed.  Here's the summary:


- turbo-frodo can do local rotamer optimization based on environment.
- SCRWL and WHAT-IF are servers for homology modeling
- Swiss PDB viewer/DeepView can also do homology modeling, but not 
natively on Linux

- mutate and regularize geometry in coot
- phenix.pdbtools from the command line (might be able to minimize only 
part of the model)




Andreas



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] mutation and minimization

[Andreas Förster]

Hey all,

I would like to introduce point mutations in a structure and quickly 
(and dirtily) minimize the new residue.  (Best rotamer dependent on 
local environment, or the like.)  What are simple approaches that don't 
involve VMD/NAMD or some such overkill.


Thanks.


Andreas



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] image file extensions

[Andreas Förster]

Dear all,

I'm trying to create some space on our server and want to compress all 
x-ray data files.  I'm wondering what extensions I should search for. 
mccd and img come to mind easily.  What other extensions are commonly used?


Thanks.


Andreas



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] image file extensions

[Andreas Förster]

Harry Powell had the most comprehensive answer, giving me the extensions 
that are used in mosflm:


.img .mar* (i.e. .mar1600, .mar2300, etc) .mccd .osc .SFRM .sfrm .image 
.ipf .cbf


In addition, finding files larger than a certain cutoff might do the 
trick too - especially if the objective is economizing disk space.


Thanks.


Andreas


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] If it is a new structure?

[Andreas Förster]

You're welcome!

Next time, irrespective of whether your structure is a new one or not, 
please upload your images to picasa, flickr, your university's file 
sharing server or some such thing and include the link in your email. 
Don't flood several thousand inboxes with megabytes of pixels.  And 
compress bitmaps, for crying out loud.  How hard can it be?


Thanks.


Andreas





On 20/12/2010 10:49, Liu Zhao  wrote:

The structure of my protein is as shown as the purple one. Another one
,as shown as green,is homologous .But the structure of my protein can't
be obtained by using molecular replacement. And both structures have
much different, especially in B chain. If my structure is a new one?
thank you for help.


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] Protein sequencing service?

[Andreas Förster]

Hey Rex,

Jeff Keen at Leeds has sequenced some of our proteins with good results.

http://www.fbs.leeds.ac.uk/proteomics


Andreas



On 24/09/2010 4:46, Rex Palmer wrote:

Can anyone please recommend a UK protein sequencing service. Our protein
is dimeric with reported molecuar weight of about 85kDa.Our funds are
somewhat limited.
Thanks in advance.
Rex Palmer
Birkbeck College, London
RexPalmer2010.homestead.com


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] database-assisted data archive

[Andreas Förster]

Dear all,

going through some previous lab member's data and trying to make sense 
of it, I was wondering what kind of solutions exist to simply the 
archiving and retrieval process.


In particular, what I have in mind is a web interface that allows a user 
who has just returned from the synchrotron or the in-house detector to 
fill in a few boxes (user, name of protein, mutant, light source, 
quality of data, number of frames, status of project, etc) and then 
upload his data from the USB stick, portable hard drive or remote storage.


The database application would put the data in a safe place (some file 
server that's periodically backed up) and let users browse through all 
the collected data of the lab with minimal effort later.


I doesn't seem too hard to implement this, which is why I'm asking if 
anyone has done so already.


Thanks.


Andreas

--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] summary - SAXS EM comparison

[Andreas Förster]

Here's a preliminary summary of the suggestions I got from the ccp4 
community regarding the problem stated below (calculate theoretical SAXS 
data from EM reconstruction):


The program em2dam, currently developed at EMBL-Hamburg (where the 
magicians of SAXS live), converts a Spider map into a pdb file, which 
can then be used as input for another EMBL-Hamburg program, crysol. 
This approach does what I want.  Nice.  Em2dam hasn't been released yet, 
but is available for testing upon request (ashku...@embl-hamburg.de).

http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html


HYDRO can also calculate scattering form factors from dummy-bead models, 
but I didn't try that out.  From the group that wrote HYDRO comes 
hydromic, a program that calculates, from an EM map, a distance 
distribution and a P vs. h list whose usefulness didn't immediately 
reveal itself to me.  Those more familiar with SAXS might find that this 
program is just what they want.

http://leonardo.fcu.um.es/macromol/programs/programs.htm


The program vol2pdb, which is part of the situs package, converts spider 
format em maps to dummy-bead models.  I couldn't suppress the feeling 
that the pdbs obtained with em2dam were closer to the truth.  Situs also 
has a SAXS tutorial that might be useful.

http://situs.biomachina.org/tutorial_saxs.html

The EMAN program proc3d with the calcsf option can calculate scattering 
curves.  The output file contains the F**2/s distribution for the map 
with max=0.0.  Some scaling might be required.  I didn't try this.

http://blake.bcm.tmc.edu/eman/

Chimera might have a SAXS function.  I didn't check.
http://www.cgl.ucsf.edu/chimera/

Thanks to all who contributed ideas and suggested approaches, and 
special thanks to Alex for sharing em2dam.



Andreas



On 23/07/2010 11:54, Andreas Förster wrote:

Dear all,

the other day I obtained SAXS data from which a low-resolution
structural model was calculated. The model is simpler/less complex than
one of the same protein that we obtained with cryo-EM.

Is there a way to estimate theoretical SAXS data from a cryo-EM
reconstruction to compare with the obtained raw data? Is there a program
that does for a reconstruction what CRYSOL does for pdbs? I understand
that there would be a huge amount of handwaving involved, but it might
help us reconcile our models.

Thanks.


Andreas




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] SAXS EM comparison

[Andreas Förster]

Thanks to all (Christoph Best, Kushol Gupta, Alexander Shkumatov, David 
J. Scott, Ruben Martinez, and Stephen Prince) who replied to my request 
concerning the calculation of theoretical SAXS scattering data from EM 
reconstructions.  I'm in the processing of testing the suggested 
solutions and will report back to the list in due course.



Andreas



On Fri, 23 Jul 2010 11:54:43 +0100, Andreas Försterdocandr...@gmail.com  said:


   Dear all, the other day I obtained SAXS data from which a
   low-resolution structural model was calculated.  The model is
   simpler/less complex than one of the same protein that we obtained
   with cryo-EM.

   Is there a way to estimate theoretical SAXS data from a cryo-EM
   reconstruction to compare with the obtained raw data?  Is there a
   program that does for a reconstruction what CRYSOL does for pdbs?
   I understand that there would be a huge amount of handwaving
   involved, but it might help us reconcile our models.


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] N-terminal sequencing

[Andreas Förster]

Beyond these (posted three weeks ago), I don't know any.
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15004.html

I use Jeff Keen's service, which very reliable and adaptable.


Andreas



On 16/04/2010 9:23, F.Xavier Gomis-Rüth wrote:

Dear CCP4ers,
does anybody know of a company that accurately but affordably makes
N-terminal sequencing ?
Thanks a lot in advance to everybody.
Best regards,
Xavier
--


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] slow graphic in mac 10.6

[Andreas Förster]

Hey Rui,

for what it's worth, I had a very similar problem.  I upgraded a MacBook 
Pro to OSX SP6 and got extra-slow graphics and a wildly flickering PyMOL 
window - only on the laptop screen, though.  On the external screen, 
PyMOL looked ok.  Ray-tracing was painfully slow in either window.


When I cloned the screen instead of extending it, the flicker 
disappeared and didn't return when I went back to the original setup of 
two contiguous screens.  All is good now.


While this is by no means an answer to your question or useful advice, 
it means at the very least that you might be able to overcome your 
problems by fiddling around.


Good luck.


Andreas



On 13/02/2010 5:10, rui wrote:

HI,Dear All,

sorry for this non-crystallgraphic question, but I think people here may
know how to fix this problem. Several days ago, I posted a question
about slow coot in my mac and people suggested me change some settings
in coot which does help. However, I still feel something is wrong. I
noticed the slow speed when I installed x11,( I switched from ppc to
macpro and need to reinstall x11 and coot etc ). Since then, I noticed
that when I open a terminal , it's very slow and if I type glxgears, it
only shows about 1400 FPS. If I open pymol, I can actually see the
images are flashing. Does anyone know why? Thanks a bunch.

Rui


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] slow graphic in mac 10.6

[Andreas Förster]

Serge,

this might indeed be the problem for some, but my MacBook is of an older 
vintage and only has one GPU.



Andreas



On 15/02/2010 10:10, Serge Cohen wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

For what it is worth (I'm fairly confident that indeed this is not the cause of 
the problem you are seeing, but better checking than missing the point):

The current MacBook Pro also have two GPU, one integrated in the chipset and a 
more powerful dedicated one.

By default only the chipset integrated one is on (to save on power consumption), so if you're doing graphics it is worth 
going in system preference -  energy saver and at the top preference window check that 
Graphics is set to Higher performance...
A bummer is that it is currently necessary to restart one's session to go from 
one setting to the other, and I'm not 100% sure that this setting is preserved 
upon reboot of the machine...

Cheers,

Serge.


Le 15 févr. 2010 à 10:44, Andreas Förster a écrit :


Hey Rui,

for what it's worth, I had a very similar problem.  I upgraded a MacBook
Pro to OSX SP6 and got extra-slow graphics and a wildly flickering PyMOL
window - only on the laptop screen, though.  On the external screen,
PyMOL looked ok.  Ray-tracing was painfully slow in either window.

When I cloned the screen instead of extending it, the flicker
disappeared and didn't return when I went back to the original setup of
two contiguous screens.  All is good now.

While this is by no means an answer to your question or useful advice,
it means at the very least that you might be able to overcome your
problems by fiddling around.

Good luck.

Andreas

On 13/02/2010 5:10, rui wrote:

HI,Dear All,

sorry for this non-crystallgraphic question, but I think people here may
know how to fix this problem. Several days ago, I posted a question
about slow coot in my mac and people suggested me change some settings
in coot which does help. However, I still feel something is wrong. I
noticed the slow speed when I installed x11,( I switched from ppc to
macpro and need to reinstall x11 and coot etc ). Since then, I noticed
that when I open a terminal , it's very slow and if I type glxgears, it
only shows about 1400 FPS. If I open pymol, I can actually see the
images are flashing. Does anyone know why? Thanks a bunch.

Rui




-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (Darwin)

iEYEARECAAYFAkt5HZQACgkQlz6UVQtc2uz5KgCgoPbmgHSgzgl3wRBxh4IEIj31
a8QAnRxkW/Ks6KmXwCJ/Gpl1tYTy3fjb
=oLb0
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--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] DLS

[Andreas Förster]

The Malvern is indeed very nice.  The only issue I have with ours is 
that it doesn't do plates.  This makes buffer screening a very laborious 
busy that is best left to graduate students.



Andreas



On 04/02/2010 2:22, Savvas Savvides wrote:

Hi Wojtek
I can easily second Dave's comment!
Best
Savvas


Savvas Savvides
Unit for Structural Biology @ L-ProBE
Ghent University
K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
Ph. +32  (0)472 928 519
http://www.LProBE.ugent.be/xray.html


On 04/02/10 14:54, David Briggsdrdavidcbri...@gmail.com  wrote:


Hiya.

My two penneth on the Malvern Zetasizer.

Simple, idiot-proof operation. Software is easy and intuative. Reports
are customisable to give you what information you want.
Problems easy to trouble shoot IMHO.

Does DLS, SLS, melting point determination.

After-care support is good from Malvern.

Not used the Wyatt instrument.

HTH,

Dave


David C. Briggs PhD
Father, Structural Biologist and Sceptic

University of Manchester E-mail:
david.c.bri...@manchester.ac.uk

Internetz: http://xtaldave.posterous.com/
Twitter: @xtaldave
Skype: DocDCB




On 4 February 2010 13:36, Wojciech Rypniewskiwojt...@ibch.poznan.pl  wrote:

Dear Fellow Crystallographers

We are going to buy a DLS instrument to help us assess crystallizability
of our proteins. I would be grateful for any opinions - either
on this BB or in my mail box (in which case I'll keep them to myself,
naturally).

We have looked more closely at two instruments:

DynaPro NanoStar from Wyatt and
Zetasizer Micro V from Malvern

and both seem to be rather similar in terms of parameters and price.

I would appreciate user opinions as to the reliability,
ease of use or any features that make a given instrument
particularly suited for assessing biological samples.

Many thanks,

Wojtek

--
--
Prof. dr hab. Wojciech Rypniewski  tel: +48-61-8528503
Institute of Bioorganic Chemistry  fax: +48-61-8520532
Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl
Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/
61-704 Poznan, Poland
--





--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] arp/warp installation

[Andreas Förster]

Dear all,

I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. 
All tests pass up to and including refmac version check (see log below). 
 After that, a Badly formed number in an if test.  What could be the 
issue?


The system is Redhat EL 5.4, tcsh.

Thanks.


Andreas



ld-andf 133% ./install.sh

ARP/wARP installer is checking your c-shell...
c-shell is installed on your machine at /bin/csh
Your login shell is: /bin/tcsh

Checking permissions for /dev/null- OK
Checking availability of sed command  - OK
Checking availability of tail command - OK
Checking availability of awk command  - OK
Checking decimal separator- OK
Checking ARP/wARP directory path  - OK
Checking ARP/wARP directory structure - OK
Checking java installation- installed version is 1.6.0
Checking java version number  - OK
Checking python installation  - installed version is 2.4.3
Checking python version number- OK
Python executables are available in 
/csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4

Checking operating system name- Linux
Checking processor type   - i686
ARP/wARP version 7.1 executables for this platform
are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux

Installing script and data files for:
 bin-athlon-Linux
 bin-i386-Darwin
 bin-i686-Linux
 bin-ia64-Linux
 bin-powerpc-Darwin
 bin-x86_64-Linux

Checking CCP4  ARP/wARP installation - OK
Checking refmac5 installation - installed version is 5.5.0109
Checking refmac5 version number   - OK
if: Badly formed number.


--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] arp/warp installation

[Andreas Förster]

As Phil realized, the leading zeros in the refmac5 version number were 
the culprit that broke the original installation script.  His modified 
version works beautifully.


Thanks.


Andreas



On 04/01/2010 11:27, Phil Evans wrote:

The attached slightly modified script fixes that problem
Phil






On 4 Jan 2010, at 11:15, Andreas Förster wrote:


Dear all,

I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up 
to and including refmac version check (see log below).  After that, a Badly formed 
number in an if test.  What could be the issue?

The system is Redhat EL 5.4, tcsh.

Thanks.


Andreas



ld-andf 133% ./install.sh

ARP/wARP installer is checking your c-shell...
c-shell is installed on your machine at /bin/csh
Your login shell is: /bin/tcsh

Checking permissions for /dev/null- OK
Checking availability of sed command  - OK
Checking availability of tail command - OK
Checking availability of awk command  - OK
Checking decimal separator- OK
Checking ARP/wARP directory path  - OK
Checking ARP/wARP directory structure - OK
Checking java installation- installed version is 1.6.0
Checking java version number  - OK
Checking python installation  - installed version is 2.4.3
Checking python version number- OK
Python executables are available in 
/csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4
Checking operating system name- Linux
Checking processor type   - i686
ARP/wARP version 7.1 executables for this platform
are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux

Installing script and data files for:
bin-athlon-Linux
bin-i386-Darwin
bin-i686-Linux
bin-ia64-Linux
bin-powerpc-Darwin
bin-x86_64-Linux

Checking CCP4  ARP/wARP installation - OK
Checking refmac5 installation - installed version is 5.5.0109
Checking refmac5 version number   - OK
if: Badly formed number.




--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] space groups not supported by Refmac5

[Andreas Förster]

Yeah, I2 works indeed just fine (for me, right now).


Andreas


Ethan Merritt wrote:

On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote:

Hi,

I have a question; recently I have encountered a few space groups which are
not supported by Refmac5. Examples include I2 and P21221. 


This is not correct.  Refmac is perfectly happy with these settings,
although there are some glitches to be careful of when you eventually
get to the point of data deposition.  (See earlier thread about
mtz2various mangling the spacegroup description when converting to *.cif).

Both these space 
groups have been identified as the best solutions for the two different

datasets I am working on using Pointless. However, I am faced with
difficulties in Refmac5, and the program fails to complete when I select
refinement cycles with Arp-waters...with the message saying 'space group not
supported'.


Ah. Perhaps this is a message from Arp/wArp? I don't know.
But having recently refined several I2 structures in refmac,
I can attest that it works fine in recent versions.

Ethan



--
Andreas Förster, Research Associate
Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] xquartz alert

[Andreas Förster]

I was so looking forward to being able to report that Apple's recent 600 
MB bugfix had got the jitters out of PyMOL on an external screen, but 
no.  It still flickers like a German disco in the 90s when I ray trace. 
 X11 2.4. should be coming out soon.  There's always hope.



Andreas



Engin Ozkan wrote:
The new OS X 10.5.7 update downgrades your X11 to 2.1.6.  There is a new 
X11 update, 2.3.3, only for 10.5.7 users.
It might be prudent to update to 10.5.7 and then xquartz 2.3.3, before 
reporting that coot or something else is suddenly broken.


As usual, very annoying...

Engin