Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

[Jens Kaiser]

Tassos,
  I'm no expert either, and there are caveats for using this formula on
correlated magnitudes. But I would assume that the intensities of twin
related reflections should be independent from each other (that's my
understanding of the sigmoid cumulative intensity distribution of
twins). Thus, I think the simple Gaussian error propagation should be
applicable to uncertainty estimates in detwinned intensities.

Cheers,

Jens

On Thu, 2013-11-07 at 08:09 +0100, Anastassis Perrakis wrote:
> Dear Jens,
> 
> 
> That formula for error propagation is correct for independent
> measurements.
> Does this assumption stand true for Intensities in twinning? I am no
> expert, but I would think not.
> 
> 
> Tassos
> 
> On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
> 
> > Fulvio, Tim,
> >   error propagation is correct, but wrongly applied in Tim's
> > example.
> > s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
> > \left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
> > \left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
> > http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
> > The uncertainty in a derived magnitude is always larger than any
> > individual uncertainty, so no subtraction, anytime. Furthermore, in
> > Tim's example you could end up with negative sigmas..
> > 
> > HTH,
> > 
> > Jens
> > 
> > 
> > On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote: 
> > > Dear Fulvio,
> > > 
> > > with simple error propagation, the error would be
> > > sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
> > > 
> > > would it not?
> > > 
> > > Although especially for theoretical aspects you should be concerned
> > > about division by zero.
> > > 
> > > Best,
> > > Tim
> > > 
> > > On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
> > > > Thank you for reply. My question mostly concern a theoretical
> > > > aspect rather than practical one. To be not misunderstood, what is
> > > > the mathematical model that one should apply to be able to deal
> > > > with twinned intensities with their errors? I mean, I+_what? I ask
> > > > this In order to state some general consideration on the accuracy
> > > > about the recovery the true intensities on varying of alpha. Thanks
> > > >  Fulvio
> > > > 
> > > > Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
> > > > University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
> > > > 
> > > > Messaggio Originale Da: herman.schreu...@sanofi.com 
> > > > Inviato:  06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
> > > > [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
> > > > from twinned crystals
> > > > 
> > > > 
> > > > Dear Fulvio, you cannot detwin perfectly twinned data with this
> > > > formula. The term (1-2α) becomes zero, so you are dividing by zero.
> > > > With good refinement programs (ShelX, Refmac), refinement is done
> > > > against twinned data, which is better than to detwin the data with
> > > > the formula you mention.
> > > > 
> > > > As I understand it, to get map coefficients, the calculated
> > > > contribution of the twin domain (Fcalc’s) is substracted from Fobs
> > > > (with the appropriate weighting factors), so what you see in coot
> > > > is detwinned electron density. In practical terms, the only thing
> > > > you have to do is to specify the TWIN keyword in Refmac.
> > > > 
> > > > Best regards, Herman
> > > > 
> > > > 
> > > > 
> > > > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
> > > > von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
> > > > CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
> > > > with intensities from twinned crystals
> > > > 
> > > > 
> > > > Dear ccp4 users
> > > > 
> > > > a question about the recovering of true intensities from merohedral
> > > > twinned crystal. Providing alpha and the twin operator one should
> > > > be able to recover the intensities from the formulas:
> > > > 
> > > > 
> > > > 
> > > > I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
> > > > 
> > > > I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
> > > > 
> > > > as stated in many papers and books*.
> > > > 
> > > > However I was wondering about the uncertainties associated to these
> > > > measurements, I mean: for all physical observable an uncertainty
> > > > should be given.
> > > > 
> > > > Hence, what is the uncertainty associated to a perfect merohedrally
> > > > twinned crystal (alpha=0.5)? It is clear that in this case we drop
> > > > in a singular value of the above formulas.
> > > > 
> > > > Please, let me know your hints or your concerns on the matter.
> > > > Probably there is something that it is not so clear to me.
> > > > 
> > > > 
> > > > 
> > > > Thanks in advance
> > > > 
> > > > 
> > > > 
> > > > Fulvio
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
> > > > Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
> > 

Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

[Anastassis Perrakis]

Dear Jens,

That formula for error propagation is correct for independent measurements.
Does this assumption stand true for Intensities in twinning? I am no expert, 
but I would think not.

Tassos

On 7 Nov 2013, at 7:53, Jens Kaiser wrote:

> Fulvio, Tim,
>   error propagation is correct, but wrongly applied in Tim's example.
>  (see http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
> The uncertainty in a derived magnitude is always larger than any individual 
> uncertainty, so no subtraction, anytime. Furthermore, in Tim's example you 
> could end up with negative sigmas..
> 
> HTH,
> 
> Jens
> 
> 
> On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:
>> 
>> Dear Fulvio,
>> 
>> with simple error propagation, the error would be
>> sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
>> 
>> would it not?
>> 
>> Although especially for theoretical aspects you should be concerned
>> about division by zero.
>> 
>> Best,
>> Tim
>> 
>> On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
>> > Thank you for reply. My question mostly concern a theoretical
>> > aspect rather than practical one. To be not misunderstood, what is
>> > the mathematical model that one should apply to be able to deal
>> > with twinned intensities with their errors? I mean, I+_what? I ask
>> > this In order to state some general consideration on the accuracy
>> > about the recovery the true intensities on varying of alpha. Thanks
>> >  Fulvio
>> > 
>> > Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
>> > University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
>> > 
>> > Messaggio Originale Da: herman.schreu...@sanofi.com 
>> > Inviato:  06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
>> > [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
>> > from twinned crystals
>> > 
>> > 
>> > Dear Fulvio, you cannot detwin perfectly twinned data with this
>> > formula. The term (1-2α) becomes zero, so you are dividing by zero.
>> > With good refinement programs (ShelX, Refmac), refinement is done
>> > against twinned data, which is better than to detwin the data with
>> > the formula you mention.
>> > 
>> > As I understand it, to get map coefficients, the calculated
>> > contribution of the twin domain (Fcalc’s) is substracted from Fobs
>> > (with the appropriate weighting factors), so what you see in coot
>> > is detwinned electron density. In practical terms, the only thing
>> > you have to do is to specify the TWIN keyword in Refmac.
>> > 
>> > Best regards, Herman
>> > 
>> > 
>> > 
>> > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> > von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
>> > CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
>> > with intensities from twinned crystals
>> > 
>> > 
>> > Dear ccp4 users
>> > 
>> > a question about the recovering of true intensities from merohedral
>> > twinned crystal. Providing alpha and the twin operator one should
>> > be able to recover the intensities from the formulas:
>> > 
>> > 
>> > 
>> > I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
>> > 
>> > I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
>> > 
>> > as stated in many papers and books*.
>> > 
>> > However I was wondering about the uncertainties associated to these
>> > measurements, I mean: for all physical observable an uncertainty
>> > should be given.
>> > 
>> > Hence, what is the uncertainty associated to a perfect merohedrally
>> > twinned crystal (alpha=0.5)? It is clear that in this case we drop
>> > in a singular value of the above formulas.
>> > 
>> > Please, let me know your hints or your concerns on the matter.
>> > Probably there is something that it is not so clear to me.
>> > 
>> > 
>> > 
>> > Thanks in advance
>> > 
>> > 
>> > 
>> > Fulvio
>> > 
>> > 
>> > 
>> > 
>> > 
>> > ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
>> > Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
>> > Fundamentals of Crystallography, 3rd edition. IUCr Texts on
>> > Crystallography No. 15, IUCr/Oxford University Press, 2011;
>> > Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
>> > 1750-1758)
>> > 
>> > --
>> > 
>> > Fulvio Saccoccia, PhD
>> > 
>> > Dept. of Biochemical Sciences "A. Rossi Fanelli"
>> > 
>> > Sapienza University of Rome
>> > 
>> > Tel. +39 0649910556
>> > 
>> 
> 

Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals; Sorry for HTML.

[Jens Kaiser]

Fulvio, Tim,
  error propagation is correct, but wrongly applied in Tim's example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
http://en.wikipedia.org/wiki/Propagation_of_uncertainty#Simplification)
The uncertainty in a derived magnitude is always larger than any
individual uncertainty, so no subtraction, anytime. Furthermore, in
Tim's example you could end up with negative sigmas..

HTH,

Jens


On Thu, 2013-11-07 at 04:44 +0100, Tim Gruene wrote:

> Dear Fulvio,
> 
> with simple error propagation, the error would be
> sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)
> 
> would it not?
> 
> Although especially for theoretical aspects you should be concerned
> about division by zero.
> 
> Best,
> Tim
> 
> On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
> > Thank you for reply. My question mostly concern a theoretical
> > aspect rather than practical one. To be not misunderstood, what is
> > the mathematical model that one should apply to be able to deal
> > with twinned intensities with their errors? I mean, I+_what? I ask
> > this In order to state some general consideration on the accuracy
> > about the recovery the true intensities on varying of alpha. Thanks
> >  Fulvio
> > 
> > Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
> > University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
> > 
> > Messaggio Originale Da: herman.schreu...@sanofi.com 
> > Inviato:  06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
> > [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
> > from twinned crystals
> > 
> > 
> > Dear Fulvio, you cannot detwin perfectly twinned data with this
> > formula. The term (1-2α) becomes zero, so you are dividing by zero.
> > With good refinement programs (ShelX, Refmac), refinement is done
> > against twinned data, which is better than to detwin the data with
> > the formula you mention.
> > 
> > As I understand it, to get map coefficients, the calculated
> > contribution of the twin domain (Fcalc’s) is substracted from Fobs
> > (with the appropriate weighting factors), so what you see in coot
> > is detwinned electron density. In practical terms, the only thing
> > you have to do is to specify the TWIN keyword in Refmac.
> > 
> > Best regards, Herman
> > 
> > 
> > 
> > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
> > von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
> > CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
> > with intensities from twinned crystals
> > 
> > 
> > Dear ccp4 users
> > 
> > a question about the recovering of true intensities from merohedral
> > twinned crystal. Providing alpha and the twin operator one should
> > be able to recover the intensities from the formulas:
> > 
> > 
> > 
> > I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
> > 
> > I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
> > 
> > as stated in many papers and books*.
> > 
> > However I was wondering about the uncertainties associated to these
> > measurements, I mean: for all physical observable an uncertainty
> > should be given.
> > 
> > Hence, what is the uncertainty associated to a perfect merohedrally
> > twinned crystal (alpha=0.5)? It is clear that in this case we drop
> > in a singular value of the above formulas.
> > 
> > Please, let me know your hints or your concerns on the matter.
> > Probably there is something that it is not so clear to me.
> > 
> > 
> > 
> > Thanks in advance
> > 
> > 
> > 
> > Fulvio
> > 
> > 
> > 
> > 
> > 
> > ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
> > Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
> > Fundamentals of Crystallography, 3rd edition. IUCr Texts on
> > Crystallography No. 15, IUCr/Oxford University Press, 2011;
> > Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
> > 1750-1758)
> > 
> > --
> > 
> > Fulvio Saccoccia, PhD
> > 
> > Dept. of Biochemical Sciences "A. Rossi Fanelli"
> > 
> > Sapienza University of Rome
> > 
> > Tel. +39 0649910556
> > 
> 

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Prof. K. Sekar]

Dear all,

there is a tool to identify invariant
water molecules in homologous protein structures
and the tool can be accessed via

http://cluster.physics.iisc.ernet.in/3dss/

best,

Sekar



> Thanks Bernhard 
>   you have helpfully distinguished between the two processes - there is
> certainly a movement of waters to symmetry replacements closer to a chain
> - and that gets documented in Remark 525 of the PDB file returned to
> authors - although then it is stripped out, I think, before the entry is
> released.
>
>  But generally a renumbering is applied to all the waters - these are not
> actually moved but are re-ordered. And of course the number count of them
> may change - in order to accommodate any waters that are swapped in or out
> of the chain during the symmetry operation.
>
>  Currently I don't think authors are given access to an audit of what is
> happening - they can of course check their favourite waters by a
> superimposition. Still have to say best way to avoid errors would be to
> check symmetry and re-order at the end of refinement, pre-deposition. 
>
> All the best 
>   Martyn 
>
>
> 
>  From: Bernhard Rupp 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Monday, 4 November 2013, 14:50
> Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
>
>
>
> As far as confusion as a result of PDB renumbering is concerned: It was
> useful to run the old REM525 standalone program (I think I got it from
> PDBe/Kim Hendrick) at the end of solvent building. It does what the PDB
> did with water renumbering when creating the REMARK 525 (probably based on
> ccp4 contact with additions). Is there an updated standalone PDB tool
> available one can use these days to avoid at least that issue?
>  
> Thx, BR
>  
> From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> MARTYN SYMMONS
> Sent: Montag, 4. November 2013 15:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
>  
> Thank you for that, Rachel
>  
> Even though the tone of your comment does not suggest that you want to
> carry on a dialogue about this, I thought I would reply in any case -
> since dialogue is what this forum is supposed to be about.
>  
> Thing is,  I was sort of looking for an explanation of why the rule was
> adopted that waters were to be renumbered from N to C terminus. If this is
> not functioning to put the waters in register across a set of related
> structures then it seems somewhat arbitrary. And other schemes might be
> suggested to be better for the "usability and interpretation of the
> structural data". 
>  
> In some cases there are only a few waters but in many structures the wwPDB
> partners renumber hundreds. And this process makes it difficult for
> authors to check the final deposited structure against the output of their
> refinement. 
>  
> I have to say that I agree with other contributors to this thread. It
> would be much better to let the refinement program authors agree on a
> default water numbering scheme. And then maintain that through
> deposition. 
>  
> I thought of six possible schemes before breakfast... one of my favourites
> was to order by B-factor - which might appeal to crystallographers.
> Another was to give priority to those in the coordination sphere of any
> metal ions - these actually get priority in the PDB as they are included
> in the LINKS records above the coordinates. These coordinated waters are
> often refined together with the metals and so it would make sense to move
> them closer to their friendly ion.    
>  
> And of course one other clearly suitable option would be to leave the
> waters in the authors' preferred order - chosen with help from their
> refinement suite. This is what happens during deposition with the residues
> of the polymers - (provided the authors chainids are suitably chosen).
> Following your link the rule for polymers is that: 'If the coordinate
> residue numbers, as provided by the author, are unique and sequential
> within a particular chain ID, the residues will not be renumbered.' 
>  
> I'm presuming that if the authors have a preferred suitable set of water
> numbers then that would be maintained similarly?
>  
> Perhaps that is what is happening in the cases I notice that do not follow
> wwPDB rules?
>  
> On Friday I was looking at TIRAP structures and in 3ub2 the protein
> construct starts at residue 78 and its final residue is 221 - but the
> associated DTT is labelled back at residue 1 in the same chain. Then the
> first ten out of eleven waters are residues 2 to 11 but then oddly the
> eleventh water is residue 222. Is there a difference in this C-terminal
> water compared with the N-terminal ones? I imagined it was perhaps
> maintained to fit in with the associated publication - or maybe started
> out life modelled as a metal ion - unfortunately I can find no mention of
> it in the paper. 
>  
> But, regardless of this distracting feature,  surely this

Re: [ccp4bb] convert orientation matrix format

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Almudena,

depending on your application there might be a different approach from
what I suggested before:
you could use my 'spots4cellnow'
(http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/spots4cellnow/) to
convert the SPOTS.XDS into reciprocal coordinates (it only applies the
maths from W. Kabsch, Acta Crystallogr. D66 (2010), pp 133-144). The
output can be read by cell_now which you have access to  if you have
access to saint / apex.
cell_now writes a p4p file including the orientation matrix.

This should be a work-around if the transformation does not fit.

Best,
Tim

On 11/05/2013 02:29 PM, Almudena Ponce Salvatierra wrote:
> Hi everyone,
> 
> I would like to know how to change matrix format from the one I get
> out of XDS to the one that comes out of SAINTS. Or the other way
> around.
> 
> My question is: is the beam along the same axis in both matrices?
> as well as the rotation axis and the third axis?
> 
> How can I convert one into the other one?
> 
> Thank you very much in advance.
> 
> Best wishes,
> 
> Almudena.

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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Re: [ccp4bb] switching space group

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Maggie,

in addition to what others explained, data integration does not depend
on the space group. It only depends on the Laue group, and P21212 and
P212121 belong to the same Laue group. You would see no difference at
all in reprocessing, and in this case Ian's suggestion is sufficient.

When I am not sure whether or not changing the space group make any
real difference to the data I like using pointless to set it right, or
even run phaser if I do have a PDB-file.

Cheers,
Tim

On 11/06/2013 07:13 PM, MAGGIE wrote:
> Hi,
> 
> I have a structure which should have space group P212121, but it
> has been processed to P21212.  It can not be solved and refined.
> Right now I do not have HKL2000, but I need change the space group
> to P212121.  Is there a way for me to do this using CCP4?
> 
> Thank you,
> 
> Maggie

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
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Re: [ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Fulvio,

with simple error propagation, the error would be
sigma(I(h1)) = (1-α)sigma(Iobs(h1))-α*sigma(Iobs(h2))/(1-2α)

would it not?

Although especially for theoretical aspects you should be concerned
about division by zero.

Best,
Tim

On 11/06/2013 05:54 PM, Fulvio Saccoccia wrote:
> Thank you for reply. My question mostly concern a theoretical
> aspect rather than practical one. To be not misunderstood, what is
> the mathematical model that one should apply to be able to deal
> with twinned intensities with their errors? I mean, I+_what? I ask
> this In order to state some general consideration on the accuracy
> about the recovery the true intensities on varying of alpha. Thanks
>  Fulvio
> 
> Fulvio Saccoccia PhD Dept. of Biochemical Sciences Sapienza
> University of Rome 5, Piazzale A. Moro 00185 phone +39 0649910556
> 
> Messaggio Originale Da: herman.schreu...@sanofi.com 
> Inviato:  06/11/2013, 17:25 A: CCP4BB@JISCMAIL.AC.UK Oggetto:
> [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities
> from twinned crystals
> 
> 
> Dear Fulvio, you cannot detwin perfectly twinned data with this
> formula. The term (1-2α) becomes zero, so you are dividing by zero.
> With good refinement programs (ShelX, Refmac), refinement is done
> against twinned data, which is better than to detwin the data with
> the formula you mention.
> 
> As I understand it, to get map coefficients, the calculated
> contribution of the twin domain (Fcalc’s) is substracted from Fobs
> (with the appropriate weighting factors), so what you see in coot
> is detwinned electron density. In practical terms, the only thing
> you have to do is to specify the TWIN keyword in Refmac.
> 
> Best regards, Herman
> 
> 
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
> von Fulvio Saccoccia Gesendet: Mittwoch, 6. November 2013 16:58 An:
> CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] uncertainites associated
> with intensities from twinned crystals
> 
> 
> Dear ccp4 users
> 
> a question about the recovering of true intensities from merohedral
> twinned crystal. Providing alpha and the twin operator one should
> be able to recover the intensities from the formulas:
> 
> 
> 
> I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
> 
> I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
> 
> as stated in many papers and books*.
> 
> However I was wondering about the uncertainties associated to these
> measurements, I mean: for all physical observable an uncertainty
> should be given.
> 
> Hence, what is the uncertainty associated to a perfect merohedrally
> twinned crystal (alpha=0.5)? It is clear that in this case we drop
> in a singular value of the above formulas.
> 
> Please, let me know your hints or your concerns on the matter.
> Probably there is something that it is not so clear to me.
> 
> 
> 
> Thanks in advance
> 
> 
> 
> Fulvio
> 
> 
> 
> 
> 
> ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M.
> Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti.
> Fundamentals of Crystallography, 3rd edition. IUCr Texts on
> Crystallography No. 15, IUCr/Oxford University Press, 2011;
> Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta Cryst. D55.
> 1750-1758)
> 
> --
> 
> Fulvio Saccoccia, PhD
> 
> Dept. of Biochemical Sciences "A. Rossi Fanelli"
> 
> Sapienza University of Rome
> 
> Tel. +39 0649910556
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.15 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFSewyuUxlJ7aRr7hoRAnP/AJ9biIGWJsHnbcQ4IaG5fusZTN0iOgCfR6bu
3po97EKDH98F881dH3CgD2M=
=2QkU
-END PGP SIGNATURE-

Re: [ccp4bb] switching space group

[Edward A. Berry]

I liked Ian Tickle's 1-line ccp4 script for changing the space group with 
mtzutils.
I believe CAD can do this also. In any case, there's no need to reprocess.
Some reflections present in the current data will be systematically absent in
the new space group, but presumably they will be eliminated in the process.

Phoebe A. Rice wrote:

If you're only changing the 2-fold axis along c to a 2-fold screw axis, you 
don't need to
go back to the raw image files and reprocess them!   Just tweak the header of 
the .sca
file and carry on (and take notes on what you did).

--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant 
Upadhyay
[vikrant192...@gmail.com]
*Sent:* Wednesday, November 06, 2013 5:13 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] switching space group

Hi Maggie,

you can re-process your data using XDS and can provide the desired space group 
in the
XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE mailto:dongmeij...@gmail.com>>
wrote:


Hi,

I have a structure which should have space group P212121, but it has been 
processed to
P21212.  It can not be solved and refined.  Right now I do not have HKL2000, 
but I need
change the space group to P212121.  Is there a way for me to do this using CCP4?

Thank you,
Maggie

Re: [ccp4bb] switching space group

[Phoebe A. Rice]

If you're only changing the 2-fold axis along c to a 2-fold screw axis, you 
don't need to go back to the raw image files and reprocess them!   Just tweak 
the header of the .sca file and carry on (and take notes on what you did).


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vikrant Upadhyay 
[vikrant192...@gmail.com]
Sent: Wednesday, November 06, 2013 5:13 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] switching space group

Hi Maggie,

you can re-process your data using XDS and can provide the desired space group 
in the XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE 
mailto:dongmeij...@gmail.com>> wrote:

Hi,

I have a structure which should have space group P212121, but it has been 
processed to P21212.  It can not be solved and refined.  Right now I do not 
have HKL2000, but I need change the space group to P212121.  Is there a way for 
me to do this using CCP4?

Thank you,

Maggie

Re: [ccp4bb] switching space group

[Vikrant Upadhyay]

Hi Maggie, 

you can re-process your data using XDS and can provide the desired space group 
in the XDS.INP file. It won't take much time.

Vikrant

Vikrant Upadhyay
Postdoctoral associate
Dr. Crina Nimigean's lab, A-1050
Department of Anesthesiology
Weill Cornell Medical College
525 East 68th Street
New York, NY 10065

On Nov 6, 2013, at 1:13 PM, MAGGIE  wrote:

> Hi,
>  
> I have a structure which should have space group P212121, but it has been 
> processed to P21212.  It can not be solved and refined.  Right now I do not 
> have HKL2000, but I need change the space group to P212121.  Is there a way 
> for me to do this using CCP4? 
>  
> Thank you,
>  
> Maggie

Re: [ccp4bb] switching space group

[Ian Tickle]

Hi Maggie

echo  symm  P212121 | mtzutils  HKLIN  in.mtz  HKLOUT  out.mtz

should do the trick.

Cheers

-- Ian


On 6 November 2013 18:13, MAGGIE  wrote:

> Hi,
>
> I have a structure which should have space group P212121, but it has been
> processed to P21212.  It can not be solved and refined.  Right now I do not
> have HKL2000, but I need change the space group to P212121.  Is there a way
> for me to do this using CCP4?
>
> Thank you,
>
> Maggie
>

[ccp4bb] switching space group

[MAGGIE]

Hi,

I have a structure which should have space group P212121, but it has been
processed to P21212.  It can not be solved and refined.  Right now I do not
have HKL2000, but I need change the space group to P212121.  Is there a way
for me to do this using CCP4?

Thank you,

Maggie

Re: [ccp4bb] Off Topic: Formulatrix NT8 nanoliter-volume dispenser

[Jim Fairman]

Hi Dileep,

We have been a user of the NT8 robot going on a year now, and we're quite
happy with it.  The initial versions of the machine had a few problems, but
engineers over at Formulatrix have worked out a majority of the bugs and
the current version of the machine functions quite well.  We use it mostly
for sitting drop tray setups and for LCP crystallization - haven't
attempted any hanging drop setups, but should work fine.  My favorite
feature of this machine is the humidity controlled chamber.  You can set
the humidity level within the chamber, and sensors keep the percent
humidity within the user-specified range.  It makes evaporation problems
with LCP setups I've experienced in the past virtually non-existent.

Customer service at Formulatrix has also been very quick to reply if
anything ever does go wrong with the machine.

Hope this helps.

Cheers, Jim




On Wed, Nov 6, 2013 at 6:53 AM, Dileep V  wrote:

> Hi there:
>
> Has anyone got experience using the Formulatrix NT8 as a 'crystallization
> robot'? Other options being considered are Art Robbins Phoenix & TTP
> Labtech's Mosquito, both of which I have used in the past.
>
> Any feedback on NT8 will be highly appreciated.
>
>
> Thanks and Regards,
> Dileep
>
>
>
>
>


-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures 
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

[ccp4bb] Error using Coot supplied with CCP4

[Antony Oliver]

Dear CCP4 / Coot community,

I am trying to use LIDIA from Coot 0.7.2 - as supplied with CCP4-6.4.0 - to 
look at a protein / ligand complex.

However, when trying to launch LIDIA from the Extensions menu of Coot - I get 
the following error.

I guess this suggests some form of fortran compile error?

Any help would be gratefully received.

Antony.


(write-pdb-file 12 "coot-ccp4/tmp-residue-for-prodrg.pdb")
arg_list ['XYZIN', 'coot-ccp4/tmp-residue-for-prodrg.pdb', 'MOLOUT', 
'coot-ccp4/.coot-to-lbg-mol', 'XYZOUT', 'coot-ccp4/.coot-to-lbg-pdb', 'LIBOUT', 
'coot-ccp4/.coot-to-lbg-lib']
forrtl: severe (180): SIGBUS, bus error occurred
Image  PCRoutineLineSource  
   
cprodrg000113FC  Unknown   Unknown  Unknown
cprodrg000111AC  Unknown   Unknown  Unknown
cprodrg00011164  Unknown   Unknown  Unknown
# 
#  
# 
# 
# 


---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: antony.oli...@sussex.ac.uk
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

[ccp4bb] R: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

[Fulvio Saccoccia]

Thank you for reply. My question mostly concern a theoretical aspect rather 
than practical one. To be not misunderstood, what is the mathematical model 
that one should apply to be able to deal with twinned intensities with their 
errors? I mean, I+_what? I ask this In order to state some general 
consideration on the accuracy about the recovery the true intensities on 
varying of alpha.
Thanks 
Fulvio

Fulvio Saccoccia PhD
Dept. of Biochemical Sciences
Sapienza University of Rome
5, Piazzale A. Moro 00185
phone +39 0649910556

Messaggio Originale
Da: herman.schreu...@sanofi.com
Inviato:  06/11/2013, 17:25 
A: CCP4BB@JISCMAIL.AC.UK
Oggetto: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from 
twinned crystals


Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α) 
becomes zero, so you are dividing by zero. With good refinement programs 
(ShelX, Refmac), refinement is done against twinned data, which is better than 
to detwin the data with the formula you mention.

As I understand it, to get map coefficients, the calculated contribution of the 
twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting 
factors), so what you see in coot is detwinned electron density. In practical 
terms, the only thing you have to do is to specify the TWIN keyword in Refmac.

Best regards,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio 
Saccoccia
Gesendet: Mittwoch, 6. November 2013 16:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] uncertainites associated with intensities from twinned 
crystals


Dear ccp4 users

a question about the recovering of true intensities from merohedral twinned 
crystal. Providing alpha and the twin operator one should be able to recover 
the intensities from the formulas:



I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)

I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)

as stated in many papers and books*.

However I was wondering about the uncertainties associated to these 
measurements, I mean: for all physical observable an uncertainty should be 
given.

Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal (alpha=0.5)? It is clear that in this case we drop in a singular value 
of the above formulas.

Please, let me know your hints or your concerns on the matter. Probably there 
is something that it is not so clear to me.



Thanks in advance



Fulvio





ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of 
Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford 
University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta 
Cryst. D55. 1750-1758)

--

Fulvio Saccoccia, PhD

Dept. of Biochemical Sciences "A. Rossi Fanelli"

Sapienza University of Rome

Tel. +39 0649910556

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Ronald E Stenkamp]

I've remained silent as this thread evolved into a discussion of how the PDB deals with 
water names and numbers.  But Nat's comment about the PDB "not advertising itself as 
anything other than an archival service" finally prodded me into saying something.

Something I've slowly come to realize is that the PDB, while it started as an archive, 
has developed into a working database.  That's why they (the PDB 
workers/organizers/managers) have gotten into this mode where they change things from the 
original deposited files.  I learned several years ago that the PDB is willing to change 
the atom names in a ligand from those previously used in the published  literature.  This 
was done in the name of "consistency" and essentially made the PDB files into 
database entries, rather than archival files since the atom names no longer matched the 
atom names used in the papers.

Given the difficulties I had in discussing this with the annotaters, I've come 
to realize that as soon as I hit the submit button on a PDB submission, I've 
lost control over what will appear in the distributed file.  In a way, it's 
been liberating to reach that point.  It reduces my sense of responsibility for 
the contents of the file.

Ron

On Wed, 6 Nov 2013, Nat Echols wrote:


On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp  wrote:

  Hmmm….does that mean that the journals are now the ultimate authority of 
what stays in
  the PDB?

  I find this slightly irritating and worthy of change.


http://www.wwpdb.org/UAB.html

"It is the current wwPDB (Worldwide PDB) policy that entries can be made 
obsolete following a request
from the people responsible for publishing it (be it the principal author or journal 
editors)."

I'm not sure I understand why things should be any different; the PDB is not 
advertising itself as
anything other than an archival service, unlike the journals which are supposed 
to be our primary
mechanism of quality control.

-Nat

Re: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

[Sabuj Pattanayek]

   Bio i   
 

 Original message 
From: herman.schreu...@sanofi.com 
Date: 11/06/2013  10:25 AM  (GMT-06:00) 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from 
twinned crystals 
 
Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α) 
becomes zero, so you are dividing by zero. With good refinement programs 
(ShelX, Refmac), refinement is done against twinned data, which is better than 
to detwin the data with the formula you mention.
 
As I understand it, to get map coefficients, the calculated contribution of the 
twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting 
factors), so what you see in coot is detwinned electron density. In practical 
terms, the only thing you have to do is to specify the TWIN keyword in Refmac.
 
Best regards,
Herman
 
 
 
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio 
Saccoccia
Gesendet: Mittwoch, 6. November 2013 16:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] uncertainites associated with intensities from twinned 
crystals
 
Dear ccp4 users
a question about the recovering of true intensities from merohedral twinned 
crystal. Providing alpha and the twin operator one should be able to recover 
the intensities from the formulas:
 
I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)
as stated in many papers and books*.
However I was wondering about the uncertainties associated to these 
measurements, I mean: for all physical observable an uncertainty should be 
given.
Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal (alpha=0.5)? It is clear that in this case we drop in a singular value 
of the above formulas.
Please, let me know your hints or your concerns on the matter. Probably there 
is something that it is not so clear to me.
 
Thanks in advance
 
Fulvio
 
 
ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of 
Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford 
University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta 
Cryst. D55. 1750-1758)
--
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences "A. Rossi Fanelli"
Sapienza University of Rome
Tel. +39 0649910556
 
 

[ccp4bb] AW: [ccp4bb] uncertainites associated with intensities from twinned crystals

[Herman . Schreuder]

Dear Fulvio,
you cannot detwin perfectly twinned data with this formula. The term (1-2α) 
becomes zero, so you are dividing by zero. With good refinement programs 
(ShelX, Refmac), refinement is done against twinned data, which is better than 
to detwin the data with the formula you mention.

As I understand it, to get map coefficients, the calculated contribution of the 
twin domain (Fcalc’s) is substracted from Fobs (with the appropriate weighting 
factors), so what you see in coot is detwinned electron density. In practical 
terms, the only thing you have to do is to specify the TWIN keyword in Refmac.

Best regards,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Fulvio 
Saccoccia
Gesendet: Mittwoch, 6. November 2013 16:58
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] uncertainites associated with intensities from twinned 
crystals


Dear ccp4 users

a question about the recovering of true intensities from merohedral twinned 
crystal. Providing alpha and the twin operator one should be able to recover 
the intensities from the formulas:



I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)

I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)

as stated in many papers and books*.

However I was wondering about the uncertainties associated to these 
measurements, I mean: for all physical observable an uncertainty should be 
given.

Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal (alpha=0.5)? It is clear that in this case we drop in a singular value 
of the above formulas.

Please, let me know your hints or your concerns on the matter. Probably there 
is something that it is not so clear to me.



Thanks in advance



Fulvio





ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of 
Crystallography, 3rd edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford 
University Press, 2011; Chandra, N., Acharya, K. R., Moody, P. C. (1999). Acta 
Cryst. D55. 1750-1758)

--

Fulvio Saccoccia, PhD

Dept. of Biochemical Sciences "A. Rossi Fanelli"

Sapienza University of Rome

Tel. +39 0649910556

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Nat Echols]

On Wed, Nov 6, 2013 at 12:39 AM, Bernhard Rupp wrote:

> Hmmm….does that mean that the journals are now the ultimate authority of
> what stays in the PDB?
>
> I find this slightly irritating and worthy of change.
>

http://www.wwpdb.org/UAB.html

"It is the current wwPDB (Worldwide PDB) policy that entries can be made
obsolete following a request from the people responsible for publishing it
(be it the principal author or journal editors)."

I'm not sure I understand why things should be any different; the PDB is
not advertising itself as anything other than an archival service, unlike
the journals which are supposed to be our primary mechanism of quality
control.

-Nat

[ccp4bb] uncertainites associated with intensities from twinned crystals

[Fulvio Saccoccia]

Dear ccp4 users
a question about the recovering of true intensities from merohedral 
twinned crystal. Providing alpha and the twin operator one should be able to 
recover the 
intensities from the formulas:

I(h1) = (1-α)Iobs(h1)-αIobs(h2)/(1-2α)
I(h2) = -αIobs(h1)+(1+α)Iobs(h2)/(1-2α)


as stated in many papers and books*.
However I was wondering about the uncertainties associated to these 
measurements, I 
mean: for all physical observable an uncertainty should be given. 
Hence, what is the uncertainty associated to a perfect merohedrally twinned 
crystal 
(alpha=0.5)? It is clear that in this case we drop in a singular value of the 
above 
formulas.
Please, let me know your hints or your concerns on the matter. Probably there 
is 
something that it is not so clear to me.

Thanks in advance

Fulvio


ref. **(C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. 
Ferraris, G. 
Gilli, P. Gilli, G. Zanotti and M. Catti. Fundamentals of Crystallography, 3rd 
edition. IUCr 
Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011; Chandra, 
N., 
Acharya, K. R., Moody, P. C. (1999). /Acta Cryst./ *D*55. 1750-1758)
-- 
Fulvio Saccoccia, PhD
Dept. of Biochemical Sciences "A. Rossi Fanelli"
Sapienza University of Rome
Tel. +39 0649910556

[ccp4bb] Off Topic: Formulatrix NT8 nanoliter-volume dispenser

[Dileep V]

Hi there:

Has anyone got experience using the Formulatrix NT8 as a 'crystallization
robot'? Other options being considered are Art Robbins Phoenix & TTP
Labtech's Mosquito, both of which I have used in the past.

Any feedback on NT8 will be highly appreciated.


Thanks and Regards,
Dileep

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Andrey,

since you mention the manual: is there a way to retrieve the manual
pages for the ccp4 programs? I often use 'man pointless' et al. to
check syntax etc and I miss the man pages in 6.4.0. Even the source
does not seem to contain them any more.

Best,
Tim

On 11/06/2013 01:52 PM, Andrey Lebedev wrote:
> Dear CCP4 Users
> 
> An update for the CCP4-6.4.0 series has just been released. This is
> the first update for both CCP4 and ARP/wARP in tandem.
> 
> The ARP/wARP component of this update will be available to those
> Mac and Linux users who have previously installed both packages via
> the CCP4 Package manager or from the joint bundle downloaded from
> CCP4 web-site. A standalone ARP/wARP package including the current
> update can be downloaded from the EMBL-Hamburg site at
> www.arp-warp.org.
> 
> The following changes will be applied to the ARP/wARP
> installation:
> 
> • The use of non-crystallographic symmetry for protein chain
> tracing has been enabled (it was accidentally disabled in version
> 7.4). • The `SAD refinement protocol' (Murshudov et al 2011) has
> undergone many fixes and now works well. • The routine for ligand
> identification has been made faster and some small bugs have been
> fixed. • A few bugs have been fixed in the ARP/wARP installer and
> shell-specific problems sometimes occurring on Linux should now be
> cured. • The manual has been updated.
> 
> The following changes will be applied to the CCP4-6.4.0
> installation:
> 
> • MrBUMP (all): a new option of model re-building after SHELXE; a
> fix for phaser_sculptor dispatcher. • Xia2 (windows): update to
> release 0.3.6.3 (fixes ctruncate issue). • aimless (all): bug
> fixes. • pointless (all): bug fixes. • ViewHKL (all): additional
> visual control to enhance weak reflections and bug fixes. •
> truncate (Mac): Fixed harvesting option of old truncate. • Molrep:
> New interface. • Update (all): Increased maximum waiting time for
> background update check in ccp4i.
> 
> Andrey Lebedev
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFSeloAUxlJ7aRr7hoRAkmxAKCU6dqpZAjaUH0nWYnlsmAuaZ392QCeP74S
ir8+bKdHF+t2eaPUfCAolnU=
=ixyQ
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Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear all

A comment to my last e-mail

If your ccp4 installation is not write-protected,
do not use sudo, just run
ccp4um

Regards

Andrey

On 6 Nov 2013, at 14:49, Lebedev, Andrey (STFC,RAL,SC) wrote:

> 
> Dear all
> 
> If you had a problem similar to that Joachim and Ingo had (see below), please 
> run
> sudo /ccp4-6.4.0/bin/ccp4um
> where  is the full path to your ccp4-6.4.0 installation,
> and uninstall the last update.
> 
> Then you can launch ccp4i and install it again as usual.
> 
> Thanks!
> 
> Andrey
> 
> On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:
> 
>> Hi,
>> 
>> I just installed the update using ccp4um.
>> All I get now is:
>> 
>>> ccp4i
>> Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
>> does not have correct file label configure
>> Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
>> does not have correct file label preferences
>> Error in startup script: can't read "array(MAPVIEWER_DEFAULT)": no such 
>> element in array
>>   while executing
>> "set viewercmd $array(MAPVIEWER_DEFAULT)"
>>   (procedure "set_default_mapviewer" line 9)
>>   invoked from within
>> "set_default_mapviewer $arrayname"
>>   ("preferences" arm line 2)
>>   invoked from within
>> "switch -- $taskname {
>>   directories {
>> catch {update_defdir_menu $arrayname}
>>   } configure {
>> # We over-write the user TYPEDEF_LIST with..."
>>   (procedure "InitialisePreferences" line 113)
>>   invoked from within
>> "InitialisePreferences preferences preferences"
>>   (file "/software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl" line 128)
>>   invoked from within
>> "source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
>>   (file "/software/ccp4-6.4.0/bin/ccp4i" line 12)
>> 
>> 
>> What went wrong?
>> 
>> Am 06.11.2013 um 13:52 schrieb Andrey Lebedev :
>> 
>>> Dear CCP4 Users
>>> 
>>> An update for the CCP4-6.4.0 series has just been released. This is the 
>>> first update for both CCP4 and ARP/wARP in tandem.
>>> 
>>> The ARP/wARP component of this update will be available to those Mac and 
>>> Linux users who have previously installed both packages via the CCP4 
>>> Package manager or from the joint bundle downloaded from CCP4 web-site. A 
>>> standalone ARP/wARP package including the current update can be downloaded 
>>> from the EMBL-Hamburg site at www.arp-warp.org.
>>> 
>>> The following changes will be applied to the ARP/wARP installation:
>>> 
>>> • The use of non-crystallographic symmetry for protein chain tracing has 
>>> been enabled (it was accidentally disabled in version 7.4).
>>> • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
>>> fixes and now works well.
>>> • The routine for ligand identification has been made faster and some small 
>>> bugs have been fixed.
>>> • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
>>> problems sometimes occurring on Linux should now be cured.
>>> • The manual has been updated.
>>> 
>>> The following changes will be applied to the CCP4-6.4.0 installation:
>>> 
>>> • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
>>> phaser_sculptor dispatcher.
>>> • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
>>> • aimless (all): bug fixes.
>>> • pointless (all): bug fixes.
>>> • ViewHKL (all): additional visual control to enhance weak reflections and 
>>> bug fixes.
>>> • truncate (Mac): Fixed harvesting option of old truncate.
>>> • Molrep: New interface.
>>> • Update (all): Increased maximum waiting time for background update check 
>>> in ccp4i.
>>> 
>>> Andrey Lebedev
>>> 
>>> 
>>> --
>>> Scanned by iCritical.
>>> 
>> 
>> Mit freundlichen Grüßen
>> 
>> Joachim Reichelt
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
>> Braunschweig | www.helmholtz-hzi.de
>> Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"
>> 
>> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
>> Bundesministerium für Bildung und Forschung
>> Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
>> Ministerium für Wissenschaft und Kultur
>> Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
>> Gesellschaft mit beschränkter Haftung (GmbH)
>> Sitz der Gesellschaft: Braunschweig
>> Handelsregister: Amtsgericht Braunschweig, HRB 477
> 


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear all

If you had a problem similar to that Joachim and Ingo had (see below), please 
run
sudo /ccp4-6.4.0/bin/ccp4um
where  is the full path to your ccp4-6.4.0 installation,
and uninstall the last update.

Then you can launch ccp4i and install it again as usual.

Thanks!

Andrey

On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:

> Hi,
> 
> I just installed the update using ccp4um.
> All I get now is:
> 
>> ccp4i
> Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
> does not have correct file label configure
> Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
> does not have correct file label preferences
> Error in startup script: can't read "array(MAPVIEWER_DEFAULT)": no such 
> element in array
>while executing
> "set viewercmd $array(MAPVIEWER_DEFAULT)"
>(procedure "set_default_mapviewer" line 9)
>invoked from within
> "set_default_mapviewer $arrayname"
>("preferences" arm line 2)
>invoked from within
> "switch -- $taskname {
>directories {
>  catch {update_defdir_menu $arrayname}
>} configure {
>  # We over-write the user TYPEDEF_LIST with..."
>(procedure "InitialisePreferences" line 113)
>invoked from within
> "InitialisePreferences preferences preferences"
>(file "/software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl" line 128)
>invoked from within
> "source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
>(file "/software/ccp4-6.4.0/bin/ccp4i" line 12)
> 
> 
> What went wrong?
> 
> Am 06.11.2013 um 13:52 schrieb Andrey Lebedev :
> 
>> Dear CCP4 Users
>> 
>> An update for the CCP4-6.4.0 series has just been released. This is the 
>> first update for both CCP4 and ARP/wARP in tandem.
>> 
>> The ARP/wARP component of this update will be available to those Mac and 
>> Linux users who have previously installed both packages via the CCP4 Package 
>> manager or from the joint bundle downloaded from CCP4 web-site. A standalone 
>> ARP/wARP package including the current update can be downloaded from the 
>> EMBL-Hamburg site at www.arp-warp.org.
>> 
>> The following changes will be applied to the ARP/wARP installation:
>> 
>> • The use of non-crystallographic symmetry for protein chain tracing has 
>> been enabled (it was accidentally disabled in version 7.4).
>> • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
>> fixes and now works well.
>> • The routine for ligand identification has been made faster and some small 
>> bugs have been fixed.
>> • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
>> problems sometimes occurring on Linux should now be cured.
>> • The manual has been updated.
>> 
>> The following changes will be applied to the CCP4-6.4.0 installation:
>> 
>> • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
>> phaser_sculptor dispatcher.
>> • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
>> • aimless (all): bug fixes.
>> • pointless (all): bug fixes.
>> • ViewHKL (all): additional visual control to enhance weak reflections and 
>> bug fixes.
>> • truncate (Mac): Fixed harvesting option of old truncate.
>> • Molrep: New interface.
>> • Update (all): Increased maximum waiting time for background update check 
>> in ccp4i.
>> 
>> Andrey Lebedev
>> 
>> 
>> --
>> Scanned by iCritical.
>> 
> 
> Mit freundlichen Grüßen
> 
> Joachim Reichelt
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
> Braunschweig | www.helmholtz-hzi.de
> Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"
> 
> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
> Bundesministerium für Bildung und Forschung
> Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
> Ministerium für Wissenschaft und Kultur
> Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
> Gesellschaft mit beschränkter Haftung (GmbH)
> Sitz der Gesellschaft: Braunschweig
> Handelsregister: Amtsgericht Braunschweig, HRB 477


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Hi Joachim

Thanks for reporting the problem

Please run 
sudo /software/ccp4-6.4.0/bin/ccp4um
and uninstall the last update for now.
There should be something wrong with your config files.
I'll trace what it could be and then contact you.

Regards

Andrey


On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:

> Hi,
> 
> I just installed the update using ccp4um.
> All I get now is:
> 
>> ccp4i
> Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
> does not have correct file label configure
> Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
> does not have correct file label preferences
> Error in startup script: can't read "array(MAPVIEWER_DEFAULT)": no such 
> element in array
>while executing
> "set viewercmd $array(MAPVIEWER_DEFAULT)"
>(procedure "set_default_mapviewer" line 9)
>invoked from within
> "set_default_mapviewer $arrayname"
>("preferences" arm line 2)
>invoked from within
> "switch -- $taskname {
>directories {
>  catch {update_defdir_menu $arrayname}
>} configure {
>  # We over-write the user TYPEDEF_LIST with..."
>(procedure "InitialisePreferences" line 113)
>invoked from within
> "InitialisePreferences preferences preferences"
>(file "/software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl" line 128)
>invoked from within
> "source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
>(file "/software/ccp4-6.4.0/bin/ccp4i" line 12)
> 
> 
> What went wrong?
> 
> Am 06.11.2013 um 13:52 schrieb Andrey Lebedev :
> 
>> Dear CCP4 Users
>> 
>> An update for the CCP4-6.4.0 series has just been released. This is the 
>> first update for both CCP4 and ARP/wARP in tandem.
>> 
>> The ARP/wARP component of this update will be available to those Mac and 
>> Linux users who have previously installed both packages via the CCP4 Package 
>> manager or from the joint bundle downloaded from CCP4 web-site. A standalone 
>> ARP/wARP package including the current update can be downloaded from the 
>> EMBL-Hamburg site at www.arp-warp.org.
>> 
>> The following changes will be applied to the ARP/wARP installation:
>> 
>> • The use of non-crystallographic symmetry for protein chain tracing has 
>> been enabled (it was accidentally disabled in version 7.4).
>> • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
>> fixes and now works well.
>> • The routine for ligand identification has been made faster and some small 
>> bugs have been fixed.
>> • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
>> problems sometimes occurring on Linux should now be cured.
>> • The manual has been updated.
>> 
>> The following changes will be applied to the CCP4-6.4.0 installation:
>> 
>> • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
>> phaser_sculptor dispatcher.
>> • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
>> • aimless (all): bug fixes.
>> • pointless (all): bug fixes.
>> • ViewHKL (all): additional visual control to enhance weak reflections and 
>> bug fixes.
>> • truncate (Mac): Fixed harvesting option of old truncate.
>> • Molrep: New interface.
>> • Update (all): Increased maximum waiting time for background update check 
>> in ccp4i.
>> 
>> Andrey Lebedev
>> 
>> 
>> --
>> Scanned by iCritical.
>> 
> 
> Mit freundlichen Grüßen
> 
> Joachim Reichelt
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
> Braunschweig | www.helmholtz-hzi.de
> Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"
> 
> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
> Bundesministerium für Bildung und Forschung
> Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
> Ministerium für Wissenschaft und Kultur
> Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
> Gesellschaft mit beschränkter Haftung (GmbH)
> Sitz der Gesellschaft: Braunschweig
> Handelsregister: Amtsgericht Braunschweig, HRB 477


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Joachim Reichelt]

Hi,

I just installed the update using ccp4um.
All I get now is:

>ccp4i
Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
does not have correct file label configure
Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
does not have correct file label preferences
Error in startup script: can't read "array(MAPVIEWER_DEFAULT)": no such element 
in array
while executing
"set viewercmd $array(MAPVIEWER_DEFAULT)"
(procedure "set_default_mapviewer" line 9)
invoked from within
"set_default_mapviewer $arrayname"
("preferences" arm line 2)
invoked from within
"switch -- $taskname {
directories {
  catch {update_defdir_menu $arrayname}
} configure {
  # We over-write the user TYPEDEF_LIST with..."
(procedure "InitialisePreferences" line 113)
invoked from within
"InitialisePreferences preferences preferences"
(file "/software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl" line 128)
invoked from within
"source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
(file "/software/ccp4-6.4.0/bin/ccp4i" line 12)


What went wrong?

Am 06.11.2013 um 13:52 schrieb Andrey Lebedev :

> Dear CCP4 Users
>
> An update for the CCP4-6.4.0 series has just been released. This is the first 
> update for both CCP4 and ARP/wARP in tandem.
>
> The ARP/wARP component of this update will be available to those Mac and 
> Linux users who have previously installed both packages via the CCP4 Package 
> manager or from the joint bundle downloaded from CCP4 web-site. A standalone 
> ARP/wARP package including the current update can be downloaded from the 
> EMBL-Hamburg site at www.arp-warp.org.
>
> The following changes will be applied to the ARP/wARP installation:
>
> • The use of non-crystallographic symmetry for protein chain tracing has been 
> enabled (it was accidentally disabled in version 7.4).
> • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
> fixes and now works well.
> • The routine for ligand identification has been made faster and some small 
> bugs have been fixed.
> • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
> problems sometimes occurring on Linux should now be cured.
> • The manual has been updated.
>
> The following changes will be applied to the CCP4-6.4.0 installation:
>
> • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
> phaser_sculptor dispatcher.
> • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
> • aimless (all): bug fixes.
> • pointless (all): bug fixes.
> • ViewHKL (all): additional visual control to enhance weak reflections and 
> bug fixes.
> • truncate (Mac): Fixed harvesting option of old truncate.
> • Molrep: New interface.
> • Update (all): Increased maximum waiting time for background update check in 
> ccp4i.
>
> Andrey Lebedev
>
>
> --
> Scanned by iCritical.
>

Mit freundlichen Grüßen

Joachim Reichelt









Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"

Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
Bundesministerium für Bildung und Forschung
Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches Ministerium 
für Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477

[ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released. This is the first 
update for both CCP4 and ARP/wARP in tandem.

The ARP/wARP component of this update will be available to those Mac and Linux 
users who have previously installed both packages via the CCP4 Package manager 
or from the joint bundle downloaded from CCP4 web-site. A standalone ARP/wARP 
package including the current update can be downloaded from the EMBL-Hamburg 
site at www.arp-warp.org.

The following changes will be applied to the ARP/wARP installation:

• The use of non-crystallographic symmetry for protein chain tracing has been 
enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes 
and now works well.
• The routine for ligand identification has been made faster and some small 
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific 
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.

The following changes will be applied to the CCP4-6.4.0 installation:

• MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and bug 
fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check in 
ccp4i.

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Bernhard Rupp]

Hmmm..does that mean that the journals are now the ultimate authority of
what stays in the PDB?

I find this slightly irritating and worthy of change.

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
Echols
Sent: Dienstag, 5. November 2013 15:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs

 

On Tue, Nov 5, 2013 at 12:22 AM, Bernhard Rupp 
wrote:

Given their otherwise almost paranoid sensitivity to ultimate author
authority 

(resulting in things like still having 2hr0 etc in the bank because certain
authors go AWOL or ignore major issues)

 

In defense of the PDB, it's not just the authors who went AWOL in that case
- it is ultimately the responsibility of the journals to retract clearly
fraudulent publications.

 

-Nat