Re: [ccp4bb] change of origin for reflections or map
On Wed, Oct 12, 2011 at 1:35 AM, James Holton jmhol...@lbl.gov wrote: My list has 8 different allowed shifts for I222, but I assume this is because the 0,0,1/2 shift is part of a symmetry operator. I guess it is a matter of semantics as to wether or not that is an allowed shift? James, the (0,0,1/2) shift is not part of any symmetry operator in I222, but I'm sure you knew that! - whereas the (1/2,1/2,1/2) shift _is_ a symmetry operator: the I centring operator in fact. This means that the lattice repeating units of the crystal structures (i.e. the set of atomic positions in the unit cell) will be identical in pairs, so in I222 (or indeed any I-centred space group) the crystal structure obtaining by shifting by (0,0,1/2) is identical in all respects to the one obtained from the (1/2,1/2,0) shift. In contrast, the structures obtained from all the other pairs, e,g, (0,0,0) and (0,0,1/2), are different in all respects, excepting that their sets of calculated amplitudes will be identical. In your terminology a non-allowed origin shift is one which would cause even the |Fc|s to differ, which is practice would mean that you would have to use a different space-group specific formula for the structure factor (so it's non-allowed only in the sense that you are not allowed to use the same structure factor formula, but you are allowed to use a different one). I prefer to call it non-equivalent origin shift (as opposed to equivalent origin or centring shift) - it's not really a question of whether it's allowed or not, it's whether it has any effect on the crystal structure. In practical terms of course it makes absolutely no difference to the result if you choose to do things that have absolutely no effect! Cheers -- Ian
Re: [ccp4bb] Ice rings... [maps and missing reflections]
Here we are I presume only worried about strong reflections lost behind an ice ring. At least that is where the discussion began. Isnt the best approach t this problem to use integration software which attempts to give a measurement, albeit with a high error estimate? The discussion has strayed into what to do with incomplete data sets.. In these cases there might be something to learn from the Free Lunch ideas used in ACORN and SHELX and other programs - set the missing reflections to E=1, and normalise them properly to an appropriate amplitude. Eleanor On 10/11/2011 08:33 PM, Garib N Murshudov wrote: In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) absent reflection with DFc, but it introduces bias. Bias becomes stronger as the number of absent reflections become larger. We need better way of estimating unobserved reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation. It may give better refinement behaviour and less biased map. Another one is integration over all errors (too many parameters for numerical integration, and there is no closed form formula) of model as well as experimental data. This would give less bia sed map with more pronounced signal. Regards Garib On 11 Oct 2011, at 20:15, Randy Read wrote: If the model is really bad and sigmaA is estimated properly, then sigmaA will be close to zero so that D (sigmaA times a scale factor) will be close to zero. So in the limit of a completely useless model, the two methods of map calculation converge. Regards, Randy Read On 11 Oct 2011, at 19:47, Ed Pozharski wrote: On Tue, 2011-10-11 at 10:47 -0700, Pavel Afonine wrote: better, but not always. What about say 80% or so complete dataset? Filling in 20% of Fcalc (or DFcalc or bin-averagedFobs or else - it doesn't matter, since the phase will dominate anyway) will highly bias the map towards the model. DFc, if properly calculated, is the maximum likelihood estimate of the observed amplitude. I'd say that 0 is by far the worst possible estimate, as Fobs are really never exactly zero. Not sure what the situation would be when it's better to use Fo=0, perhaps if the model is grossly incorrect? But in that case the completeness may be the least of my worries. Indeed, phases drive most of the model bias, not amplitudes. If model is good and phases are good then the DFc will be a much better estimate than zero. If model is bad and phases are bad then filling in missing reflections will not increase bias too much. But replacing them with zeros will introduce extra noise. In particular, the ice rings may mess things up and cause ripples. On a practical side, one can always compare the maps with and without missing reflections. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] Ice rings... [maps and missing reflections]
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/11/2011 09:58 PM, Ethan Merritt wrote: On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote: In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) absent reflection with DFc, but it introduces bias. Bias becomes stronger as the number of absent reflections become larger. We need better way of estimating unobserved reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation. I don't quite follow how one would generate multiple imputations in this case. Would this be equivalent to generating a map from (Nobs - N) refls, then filling in F_estimate for those N refls by back-transforming the map? Sort of like phase extension, except generating new Fs rather than new phases? Some people call this the free-lunch-algorithm ;-) Tim Ethan [...] - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOlVi4UxlJ7aRr7hoRAlU+AKDo+c449pUQ/1cnQAl6SMRqzVkp6wCcDETj GHB8hFXt1McbxWHfpUAsHtE= =FOWk -END PGP SIGNATURE-
Re: [ccp4bb] change of origin for reflections or map
If you have two pdb files - one for each ha solution, you can use csymmatch -pdbin-ref soln1.pdb -pdbin soln2.pdb -origin-hand -connetivity-radius 1 Eleanor On 10/11/2011 10:58 PM, George M. Sheldrick wrote: There are 4 possible origins in I222. There is a simple but inelegant way to check. Run the SHELXE job for the second dataset four times, first with no MOVE instruction, then with one of the following MOVE instructions inserted between UNIT and the first atom in the *_fa.res file from SHELXD: MOVE 0.5 0 0 MOVE 0 0.5 0 MOVE 0.5 0.5 0 one of these should give you phases with the same origin as your first dataset, so if you display both maps from the .phs files in COOT they will superimpose. George On Tue, Oct 11, 2011 at 11:29:14PM +0200, Klaas Decanniere wrote: Hi, I have two solutions from the ShelX C/D/E pipeline I would like to compare (different datasets, same protein). They seem to have different origins. Space group is I222, with a choice of 8 origins. How can I find and apply the correct shift to have the phase sets on a common origin? The information on http://www.ccp4.ac.uk/html/alternate_origins.html and http:/ /www.ccp4.ac.uk/html/non-centro_origins.html explain it very well, but thy don't point to the tools to use. Is it a matter of reindex and trying all 8 possibilities? thanks for your help, Klaas Decanniere
[ccp4bb] help me to determine ligand's b fator?
Dear Everybody, I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. By the way, are there a software to determine a new pdb's all parameters such as Rsym, I/σ, Redundancy, Solvent molecules' b factors? Thanks
Re: [ccp4bb] help me to determine ligand's b fator?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , A PDB file is a coordinate file. The quantities you mention, Rsym, I/sigI, and Redundancy are quantities calculated from the measured data and can therefore not be determined from a PDB file. The PDB file also contains the B-factor, so in order to find out the B-factors of some coordinates in the PDB file, you can open the file with any text editor of your choice and look at its entries. Best wishes, Tim On 10/12/2011 01:53 PM, 王瑞 wrote: Dear Everybody, I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. By the way, are there a software to determine a new pdb's all parameters such as Rsym, I/σ, Redundancy, Solvent molecules' b factors? Thanks - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOlY9gUxlJ7aRr7hoRAt4cAKCzxQevEo8lo5oP4kde909nPMcb4QCgvk1u iFnvewprn+436CcS0ThHyZg= =O1Zt -END PGP SIGNATURE-
Re: [ccp4bb] help me to determine ligand's b fator?
On 12/10/11 12:53, 王瑞 wrote: Dear Everybody, I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. You can use Coot to generate a new molecule for your residue selection (or ligand) and then use the functions: (average-temperature-factor imol) (median-temperature-factor imol) (standard-deviation-temperature-factor imol) You can also use bfactan, which makes an xml file with temperature factor statistics, IIRC. Paul.
[ccp4bb] Definition of B-factor (pedantry)
I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
Re: [ccp4bb] Definition of B-factor (pedantry)
Not sure if this is helpful Phil, but SCALEIT output includes various
definitions taken from the Willis and Prior book.
But then there is the problem of converting the amplitude B factors to
real space..
I attach my anisotropy notes..
It doesnt address the ? of sensible conventions!!
E
On 10/12/2011 02:55 PM, Phil Evans wrote:
I've been struggling a bit to understand the definition of B-factors,
particularly anisotropic Bs, and I think I've finally more-or-less got my head
around the various definitions of B, U, beta etc, but one thing puzzles me.
It seems to me that the natural measure of length in reciprocal space is d* =
1/d = 2 sin theta/lambda
but the conventional term for B-factor in the structure factor expression is
exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2)
Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the
factor of 4?
Or should we just get used to U instead?
My guess is that it is a historical accident (or relic), ie that is the
definition because that's the way it is
Does anyone understand where this comes from?
Phil
+
+
Scaleit:
+
+
Anisotropic temperature factor (REFINE ANISOTROPIC) (default)
C * exp(-(h**2 B11 + k**2 B22 + l**2 B33 +
2hk B12 + 2hl B13 + 2kl B23))
T he anisotropic scale is applied to the derivative F as
(derivative scale)* exp( - (B11*h**2 + B22*k**2 + B33*l**2 + 2*(B12*h*k +
B13*h*l + B23*k*l) ) )
An equivalent form of the anisotropic temperature factor is where
beta11 = B11/(a*)**2 etc
exp(-0.25( h**2 * (a*)**2 * beta11 + k**2 * (b*)**2 * beta22 + l**2 * (c*)**2
* beta33
+ 2*k*l*(b*)*(c*)*beta23 + 2*l*h*(c*)*(a*) *beta31 + 2*h*k*(a*)*(b*)
*beta12))
(This means the Uij terms of an anisotropic temperature factor is equal to
betaij/(8*pi**2.)
For derivative : 1
beta matrix - array elements beta11 beta12 beta13
beta21 beta22 beta23,
beta31 beta32 beta33
-2.60940.0.
0. -2.60940.
0.0. -0.9378
+
Note: REFMAC5 outputs betaij/4
The isotropic equivalent is ::
exp(-B (sin**2(theta)/lamda**2) ) =
exp(-0.25( h**2 * (a*)**2 * B + k**2 * (b*)**2 * B + l**2 * (c*)**2
* B
+ 2*k*l*(b*)*(c*)*cosAS*B + 2*l*h*(c*)*(a*)*cosBS*B +
2*h*k*(a*)*(b*)*cosGS*B))
+
+
REFMAC code:
+
+
S1 = FLOAT(IHH(1))*RCELL(1)
S2 = FLOAT(IHH(2))*RCELL(2)
S3 = FLOAT(IHH(3))*RCELL(3)
S11 = S1*S1
S22 = S2*S2
S33 = S3*S3
S12 = 2.0*S1*S2
S13 = 2.0*S1*S3
S23 = 2.0*S2*S3
SBS = B_LS_ANISO_OVER(1)*S11 + B_LS_ANISO_OVER(2)*S22 +
B_LS_ANISO_OVER(3)*S33 + B_LS_ANISO_OVER(4)*S12 +
B_LS_ANISO_OVER(5)*S13 + B_LS_ANISO_OVER(6)*S23
EXPAN = EXP(-SBS)
+
+
From RWBROOK and SHELXL
+
+
C
C PDB files contain anisotropic temperature factors as orthogonal Uo_ijs
multiplied by 10**4.
C The order is: Uo11 Uo22 Uo33 Uo12 Uo13 Uo23
C
C Shelx defines Ufn_ij to calculate temperature factor as:
C T(aniso_Ufn) = exp (-2PI**2 ( (h*ast)**2 Ufn_11 + (k*bst)**2 Ufn_22 +
(l*cst)**2 Ufn_33
C+ 2hk*ast*bst*Ufn_12 + 2hl*ast*bst*Ufn_13+
2kl*bst*cst*Ufn_23)
C
C Note: Uo_ji == Uo_ij and Uf_ji == Uf_ij.
C
C 10**4*[Uo_ij] listed on ANISOU card satisfy the relationship:
C [Uo_ij] = [RFu]-1 [Ufn_ij] {[RFu]-1}T
C [Ufn_ij] = [RFu] [Uo_ij] {[RFu]}T
Cwhere [Rfu] is the normalised [Rf] matrix read derived from the SCALEi
cards.
ie Rf11 Rf12 Rf13 = SCALE1(1) SCALE1(2) SCALE1(3)
Rf21 Rf22 Rf23SCALE2(1) SCALE2(2) SCALE2(3)
Rf31 Rf32 Rf33SCALE3(1) SCALE3(2) SCALE3(3)
and Rfu11 Rf12 Rfu13 = Rf11/FAC1 Rf12/FAC1 Rf13/FAC1
where FAC1 = SQRT(Rf11**2 +Rf12**2 +Rf13**2) etc.
For conventional SCALEi FAC1 = a*, etc but I am not sure if it is always
true..
If it is and you
Re: [ccp4bb] help me to determine ligand's b fator?
I made a simple script for this, perhaps you can edit it for your case.
Just save it as baverage.sh, then run it as ./baverage.sh your.pdb.
#!/bin/bash
echo --
grep '^ATOM' $1|cut -b61-66|cat |awk '{sum+=$1} END { print Protein
Average B =,sum/NR;printProtein Atom Number =, NR}'
grep '^HETATM' $1|grep -v 'HOH'|cut -b61-66 |cat|awk '{sum+=$1} END {print
Ligand/Ion Average B =,sum/NR;print Ligand/Ion Atom Number =, NR}'
grep '^HETATM' $1|grep 'HOH'|cut -b61-66|cat |awk '{sum+=$1} END {print
Water Average B =,sum/NR;print Water Number =, NR}'
echo --
-
best,
xiaopeng
Re: [ccp4bb] help me to determine ligand's b fator?
Hi, as Tim pointed out Rsym, I/sigma, Redundancy could not be obtained from a pdb, but you find it in the ouptut of SCALA, XSCALE, or similar scaling programs. I use Moleman2 from the Uppsala Software Factory to get the B values out of my pdb. F.e. Bf St Type provide B-Factors for every component in the file. Christian Am Mittwoch 12 Oktober 2011 13:53:56 schrieb 王瑞: Dear Everybody, I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. By the way, are there a software to determine a new pdb's all parameters such as Rsym, I/σ, Redundancy, Solvent molecules' b factors? Thanks
Re: [ccp4bb] Definition of B-factor (pedantry)
Hi Phil My understanding is that when the B factor was devised it was believed that it wouldn't represent any physical reality and was initially at least widely regarded as a garbage dump for errors. So it made no difference whether or not it was related to the natural length in reciprocal space, it was just a number, a fudge factor used to fit the data. Bs^2 is simplest to calculate from theta (which can be measured directly from the film or diffractometer setting), lambda (which is fixed of course) and B - particularly if you don't have a computer! Also a significant point may be that the scattering factors were tabulated as a function of s=sin(theta)/lambda (but you could equally well ask why 2sin(theta)/lambda wasn't used there). So it's more convenient to have B multiplying s^2 since you can simply add B to the constant part of the Gaussian scattering factor function. Of course they could have absorbed the extra factor of 2 into lambda (i.e. use lambda/2 instead of lambda) but maybe no-one thought of that! U, the mean square displacement, is the quantity which is directly related to the physics so if it's realism you're after, use U, not B (or beta). Cheers -- Ian On Wed, Oct 12, 2011 at 2:55 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
[ccp4bb] How to make a geometric and energetic statistics for 20 NMR structures calculated by CNS program?
Hi, all I don't know how to make a geometric and energetic statistics for 20 NMR solution structures calculated by CNS program. How to calculate r.m.s. deviations from idealized geometry; and how to calculate bond, angle, improper, vdw, NOE, cdih, and total energy? The pdb output files by CNS seems not contain these informations. Should I use another software? Thanks. Huayue Li, Ph. D College of Pharmacy Pusan National University Geumjeong-gu, Jangjeon-dong Busan 609-735, Korea Tel: +82-51-510-2185
[ccp4bb] Akta Prime
Dear all, We have an AktaPrime and GE Lifesciences stop servicing these instruments because they are getting old. Does anyone know of a third party company that gives contracts to maintain these instruments? Thank you. Mike Colaneri
Re: [ccp4bb] Ice rings... [maps and missing reflections]
Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/11/2011 09:58 PM, Ethan Merritt wrote: On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote: In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) absent reflection with DFc, but it introduces bias. Bias becomes stronger as the number of absent reflections become larger. We need better way of estimating unobserved reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation. I don't quite follow how one would generate multiple imputations in this case. Would this be equivalent to generating a map from (Nobs - N) refls, then filling in F_estimate for those N refls by back-transforming the map? Sort of like phase extension, except generating new Fs rather than new phases? Some people call this the free-lunch-algorithm ;-) Tim Doesn't work- the Fourier transform is invertable. As someone already said in this thread, if the map was made with coefficients of zero for certain reflections (which is equivalent to omitting those reflections) The back-transform will give zero for those reflections. Unless you do some density modification first. So free-lunch is a good name- there aint no such thing!
Re: [ccp4bb] help me to determine ligand's b fator?
Hello, 2011/10/12 Xiaopeng Hu huxp...@mail.sysu.edu.cn I made a simple script for this, perhaps you can edit it for your case. Just save it as baverage.sh, then run it as ./baverage.sh your.pdb. Here is another option: phenix.pdbtools model_statistics=true model.pdb or phenix.model_vs_data model.pdb data.hkl which, among other statistics, will give you min/max/mean B-factor values for macromolecule, ligands, solvent. Pavel
Re: [ccp4bb] Definition of B-factor (pedantry)
This may answer some of your questions or at least give pointers: Grosse-Kunstleve RW, Adams PD: On the handling of atomic anisotropic displacement parameters. Journal of Applied Crystallography 2002, 35, 477-480. http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf Pavel On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
Re: [ccp4bb] Ice rings... [maps and missing reflections]
On Wednesday, October 12, 2011 01:12:11 pm Edward A. Berry wrote: Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/11/2011 09:58 PM, Ethan Merritt wrote: On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote: In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) absent reflection with DFc, but it introduces bias. Bias becomes stronger as the number of absent reflections become larger. We need better way of estimating unobserved reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation. I don't quite follow how one would generate multiple imputations in this case. Would this be equivalent to generating a map from (Nobs - N) refls, then filling in F_estimate for those N refls by back-transforming the map? Sort of like phase extension, except generating new Fs rather than new phases? Some people call this the free-lunch-algorithm ;-) Tim Doesn't work- the Fourier transform is invertable. As someone already said in this thread, if the map was made with coefficients of zero for certain reflections (which is equivalent to omitting those reflections) The back-transform will give zero for those reflections. Unless you do some density modification first. So free-lunch is a good name- there aint no such thing! Tim refers to the procedure described in Sheldrick, G. M. (2002). Z. Kristallogr. 217, 644–65 which was later incorporated into shelxe as the Free Lunch Algorithm. It does indeed involve a form of density modification. Tim is also correct that this procedure is the precedent I had in mind, although I had forgotten its clever name. cheers, Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Ice rings... [maps and missing reflections]
Dear Ethan, Thankyou for the reference, but actually it's the wrong paper and anyway my only contribution to the 'free lunch algorithm' was to name it (in the title of the paper by Uson et al., Acta Cryst. (2007) D63, 1069-1074). By that time the method was already being used in ACORN and by the Bari group, who were the first to describe it in print (Caliandro et al., Acta Cryst. Acta Cryst. (2005) D61, 556-565). As you correctly say, it only makes sense in the context of density modification, but under favorable conditions, i.e. native data to 2A or better, inventing data to a resolution that you would have liked to collect but didn't can make a dramatic improvement to a map, as SHELXE has often demonstrated. Hence the name. And of course there is no such thing as a free lunch! Best regards, George On Wed, Oct 12, 2011 at 01:25:12PM -0700, Ethan Merritt wrote: On Wednesday, October 12, 2011 01:12:11 pm Edward A. Berry wrote: Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/11/2011 09:58 PM, Ethan Merritt wrote: On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote: In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) absent reflection with DFc, but it introduces bias. Bias becomes stronger as the number of absent reflections become larger. We need better way of estimating unobserved reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation. I don't quite follow how one would generate multiple imputations in this case. Would this be equivalent to generating a map from (Nobs - N) refls, then filling in F_estimate for those N refls by back-transforming the map? Sort of like phase extension, except generating new Fs rather than new phases? Some people call this the free-lunch-algorithm ;-) Tim Doesn't work- the Fourier transform is invertable. As someone already said in this thread, if the map was made with coefficients of zero for certain reflections (which is equivalent to omitting those reflections) The back-transform will give zero for those reflections. Unless you do some density modification first. So free-lunch is a good name- there aint no such thing! Tim refers to the procedure described in Sheldrick, G. M. (2002). Z. Kristallogr. 217, 644–65 which was later incorporated into shelxe as the Free Lunch Algorithm. It does indeed involve a form of density modification. Tim is also correct that this procedure is the precedent I had in mind, although I had forgotten its clever name. cheers, Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Definition of B-factor (pedantry)
Indeed that paper does lay out clearly the various definitions, thank you, but I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather than d*^2). I think James Holton's reminder that the definition dates from 1914 answers my question. So why do we store B in the PDB files rather than U? :-) Phil On 12 Oct 2011, at 21:19, Pavel Afonine wrote: This may answer some of your questions or at least give pointers: Grosse-Kunstleve RW, Adams PD: On the handling of atomic anisotropic displacement parameters. Journal of Applied Crystallography 2002, 35, 477-480. http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf Pavel On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
Re: [ccp4bb] Definition of B-factor (pedantry)
I think the PDB decided to store B instead of U because unless the B factor was 80, there would always be a leading 0. in that column, and that would just be a pitiful waste of two bytes. At the time the PDB was created, I understand bytes cost about $100 each! (But that could be a slight exaggeration) -James Holton MAD Scientist On Wed, Oct 12, 2011 at 2:56 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Indeed that paper does lay out clearly the various definitions, thank you, but I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather than d*^2). I think James Holton's reminder that the definition dates from 1914 answers my question. So why do we store B in the PDB files rather than U? :-) Phil On 12 Oct 2011, at 21:19, Pavel Afonine wrote: This may answer some of your questions or at least give pointers: Grosse-Kunstleve RW, Adams PD: On the handling of atomic anisotropic displacement parameters. Journal of Applied Crystallography 2002, 35, 477-480. http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf Pavel On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
Re: [ccp4bb] help me to determine ligand's b fator?
Thank you for all your advice.They are all good suggestions! 2011/10/12 王瑞 wangrui...@gmail.com Dear Everybody, I am sorry for a little off-topic. Could anyone tell me how to determine a protein, peptide and ligand of a new pdb's b factor? I know there are rampage and sfcheck to validate in ccp4, but I only found a overall b factor in their result. By the way, are there a software to determine a new pdb's all parameters such as Rsym, I/σ, Redundancy, Solvent molecules' b factors? Thanks
Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic
Michael, Unfortunately, I actually don't know who serves these machines apart from GE. Because you brought up the subject of GE equipment and service, I thought I would ask the community about the best options for routine crystallographic scale FPLC. In my opinion, following the takeover of Pharmacia by GE the the price of GE machines, replacement parts, and service has skyrocketed and GE service reps seem determined to squeeze and extort every dollar they can. Personally, I'd love to never do business with GE again. However, in some ways, they are the only game in town. GE is the de facto standard for our line of work and the Akta line are very good machines. However, GE's consistent price gouging and outright crooked service practices encourage me look elsewhere. I've used systems from AP-biotech (junk) and have heard some good things about Bio-rad. What does the community at large think? Are there other good options? Does anyone have some spare millions and manufacturing connections in India/China to consider starting a competing company? Sorry to hijack your thread Michael. Let me know what you find out. The less money I send to GE the better. --Paul From: Michael Colaneri colane...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, October 12, 2011 2:28 PM Subject: [ccp4bb] Akta Prime Dear all, We have an AktaPrime and GE Lifesciences stop servicing these instruments because they are getting old. Does anyone know of a third party company that gives contracts to maintain these instruments? Thank you. Mike Colaneri
Re: [ccp4bb] change of origin for reflections or map
Hello, The more I read this mailing list, the more I feel the crystallographer is a very special human being: - he lives in the Fourier space - when he goes to the Cartesian space, he restricts himself to a small box that is replicated to the infinity using symmetry operators and origin shifts That being said, some live in a world made of zero and ones... Regards, F.
Re: [ccp4bb] Definition of B-factor (pedantry)
At this point I usually chime in with an explanation of why the Protein Data Bank made some choice or other in the early days but on the matter of U vs. B I have not information to contribute. I can point out the at that time characters were stored in display code on a CDC 6600 and display code used 6 bits so 'bytes' at that time were less obese. 6 bits per character explains, of course, why lower case characters were not routinely used. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Wed, 12 Oct 2011, James Holton wrote: I think the PDB decided to store B instead of U because unless the B factor was 80, there would always be a leading 0. in that column, and that would just be a pitiful waste of two bytes. At the time the PDB was created, I understand bytes cost about $100 each! (But that could be a slight exaggeration) -James Holton MAD Scientist On Wed, Oct 12, 2011 at 2:56 PM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Indeed that paper does lay out clearly the various definitions, thank you, but I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather than d*^2). I think James Holton's reminder that the definition dates from 1914 answers my question. So why do we store B in the PDB files rather than U? :-) Phil On 12 Oct 2011, at 21:19, Pavel Afonine wrote: This may answer some of your questions or at least give pointers: Grosse-Kunstleve RW, Adams PD: On the handling of atomic anisotropic displacement parameters. Journal of Applied Crystallography 2002, 35, 477-480. http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf Pavel On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me. It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda but the conventional term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2) Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4? Or should we just get used to U instead? My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is Does anyone understand where this comes from? Phil
[ccp4bb] Monomers in COOT
Dear All, For all monomers (3 letter) used in COOT, where can i find the full names of the whole library? Many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] Monomers in COOT
try file search monomer library. Hit search without typing anything. It will give you what it has. Jackie Vitali 2011/10/12 Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk Dear All, For all monomers (3 letter) used in COOT, where can i find the full names of the whole library? Many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
