Re: [ccp4bb] Heavy atom sites?

Hi Pu Obviously your SAD & SIRAS solutions can't both be right, one must have the inverted handedness: I would guess it's the SIRAS solution that's wrong, since the SAD solution seems to have given you an interpretable map. The reason for getting the wrong hand in the SIRAS case is probably that

Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?

On Wed, Sep 1, 2010 at 4:26 AM, Ed Pozharski wrote: > The > reason you see the missing region in (2mFo-DFc) map is because it is > effectively the sum of model map (mFo) which shows you the parts of the > model you have already placed and difference map (mFo-DFc) which shows > you the regions whic

Re: [ccp4bb] Fd-3m with pdbset

It seems that it's the new addition of ':n' which has pushed it over the limit of the 11 char field. Has this been thought through? I can see that the ':n' qualifier is necessary to disambiguate alternate origins. Without the redundant formatting spaces 9 chars would be sufficient even for 'P 4

Re: [ccp4bb] Method to calculate the axis of an alpha helix

Hi Yuan You might want to look at the 'exponential map' as an alternative to quaternions. This article evaluates all the various representations of rotations, including Eulerian angles, polar angles, rotation matrices, quaternions etc: http://webhome.cs.uvic.ca/~blob/courses/485c/notes/pdf/expma

Re: [ccp4bb] Method to calculate the axis of an alpha helix

actly identical: the expressions for angle & axis vector are quite different as can be seen from the above definitions. However for a given rotation they clearly must have the same value (by definition!) if that's what you mean. Cheers -- Ian > > Regards, > > Yuan SHANG >

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

I should just like to point out that the main source of the disagreement here seems to be that people have very different ideas about what a 'model' is or should be. Strictly a model is a purely mathematical construct, in this case it consists of the appropriate equation for the calculated structu

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

Dirk Personally I wouldn't make use of the deposited Fcalcs, I would insist on having the refined model, not only for the reasons Pavel gave, but also because it's never clear which mathematical model was used to produce the deposited Fcalcs. There are 2 problem areas (at least 2 I can think of r

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

> Oh, goodness, I see: even here, we would need clear rules what the > calculated structure factors are, which weights are were, which bulk solvent > correction was applied ... a maze, too! Fortunately the X-ray & restraint weights/target values are not an issue here: varying them changes the refi

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

Hi Florian, Tight NCS restraints or NCS constraints (they are essentially the same thing in effect if not in implementation) both reduce the effective parameter count on a 1-for-1 basis. Restraints should not be considered as being added to the pool of X-ray observations in the calculation of the

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

Mon, Sep 20, 2010 at 9:20 AM, Dirk Kostrewa wrote: >  Hi Ian, > > Am 19.09.10 15:25, schrieb Ian Tickle: >> >> Hi Florian, >> >> Tight NCS restraints or NCS constraints (they are essentially the same >> thing in effect if not in implementation) both reduce the effect

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

case: > > = f - (m - r + Drest) = f + r - m - Drest > > it certainly appears from this that the number of X-ray data (f) and > the number of restraints (r) are being added. > > However if you consider the test set residual: > >  = f + (m - r + Drest) = f -

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

of the algebra, I didn't have to introduce it. If the form of the obs/param ratio that you are suggesting came out of the algebra in the same way I would be happy to accept it, but AFAICS it doesn't. Cheers -- Ian On Mon, Sep 20, 2010 at 12:22 PM, Ian Tickle wrote: > Hi Dirk >

Re: [ccp4bb] how to decide an ideal "Weight matrix" value in REFMAC

Hi Hailiang The short answer is that the optimal X-ray weighting factor minimises Rfree, or better -LLfree. However this is tricky to carry out in practice since it means you have to run several jobs adjusting the weight manually each time to find the optimum.  Also, ideally the same procedure sh

Re: [ccp4bb] how to decide an ideal "Weight matrix" value in REFMAC

that I referred to briefly. Cheers -- Ian On Tue, Sep 21, 2010 at 9:42 PM, Ian Tickle wrote: > Hi Hailiang > > The short answer is that the optimal X-ray weighting factor minimises > Rfree, or better -LLfree. > > However this is tricky to carry out in practice since it means

Re: [ccp4bb] how to decide an ideal "Weight matrix" value in REFMAC

> (1). Can I say the X-ray weighting is optimal when it yields the smallest > Rfree, meanwhile RMS-Z(bonds) is smaller than "0.85 - 0.146*resolution" > (angles also maybe)? The weighting is optimal when the free likelihood is maximised with respect to the weights, or equivalently when the negative

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

Hi Gerard & Pavel Isn't this the proviso I was referring to, that one cannot in practice use an infinite weight because of rounding errors in the target function. The weight just has to be 'big enough' such that the restraint residual becomes sufficiently small that it's no longer significant. I

Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio

chains when the ASU is made. At this point I > guess the copies can bump and so apply a force on each other but that is a > local, and likely to be perturbing, force. > > best wishes >  Martyn > > Martyn Symmons > Cambridge > > > > --- On Thu, 23/9/10, Ian Tick

Re: [ccp4bb] .cv to .mtz conversion

Hi, There are 2 basic ways of approaching this problem: the good and the bad (I won't even mention the ugly!). The bad ways all involve counting columns and working out Fortran formats. This is because it cannot be safely assumed that the file has been written with fixed length records, which is

Re: [ccp4bb] R factor & R free struck

On Sun, Oct 3, 2010 at 6:34 PM, J. Preben Morth wrote: > hi > remember to reindex your data to P21212 in case you used Phaser to search > all alternative orthorhombic SG's and it found P22121 > Preben > > Hi, re-indexing the data without also remembering to transform the co-ordinates (using the m

Re: [ccp4bb] relation between wavelength and inter-atomic distances

Hi Carlos Well, diffraction is a consequence of the crystal lattice repeat (or it could be a 1-D repeat in a fibre), for without the lattice there could be no diffraction, only scattering. But the lattice repeat is obviously directly related to the average distance between atoms and the number of

Re: [ccp4bb] crystal friendly solvents that are useful for dissolving hydrophobic small molecules?

There's also NMP (N-methyl-2-pyrrolidone). -- Ian > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Green, Todd > Sent: 22 January 2007 20:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [CCP4BB] crystal friendly solvents that are useful > for dissolvin

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

I believe the recommended procedure is to refine against all data before submission, using the same set of parameters and weights as for the last refinement against the working set alone, after all why throw away 5% (or even 10% in some cases) of your hard-won data? The purpose of Rfree is 1) to c

[ccp4bb] MTZ to Shel-X?

All, I thought this would be a simple task, but for the life of me I can't see how to do it! All I want to do is convert an MTZ file to Shel-X format for refinement. I thought it would take me 2 secs, but it's taken me at least 5 attempts, and it's still not right! First I tried mtz2various w

Re: [ccp4bb] RMSD

I believe some programs give the unweighted RMSD, others weighted by inverse variance (of course often they don't tell you which one!). I prefer the latter as it's less skewed by distances with big variances. Of course if the variances are all equal then it won't make any difference. -- Ian > --

[ccp4bb] Can't choose full H-M symbol for conventional cell ?

We're having some problems essentially because AFAICS Mosflm (and also D*Trek) don't recognise the 'full' Hermann-Mauguin symbols for space groups. For example for space group no 18 with the 'short' H-M symbol 'P 2/1 2/1 2' in the setting with 'full' H-M symbol 'P 2 2/1 2/1' the programs choose

Re: [ccp4bb] Warning messages from Refmac.

All - I'm refining some structures in SG P22121 and I lots of warning msgs from Refmac: "===> Warning: No such space group in ASYLIM". The job seems to run fine & I can't see anything untoward with the results or the output files, so I was just wondering whether I need be concerned about the mes

Re: [ccp4bb] Warning messages from Refmac.

lways follow the science, it should never lead or limit it. Ralf Grosse-Kunstleve has done an excellent job of tabulating the properties of all space groups (in $CLIBD/syminfo.lib) in machine-readable form, so there's no longer any excuse for not doing it properly! Cheers -- Ian >

Re: [ccp4bb] Highest shell standards

I don't understand why should D be low for an incomplete shell? According to Randy's tutorial: D includes effects of: difference in position or scattering factor missing atoms difference in overall scale or B-factor i.e. all kinds of error in the SF model, but this is surely uncorrelated with

Re: [ccp4bb] Nature policy update regarding source code

In any case, does Nature Methods actually publish any papers that fall into the category (quote) "custom-designed software necessary for the method's implementation" where "a software program is the focus of the report", at least in the area of macromolecular structure determination? Come to that,

Re: [ccp4bb] Nature policy update regarding source code

It seems to me to be important in this context to draw the distinction between _software_ which is about the most ephemeral thing I can think of (OK maybe butterflies are more so) - e.g. try compiling code published > 5 years ago - and _algorithms_ which if well constructed are potentially everlast

Re: [ccp4bb] Can I change the e-mail address

Hi Jian If you haven't done so already you should register at the JISCMAIL site (http://www.jiscmail.ac.uk/) using your old address, then login & unsubscribe from the list(s). Then repeat the process with your new address & re-subscribe to the list(s) you want. -- Ian > -Original Message---

Re: [ccp4bb] truncate error on x86_64

Hi Daniele I recently made a change in truncate (added cumulative distribution for twinned intensities), however I'm not sure whether 6.0.2 incorporates that change. I've not seen either of the problems you report before, all I can suggest is you re-compile truncate with the debug (-g switch),

Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

Hi Bernhard This subject has indeed come up repeatedly and it has never in my view been clearly explained why the optimal RMS(calc-target) geometry value (i.e. bond length, bond angle etc.) in restrained refinements must always be <= RMS(obs-mean(obs)) = SD(obs) from unrestrained refinements, assu

Re: [ccp4bb] Summary - Valid to stop Refmac after TLS refinement?

I see that Dale and I are in pretty well complete agreement on this subject (even though I honestly hadn't read Dale's response when I sent mine!) - I think we now have a definitive explanation, so hopefully this will be the last time that this question comes up, or if not at least we now have a

[ccp4bb] Groundhog Day syndrome?

We've seem to be experiencing the 'Groundhog Day' syndrome again, and no I didn't hit 'Send' accidentally! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle > Sent: 10 April 2007 11:21 >

Re: [ccp4bb] twin fraction varies between crystals?

I seem to recall a discussion at some Study Weekend where someone reported a needle crystal in which the twin fraction appeared to vary continuously from 0 at one end of the needle to 0.5 at the other! You just had to make sure you picked the right end to collect the data! -- Ian > -Origina

Re: [ccp4bb] twin fraction varies between crystals?

Here's an interesting paper on "The Genesis of Twinned Crystals" (from 1945! - it's even printed on simulated aged paper and if you look closely the "aging" has an unrealistic plane-group pattern!): http://www.minsocam.org/msa/collectors_corner/arc/twinorig.htm It's by the eminent crystallograp

Re: [ccp4bb] truncate Wilson printout

Hi Bernhard I'm sure you're right: it must be a typo. I think the problem is that people get into the habit of including the minus sign in EXP(-B*2*SINTH**2/L**2), e.g. when writing the expression for structure factor, without thinking whether the formula is actually applicable to the particula

Re: [ccp4bb] R and Rfree

Hi U Sam When you say "R increases and Rfree decreases or vice versa" it's important to consider which variables they are increasing/decreasing with respect to. During a given run of Refmac (or whatever) with N iterations, where you optimise a *fixed* set of atomic/group/overall parameters with

Re: [ccp4bb] can truncate import Rfree?

Hi, the distributed version of truncate (from v 6.0 I think) has an option to assign label FreeR_flag on input & copy to output, this is an option I added because we needed it here. Unfortunately the relevant info doesn't seem to have made it to the man page, sorry about that. Cheers -- Ian > -

Re: [ccp4bb] can truncate import Rfree?

y also the case that there are many useful undocumented features. C'est la vie! > -Original Message- > From: Tim Grune [mailto:[EMAIL PROTECTED] > Sent: 03 May 2007 10:18 > To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] can truncate import Rfree? >

Re: [ccp4bb] How to run ccp4 in php script?

Hi Yang Li Are you sure it's not just a file permission problem? If the Apache account does not have read access to /home/prog then even if you make a local copy of ccp4.setup so Apache can read it, the script will report that the directory /home/prog/ccp4/ does not exist. In fact if Apache does

Re: [ccp4bb] How to determine ligand binding from diffraction pattern?

Hi Joe In principle, a FOM-weighted difference Fourier using the known phases of the apo structure is in essence a comparison of the diffraction patterns, however in practice it relies on the apo & ligand-bound crystals being highly isomorphous. The problem is that changes in the diffraction due

Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > Sent: 30 May 2007 10:16 > To: Schubert, Carsten [PRDUS] > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] How to determine ligand binding from > diffraction pat tern? > > 2) There

Re: [ccp4bb] Is anomalous signal a different wavelength?

I think it's to do with the Uncertainty Principle. You can't say for sure that a particular X-ray photon has gone off in that direction (if you could you would know both its position and momentum accurately which is not allowed). If you integrated the momentum over all possible outcomes I'm sure

Re: [ccp4bb] Problem with ligand refinement in REFMAC5

Hi Andreas I can't explain your first problem, but I may be able to explain your second one. My take from the Refmac code is that a VDW repulsion restraint between any pair of atoms is included ONLY if the atoms are NOT bonded or related by a bond angle (obviously) OR the occupancy sum is > 1.

[ccp4bb] Problem reading syminfo.lib

All- I've written a program which reads all the space-group info in syminfo.lib (in order to generate Cheshire groups - currently syminfo.lib only contains the limits of the Cheshire cell - it doesn't list the elements of the group which is what I need). However I'm running into a problem: s/r MS

Re: [ccp4bb] CCP4 Wiki

-Original Message- From: [EMAIL PROTECTED] on behalf of James Stroud Sent: Fri 7/27/2007 9:03 PM To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] CCP4 Wiki >On Friday 27 July 2007 06:10, Anastassis Perrakis wrote: >> Being a small contributor to the Greek Wiki, which has far less >> subsc

Re: [ccp4bb] mr query

Hi Simon You didn't say whether you have just 1 mol/a.u. or more than one. In the latter case you can get the effect you observe because as well as considering possible origin shifts you also have to consider the possibility that say the A and B molecules have been switched, i.e. like the origin

Re: [ccp4bb] CCP4 rotation convention

Hi Bernhard Yes you are right, these descriptions cannot be talking about the same overall rotation, assuming the angles are defined in the same way of course (i.e. assuming that alpha & gamma have not been switched round in the J.Appl.Cryst. paper you refer to). The 'Crowther' convention (used c

Re: [ccp4bb] CCP4 rotation convention

Hi folks I hate to say this but I think everyone here has got it wrong to some degree (including myself - and I hereby retract my previous e-mail and issue the correction below!). If you don't believe me then read & digest Jorge Navaza's article "Rotation functions" in Int. Tab. Vol. F (sect 13

Re: [ccp4bb] step 1 & step 2

> -Original Message- > From: Bernhard Rupp [mailto:[EMAIL PROTECTED] > Sent: 13 August 2007 22:14 > To: Ian Tickle > Subject: step 1 > > I think I understand what you sent last, but > but I am slow and need this in simple words: My first point which I would str

Re: [ccp4bb] CCP4 rotation convention

om: Eleanor Dodson [mailto:[EMAIL PROTECTED] > Sent: 14 August 2007 10:01 > To: Ian Tickle > Subject: Re: [ccp4bb] CCP4 rotation convention > > I think you are foolish to believe the literature! > The only information I trust is the rotation matrix to be applied to > coor

Re: [ccp4bb] CCP4 rotation convention

Bernhard - In case you're still trying to follow the convoluted arguments in my previous long answer, here's the short answer (for your summary!): Replace the word 'new' (twice) in this sentence in Phil's AC 2001 article with the word 'fixed': "... rotate by gamma around z, then by beta around t

Re: [ccp4bb] CCP4 rotation convention

t in 2 secs. I trust I have convinced you! Cheers -- Ian > -Original Message- > From: Bernhard Rupp [mailto:[EMAIL PROTECTED] > Sent: 15 August 2007 07:39 > To: Ian Tickle > Subject: RE: [ccp4bb] CCP4 rotation convention > > Ian, my question is actually ge

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

ED] > Sent: 15 August 2007 10:51 > To: Ian Tickle > Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK > > Your message is being returned to you unprocessed because > it appears to have > already been distributed to the CCP4BB list. That is, a > message with identical &g

Re: [ccp4bb] CCP4 rotation convention

therwise I stand by everything I said! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle > Sent: 15 August 2007 10:47 > To: [EMAIL PROTECTED] > Cc: CCP4BB@jiscmail.ac.uk > Subject: RE: [ccp4bb] CCP4 rotation c

Re: [ccp4bb] Wasp web server

Be aware that WASP does not take into account symmetry-related atoms when analysing the co-ordination sphere of a potential ion; this becomes clear when you look at the source code (http://biochem.wustl.edu/~enrico/wasp.htm) & see that it only reads the ATOM & HETATM records from the PDB file, a

Re: [ccp4bb] Wasp web server

tting potential ligands then it's not going to make the correct identification! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle > Sent: 21 August 2007 17:25 > To: Jacob Keller > Cc: CCP4BB@jiscmail.ac.uk

Re: [ccp4bb] MSE

Phil, Now you've opened this can of worms I'd like to add phosphoserine, phosphothreonine & phosphotyrosine to the wish-list of things that look like amino-acids to me. So to extend Clemens' suggestion to cover all these: % egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb > sta

Re: [ccp4bb] How many twinned crystals?

In the past twinned crystals must have been much more frequent than published twinned structures because the traditional reaction of crystallographers to twinning has been either to find a way of inhibiting it or chucking the crystals in the bin and finding a non-twinned form. But I guess that's

Re: [ccp4bb] anisotropic scaling in refmac versions

I think this isn't a problem in the latest version of Refmac (0040 I think), so try downloading it from the York site. -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Alejandro Buschiazzo > Sent: 19 September 2007 13:20 > To: Lari Lehtio >

Re: [ccp4bb] arp/warp in p22121

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin > Sent: 18 September 2007 12:48 > To: [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] arp/warp in p22121 > > Dear Florian, > > ARP/wARP supports 65 space groups where pr

Re: [ccp4bb] arp/warp in p22121

I'm confused now, sticking to the IUCr convention should not require any axis permutation. My beef is specifically against unnecessary axis permutations! Surely it's when the program doesn't support the convention that you are forced to permute the axes? Besides I did solve a structure in P22121

Re: [ccp4bb] arp/warp in p22121

rthorhombic), and therefore any program which doesn't support that convention for any space group forces you to permute the axes completely unnecessarily. -- Ian > -----Original Message- > From: Sue Roberts [mailto:[EMAIL PROTECTED] > Sent: 19 September 2007 16:38 > To: Ia

Re: [ccp4bb] arp/warp in p22121

On second reading maybe I misunderstood what you were saying. If Phaser reads an MTZ file which doesn't conform to the convention (e.g. a<=b<=c NOT true in primitive orthorhombic) then it certainly should not by default permute the axes on output, I agree that that certainly would cause confusion.

Re: [ccp4bb] anisotropic scaling in refmac versions

ed Refmac 5.3.0037 to refine a structure. Is there a > problem with this version too? > Thank you in advance, > Madhavi > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Ian Tickle > Sent: Wednesday, September 19, 2007

Re: [ccp4bb] anisotropic scaling in refmac versions

turned on (even though it's the default) and there were no Bij's output. -- Ian > -Original Message- > From: Benini, Stefano [mailto:[EMAIL PROTECTED] > Sent: 20 September 2007 09:56 > To: Ian Tickle > Subject: RE: [ccp4bb] anisotropic scaling in refmac version

Re: [ccp4bb] arp/warp in p22121: what to do in Pointless

ie suppose you have a crystal which when indexed with a <= b > <= c and > Pointless decides unambiguously for the sake of argument) that the > axis along a is a 2-fold and the other two are 2(1) screws, ie space > group P 2 21 21. > > At present this will be reindexed

Re: [ccp4bb] Past CCP4 meeting on problem structures

Hi Bernhard You may be referring to the one I was involved in organising: http://epubs.cclrc.ac.uk/bitstream/946/DL-SCI-R28.pdf Cheers -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp > Sent: 26 September 2007 19:38 > To: CC

Re: [ccp4bb] R-sleep

The question is how significant is this bias, and is the cure (i.e. leaving out more reflections from the working set) worse than the disease? For refinements at 'medium' typical resolution (around 2.5 to 2 Ang) we are working with an observation/parameter count ratio of say < 3 (naturally I'm

Re: [ccp4bb] R-sleep

nal Message- > From: Peter Adrian Meyer [mailto:[EMAIL PROTECTED] > Sent: 01 October 2007 16:50 > To: Ian Tickle > Cc: ccp4bb@jiscmail.ac.uk > Subject: Re: [ccp4bb] R-sleep > > This raises a slightly tangential question though - how do we know how > what obs/param ratio is

Re: [ccp4bb] atomic FF used in SFALL

In any case it will become a Gaussian because presumably the atomic B's are added to the b terms for the density calculation? -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > Sent: 11 October 2007 09:26 > To: [EMAIL PROTECTE

Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

I like it! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > Sent: 09 November 2007 13:51 > To: Phil Evans > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's > > As I often say!!! T

Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

Merely encoding our state of knowledge of the space group into the file header doesn't introduce any additional constraint. The very fact that we are uncertain of the correct space group, whether or not that information is encoded, is already a constraint on what operations can be sensibly perform

Re: [ccp4bb] Malonate Crystals?

Hi Jacob, birefringence, the variation in refractive index depending on the direction of the plane of polarisation of the incident light has nothing to do with chirality, it's a consequence of anisotropy of the refractive index tensor, thus a crystal in any crystal system other than cubic may be bi

Re: [ccp4bb] Malonate Crystals?

Jacob, ITC vol A (5th ed), sect. 10.2 (pp 804-7) contains the full low-down on physical methods of detecting anisotropy & chirality of crystals (see sect 10.2.4 for optical properties). -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On

Re: [ccp4bb] Symmetry of crystallographic stereographic projections?

Hi Dirk There's a useable (though slightly incomplete) description of the symmetry of SRF's in the POLARRFN doc, though this only talks about the symmetry of the stereographic projection itself and then only about the effect of crystallographic dyads. Higher order rotations about z will obviously

Re: [ccp4bb] Symmetry of crystallographic stereographic projections?

symmetry-equivalent peaks that have some rule for > Phi, Psi, Kappa that includes a "Phi-180" term ... but this > is why I'm looking for a good reference ... > > Best regards, > > Dirk. > > Am 22.11.2007 um 15:10 schrieb Ian Tickle: > > >

Re: [ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs > Sent: 02 December 2007 10:07 > To: [EMAIL PROTECTED] > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rotation search using the Patterson in > a non-spherical neighbourhood of the o

Re: [ccp4bb] Rotation search using the Patterson in a non-spherical neighbourhood of the origin

> > Ian, > > I agree with your description, but not quite with your > conclusion. In the > original poster's problem one of the cell axes is so short > that at most a < 20 > Angstrom Patterson outer radius can be used in a > Patterson-based rotation > function. This will inevitably lead

Re: [ccp4bb] refmac5.3 vs refmac5.4

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis > Sent: 05 December 2007 13:45 > To: Jianghai Zhu > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refmac5.3 vs refmac5.4 > > > On Dec 5, 2007, at 14:05, Jianghai Zhu wrote: >

Re: [ccp4bb] CCP4 rotation convention

Hi Tilman That's great! Your derivation for the 'rotating axes' case is essentially the same as one I derived for myself and also agrees with that of Jorge Navaza (ITC Vol F, sect A13.2.1.1 p.273), but it's nice to have it all readily accessible on a webpage. BTW I note that you hide the full

Re: [ccp4bb] CCP4 rotation convention

rotations about *rotating* axes in the *fixed* observer frame of reference (same proviso applies). Hope I haven't thoroughly confused everyone, I think the bottom line here is: avoid the 'rotating observer' and 'rotating axes' ways of thinking about this, always keep the

Re: [ccp4bb] bond lengths, angles, ideality and refinements

Hi William & others, Indeed, phenix.refine uses cross-validation to optimise the scaling of the X-ray & B-factor weights. All I did was demonstrate that you can do essentially the same thing as phenix.refine but using Refmac instead. I don't claim to have done anything new, except I modified

Re: [ccp4bb] Perl

I'm rather surprised that is the complete explanation, for the simple reason that Perl (or any program for that matter) already inherits all the environment variables from the shell in which it is run, including PATH, CINCL, CLIBD_MON etc which would be needed to run pdbset, refmac etc. In fact so

Re: [ccp4bb] Spacegroup choices, reindexing and so on

Hi Manfred I agree with everything you say except the last bit about re-indexing! For those space groups with alternate settings, e.g. those with standard names C2 or P2221 or P21212, why is it necessary to re-index to the 'standard setting' when the data will have been already indexed correctly

Re: [ccp4bb] Spacegroup choices, reindexing and so on

Message- > From: Manfred S. Weiss [mailto:[EMAIL PROTECTED] > Sent: 21 January 2008 11:13 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on > > > Dear Ian, > > I thought that in cases of for instance P

Re: [ccp4bb] Spacegroup choices, reindexing and so on

!). Cheers -- Ian > -Original Message- > From: Pietro Roversi [mailto:[EMAIL PROTECTED] > Sent: 21 January 2008 11:10 > To: Ian Tickle > Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on > > Dear Ian, > I would agree with everyhtin

Re: [ccp4bb] ADP variance restriction in phenix

Hi Tim Sorry I can't help you with Phenix, I would just like to point out that from a theoretical standpoint it's very difficult to say a priori what the value of the ADP variance should be. Since the resolution is 2.4 I assume you're talking about isotropic ADP's. Essentially all of the contrib

Re: [ccp4bb] an over refined structure

Hi Sun Tang Unfortunately there's no such thing as a fixed value for the maximum acceptable Rfree-Rwork difference that applies in all circumstances, because the 'normal' difference depends on a number of factors, mainly the observation/parameter ratio, which depends in turn on the resolution a

Re: [ccp4bb] an over refined structure

have opinions on how many waters you expect to find at various resolutions. HTH -- Ian > -Original Message- > From: Sun Tang [mailto:[EMAIL PROTECTED] > Sent: 04 February 2008 22:32 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] an over refined s

Re: [ccp4bb] an over refined structure

When you say that "NCS is only a local, not global, crystal symmetry" what you actually mean is that "NCS is only a local not global *group* symmetry", i.e. NCS symmetry obviously *is* global if symmetry is defined (as in physics) as *any* operator which superposes (more or less) 2 copies of the mo

Re: [ccp4bb] counting constraints?

Peter, Bart Actually the restraint weight doesn't affect the restraint count one iota and as far as counting is concerned each restraint has exactly one 'vote' in the count. However there is an important proviso: the restraints must be completely independent to contribute fully to the count. Sup

Re: [ccp4bb] counting constraints?

Peter, Sorry I re-read your e-mail & realised you're asking a slightly different question from the one I answered. Of course you count the restraints in your structure, not the ones in the dictionary, so in the example you give there would be 4 not 1. Each bond, angle, torsion, VDW contact, B-fa

Re: [ccp4bb] counting constraints?

; From: Bart Hazes [mailto:[EMAIL PROTECTED] > Sent: 14 February 2008 18:32 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] counting constraints? > > > Thanks Ian, > > I saw experimental observations and restraints (empirical > observations) &

Re: [ccp4bb] counting constraints?

on. HTH! -- Ian > -Original Message- > From: Meyer, Peter [mailto:[EMAIL PROTECTED] > Sent: 14 February 2008 23:04 > To: Ian Tickle > Subject: RE: counting constraints? > > Ian, > > Thanks for the quick answers. > > > > different question f

Re: [ccp4bb] counting constraints?

[mailto:[EMAIL PROTECTED] > Sent: 14 February 2008 19:09 > To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] counting constraints? > > The point where this restraint discussion regarding > counting of restraints seems to become murky imho, is when > it comes to &#

Re: [ccp4bb] polarrfn, pltdev

Hi Thomas I normally run pltdev on the whole map, did you try that? There may be a problem just plotting one section because I think it may rescale the SRF values to the origin value on the first section, so if that happens to be zero on the kappa=180 section you'll get division by zero. The ori

Re: [ccp4bb] changing names of many files

Beware that 'rename' on Fedora/Redhat and the like works differently from 'rename' on Debian/Ubuntu etc. Both are in /usr/bin but the former is an executable and the latter is a Perl script (it's apparently installed with Perl), and is probably descended from your 'rename-alot' (the syntax appears

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