Re: [ccp4bb] the f' and f'' of heavy cluster

these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

. -- 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] Off-topic: Best Scripting Language

Medical Scientist Training Program email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu *** -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

It is dual bootable Linux/Windows George On 11/20/2012 05:56 PM, William Scott wrote: Presumably then it was running Linux? On Nov 20, 2012, at 7:39 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: I have never understood why Macs are so popular, although in this part

Re: [ccp4bb] Fwd: Re: [ccp4bb] The information of shelxc_fa.lst

. Can you give me a short introduction about the 'mult' indicates and the rule of peaks selection? Thank you very much! Best wishes! Ding wei -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

Re: [ccp4bb] a challenge

a solution is in place. Neither would make an excellent macromolecular crystallographer by necessity. Tassos -- 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] statistics from a structure factors file

9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu -- 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] x86-64

Is it possible to set compile flags to produce something (.o) which will link with th distributed libraries, and produce an executable which will run on other (32-bit) Linux machines? In the mean time, I'm doing a complete source build on the 64-bit machine Phil -- Prof. George M. Sheldrick FRS

Re: [ccp4bb] fromm .fcf to .map for coot

=660600bcd=EMAILFOOTERAVERAGE -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582

Re: [ccp4bb] MTZ to Shel-X?

back to the BB. Kevin George M. Sheldrick wrote: Dear Ian, It is all part of a diabolical CCP4 plot to make it as inconvenient as possible to move from a REFMAC refinement to SHELXL! I hope that i do not get excommunicated like DVD for this comment

Re: [ccp4bb] MTZ to Shel-X?

Martyn Winn wrote: Yes, there is: C input FP(+) IF(LOOKUP(23).GT.0 .AND. IFSQ.NE.0) + SCCHK = 9.00/(RANGES(2,LOOKUP(23))* RANGES(2,LOOKUP(23))) C IF (SCAL.GE.SCCHK .AND.IFSQ.NE.0) SCAL = SCCHK IF(IFSQ.NE.0) WRITE(6,'(/,a,/,a,F8.4,/)') + ' *** You are

Re: [ccp4bb] refmac vs shelx refinement

SHELX does not need a parameter to control the relative weights of restraints and X-ray data, it is performed automatically. However you can change the restraint esds, either individually or globally using DEFS, though the default values are generally OK. There is bound to be some difference

Re: [ccp4bb] ccp4 pdb format

need to edit the .pdb file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 20 Mar 2007, yang li wrote: Hi: Now I need to input a heavy atom pdb

Re: [ccp4bb] shelxl, refinement of occupany

that after all your emails on the subject you still can't spell 'SHELX'! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 21 Mar 2007, U Sam wrote: I

Re: [ccp4bb] Scale factor in ccp4

A less convoluted method is to read both .sca files into xprep, scale them together and write out the combined .sca file. George 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

Re: [ccp4bb] MAD and twinning

. Even if you get the same twin fraction for each wavelength independently and the merging R-index is not too bad, they could still be indexed inconsistently! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel

[ccp4bb] SHELX Workshop at ACA Meeting

George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582

Re: [ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 15 Jun 2007, U Sam wrote: Deliang, That's right, coot closes if you want to open map from shelxpro which

[ccp4bb] conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format

I understand that when Coot reads the .fcf file it makes SigmaA weighted maps, i.e. 2mFo-DFc and mFo-DFc. These are the maps you should usually be looking at during the refinement. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4

Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

You can use SHELXPRO to generate ligand restraints, reading in the ligand from the CSD or as a SHELX file (which if necessary can be generated from a PDB file using SHELXPRO). You may have to add some extra restraints by hand (e.g. FLAT, CHIV). George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] Linux Crystallography PC with Core 2 Duo CPU?

location with SHELXD) or different solvent content (density modification with SHELXE). Several GUIs already do this automatically. Molecular replacement programs (and Refmac) would be good candidates for exploiting multiple CPU machines! George Prof. George M. Sheldrick FRS Dept. Structural

Re: [ccp4bb] difference density ripples around Hg atoms

refines against the native data and so does not see the mess. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Wed, 1 Aug 2007, Bart Hazes wrote: Hi Klemens

Re: [ccp4bb] PDB format survey?

format also has no answer yet to this problem, maybe the same solution could be found for both MMCIF and CIF?! Best wishes, George 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

Re: [ccp4bb] SAD: Refine against anomalous data

separately. There is a suitable option in SCALA and SADABS and possibly in other scaling programs as well. Best wishes, George 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

Re: [ccp4bb] The importance of USING our validation tools

to the request for the essential experimental evidence, i.e. the raw diffraction data, to be produced. Protein crystallography is an experimental science just like any other, even if the results it produces usually stand the test of time better. George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] The importance of USING our validation tools

Dominika is entirely correct, the F and (especially) sigma(F) values are clearly inconsistent with my naive suggestion that columns could have been swapped accidentally in an mtz file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4

Re: [ccp4bb] The importance of USING our validation tools

PS. A completely unimportant correction to my comment on the MolProbity output for 2HR0: every residue is indeed an outlier in at least one test, but in three cases it is only the CB-deviation test, not the other three tests that I mentioned. George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] The importance of USING our validation tools

Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sun, 19 Aug 2007, Alexander Aleshin wrote: I do not think the small molecule approach proposed by George Sheldrick

Re: [ccp4bb] Posting again: Is the H-bond length in CYS.cif library correct?

For what it is worth, SHELXL sets the S-H distance to 1.20A. As with other bonds to hydrogen, this allows for apparent shortening to fit the electron distribution and also librational effects. An S-H distance determined by neutron diffraction would be longer. George Prof. George M. Sheldrick

Re: [ccp4bb] Strange diffraction images

and EVALCCD are able to integrate such diffraction patterns and SADABS is able to scale them. However the case in point is probably commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

Re: [ccp4bb] Strange diffraction images - PS

: http://www-xray.fzu.cz/jana/Jana2000/jana.html However the case in point is probably commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582

Re: [ccp4bb] How many twinned crystals?

most of the discussion in this list has been about merohedral twins so far. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 31 Aug 2007, Ian Tickle wrote

Re: [ccp4bb] How many twinned crystals?

Crystals with messy spots smeared out in one direction with sometimes more than one maximum are probably better described as split crystals rather than twins, but if the splitting of the spots is clear enough the same procedures can be used to integrate them. George Prof. George M. Sheldrick

Re: [ccp4bb] just how bad can phases be and still help

. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sat, 8 Sep 2007, Dunten, Pete W. wrote: Here's one - FOM 0.5 after shelxe, SAD phases, not traceable Lots

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

understands 413 different space groups! Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 24 Sep 2007, Phil Evans wrote: I think

Re: [ccp4bb] Rfree statistics in SHELXL

resolution shell you may only about 100 reflections in your free R set, so the free R value will have a very large esd and so could be misleading. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39

Re: [ccp4bb] Rfree statistics in SHELXL

Boaz, If you had used the U option in SHELXPRO to update from .res to .ins the free R should have been included in the deposition PDB file by the B option! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany

Re: [ccp4bb] torsion restraints and phi/psi

three programs in their current rather primitive form does not prevent one from getting plenty of Ramachandran outliers, so the Ramachandran plot is still a good diagnostic tool. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077

Re: [ccp4bb] coot: Show Symmetry

line. An elegant way around this problem is to read the .res file from SHELXL into Coot instead, or you can edit the CRYST1 line in the .pdb file. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

server is an excellent source of ligand geometries and restraints for such refinements. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 17 Dec 2007

Re: [ccp4bb] SHELEX .pdb and .res output and MLPHARE HA file

In this case I would recommend searching for more Se atoms, e.g. FIND 6 or 8 for SHELXD. If you then input the results into SHELXE (or are using these programs via hkl2map) you do not need use MLPHARE as well. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University

[ccp4bb] SHELX reference

not expect anyone to actually read it, but for those who wish to do so, it is available as Open Access at: http://journals.iucr.org/a/issues/2008/01/00/issconts.html George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen

Re: [ccp4bb] Sulfate ion on 2-fold axis

(in any space group), this can be very useful for high-resolution refinements. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 11 Jan 2008, Charlie

Re: [ccp4bb] Python 3.0 breakage

That's interesting. I'm glad that I am still using FORTRAN; SHELX-76 still compiles and runs unchanged with any modern FORTRAN compiler. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

[ccp4bb] an over refined structure

the geometric restraints we increase p, which then leads to a larger 'allowed' R-factor ratio! Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582

Re: [ccp4bb] Announcement: two crystallographic wikis

of work. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 7 Feb 2008, Kay Diederichs wrote: Dear all, I want to bring two crystallographic

Re: [ccp4bb] xprep vs shelxc

them as required. XPREP does lots of other things that can be useful for experimental phasing, e.g. space group determination, merging data, twinning detection and anisotropic scaling. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4

[ccp4bb] SHELX precompiled binaries

! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582

Re: [ccp4bb] MTZ cell troubles after sortmtz reindexing from P321 to C2

inputting unmerged data in such cases! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Fri, 7 Mar 2008, Pietro Roversi wrote: Dear all, after much

Re: [ccp4bb] Missing reflections

. This will in general improve the appearence of the map at the cost of introducing a little model bias. As far as I know these 'unobserved' reflections are not used in calculating the difference map. CNS is probably like SHELXL, I'm not sure what phenix.refine does. George Prof. George M. Sheldrick FRS

Re: [ccp4bb] [phenixbb] Rant: B vs TLS, anisou, and PDB headers

. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Sat, 29 Mar 2008, Pavel Afonine wrote: Hi Frank, Hi Frank, All your reasons

Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5

that since this is a Wiki, users are encouraged to contribute! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 3 Apr 2008, U Sam wrote: How one can fix

Re: [ccp4bb] Arp/warp space group P 21 2

SHELX has been able to handle P 21 2 21 and other such space groups without any problems for the last 38 years! George 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

Re: [ccp4bb] Coot and Hs

I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077

Re: [ccp4bb] program for distribution of distances

to the much more recent Microsoft program with the same name). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 24 Jun 2008, harry powell wrote: Hi

Re: [ccp4bb] Refmac unrestrained refinement on ligands only

are B-value dependent distance and other restraints, so they are tighter if the B-values are higher and vice versa. George 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

Re: [ccp4bb] question on scalepack

An easy way is to start XPREP, then give the name of the .sca file when prompted for a datafile, and hit Enter several times until the table of statistics appears. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen

Re: [ccp4bb] Using multiple crystals for structure solution in P1 using MAD/SAS/SAD

but am getting lazy and senile. Best wishes, George 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 On Wed, 23 Jul 2008, Bram Schierbeek wrote: Hi Hari, I have

Re: [ccp4bb] Acorn question

shelxe can do a pretty good imitation of Acorn (amongst other things) and is kinder to your computer. George 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 On Wed

Re: [ccp4bb] convert and direction cosines

If you are desparate, XPREP can apply symmetry transformations to direction cosines (assuming that they are defined according to the (1976) SHELX convention, i.e. relative to the crystal reciprocal axes). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University

Re: [ccp4bb] Wilson plot from truncated.mtz

Ian, SHELXL users would also be very happy if mtz files routinely contained F^2 and its esd, but I had long regarded this as a lost cause. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

[ccp4bb]

. There are also some new powerpoints on crystallographic methods and pdfs of selected recent papers. George 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] Wilson plot from truncated.mtz

negative because of experimental errors) avoids this problem but we still need F(obs) (and hence TRUNCATE) to calculate a map. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax

Re: [ccp4bb] Wilson plot from truncated.mtz

Dear Ian, I agree entirely about the k-curve approach. SHELX/S/C/D/E have always used it to derive E-values. Best wishes, George 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

Re: [ccp4bb] how to calculate the occupancy of two Mixed ligand binding modes at the single active site

SHELXL has been able to refine such occupancies (e.g. as p and 1-p for the two ligands, i.e. one extra parameter) for many years, and if I have understood correctly last week's version of phenix_refine can do so too. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University

Re: [ccp4bb] Wilson plot from truncated.mtz

on the refinement will be to reduce all B-values a little, i.e. it will lead to a biassed model. This is of course a purely theoretical discussion, there is no need for anyone to retract their published structures. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University

Re: [ccp4bb] program to rotate atoms with anisotropic B factors

crystallographer who happens to have it. George 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 On Wed, 10 Sep 2008, Pavel Plevka wrote: Dear all, I am looking for a program

Re: [ccp4bb] Non-integer epsilons for rotation axes.

I think that you are looking for A.J.C. Wilson, Acta Cryst. 17 (1964) 1591-2. George 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 On Wed, 17 Sep 2008, Ian

Re: [ccp4bb] disulfide bonds, SE sample, and Xray absorption edges

. This will produce an analysis of the anomalous density at the sites that you inputted and a list of peaks in the anomalous map. I also suggest that you look at the anomalous density by feeding the .pha file from SHELXE (generated if -b is set) into e.g. Coot. George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] Scaling of intensities

compromising them in any way, but I appreciate that I am in a small minority. George 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 On Fri, 7 Nov 2008, Andy Torelli wrote

Re: [ccp4bb] Scaling of intensities

, and may depend more on the technical details of the refinement program you are using. Best wishes, George 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 On Fri, 7 Nov

Re: [ccp4bb] meaning of R free of perfect twin

. A disadvantage is the the maps may not be quite as good as when the free R reflections are selected randomaly. George 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 On Mon, 8

Re: [ccp4bb] R pim and Rmeans

When discussing this issue, perhaps we should not lose sight of the fact that the statistics behind Rp.i.m. assume 'independent observations'. Surely doing more than one rotation about the same axis is likely to repeat the same systematic errors? George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] updated XDS binaries available

Is it really essential to force users to update XDS every four months, especially when No other changes were made to the binaries? George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068

Re: [ccp4bb] indexing choice for C2

A safe approach is to integrate in P1 and let XPREP sort it out. George 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 On Sat, 13 Dec 2008, Peter Zwart wrote

Re: [ccp4bb] OT - Software articles / databases

I am equally upset by the fact that citations in the supplementary material tend not to get into the citation indices, though it is not quite so bad for SHELX because it tends to be cited in less prestigeous journals that make less use of supplementary material! George Prof. George M

Re: [ccp4bb] unstable refinement

. A stable refinement in which R decreases but Rfree goes through a minimum and then starts to rise might be a useful indication of overfitting?! Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49

Re: [ccp4bb] Importance of low order reflections?

reflections (especially if the home system has a kappa or three-circle goniometer) and may well be measured more precisely at low resolution, as well as suffering much less from radiation damage. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4

Re: [ccp4bb] Refmac5 - high res (1.2A) refinement problem

It would be possible to model all of that with SHELXL, but it is a complex problem and would need time and patience with any program. One advantage of SHELXL would be the flexible refinement of occupancies for the different conformations. George Prof. George M. Sheldrick FRS Dept. Structural

Re: [ccp4bb] .phs file conversion

Bram, If you use the beta-test autotracing SHELXE, the .pdb file containing the poly-Ala trace also contains the space group. You presumably meant that the space group is missing from the SHELXL and SHELXD .pdb files, but of course you can read the .res files into Coot. George Prof. George M

Re: [ccp4bb] restraints for 4Fe4S in shelxl

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 On Wed, 11 Mar 2009, Guenter Fritz wrote: Dear All, I am looking for a set of suitable restraints for 4Fe4S clusters in shelxl

Re: [ccp4bb] fake images

with the ca. 50% of the structure that is rather poorly modeled - the 'solvent' region. Best wishes, George 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 On Fri, 20

Re: [ccp4bb] fake images

the frames, but it will surely make fraud more difficult to detect! George 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 On Fri, 20 Mar 2009, George M. Sheldrick wrote

Re: [ccp4bb] Structure idealisation Refmac_5.5.0072

Dear Ian, If one has sufficiently high resolution data, full matrix refinement with SHELXL might be the best way to get real convergence. The installation of the program also converges faster (zero dependence!). Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry

Re: [ccp4bb] chiral volume target value

)); if there is a D-Ala in the structure as well: CHIV_DAL 29 CA (i.e. -1*fv(3)). I think that I will have to add all this to Kay's Wiki. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

scattering increases the noise at lower resolution, which is less serious. George 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 On Wed, 22 Apr 2009, Gerard

Re: [ccp4bb] Charge flipping.

) native data, the data are much less borderline and charge flipping in P1 is a good way to explore phase space. George 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] Charge flipping - PS.

than when you are just searching for peaks. George 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 On Mon, 24 May 2010, George M. Sheldrick wrote: I have also played

Re: [ccp4bb] Recommendations for (linux) crystallography workstation, server?

computing developments, but have more important ways of spending our time! George (with much help from Tim) 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 On Thu, 3

Re: [ccp4bb] Computing hardware

why they were not full yet ... George 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 On Fri, 4 Jun 2010, David Schuller wrote: Regarding computer hardware choices

Re: [ccp4bb] Not a Job Advertisement

Atul, Your space group and cell are rather inconsistent, maybe if you fixed them it would help. If it is really trigonal, it could be merohedrally twinned, I think that REFMAC can now handle that automatically. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University

Re: [ccp4bb] Impact Factor of Acta Crystallographica A is 49.9

reference for Ton's CIFCHECK program that is almost universally used for checking small molecule refinements before deposition). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax

Re: [ccp4bb] Crystal growth time lapse movies.

Dear David, You are welcome to use this movie from our homepage: http://shelx.uni-ac.gwdg.de/xtal/xtal.htm#xtalgrowth Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068

Re: [ccp4bb] cphasematch

shelxe by using the beta-test version that does iterative main-chain tracing (available by sending me an email while I am still developing it). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39

Re: [ccp4bb] process data in R32

programs do it this way already, but unfortunately there are still a few black sheep. George 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 On Thu, 12 Aug 2010, Phil

Re: [ccp4bb] Heavy atom sites?

to break the enantiomer ambiguity. MAD and SIRAS will in general behave like SAD. However if your isomorphous difference is large and the anomalous signal is lost in the noise, they might be dominated by it and so tend to behave more like SIR. George Prof. George M. Sheldrick FRS Dept. Structural

Re: [ccp4bb] Heavy atom sites?

have to be inverted at a point that is not at the origin (e.g. x, y, z - 1-x, 0.5-y, 0.25-z for I4122). Fortunately SHELXE and some other programs know this and apply the correct inversion automatically. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen

Re: [ccp4bb] Local real-space refinement by phenix

, as in fact most users do. 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 On Wed, 25 Aug 2010, Hailiang Zhang wrote: Hi there: As I understand, phenix.refine do real

Re: [ccp4bb] Fd-3m with pdbset

, alternative settings, specified in IT or not, cause no problems. But then we would not have had this thread (or the H3/R3 and P21221 threads). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021

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