Re: [ccp4bb] Intensities and amplitudes

am.ac.uk > > On 1 Dec 2014, at 20:49, Mohamed Noor wrote: > >> Dear crystallographers >> >> Is there any reason for using one data type over the other? Are there any >> errors associated with the French and Wilson I-to-F conversion step? >> >> Thanks. &

Re: [ccp4bb] Refinement of Iron-sulphur clusters

edistribute/work the dictionaries sent then we would > be happy > (please email off-list). > > Dr Oliver Smart > Director SmartSci Limited http://www.smartsci.uk/ > & Consultant Global Phasing Ltd http://www.globalphasing.com/ > -- 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] the f' and f'' of heavy cluster

f''10.5. The autosharp result said 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] observed criterion sigma

in the "Observed criterion sigma" value >> required during pdb deposition. Does it depends on the methods of data >> integration and scaling ? if yes then what are the values for the data >> processed through scalepack2mtz (HKL2000) and scala (mosflm).. >> >>

Re: [ccp4bb] statistics from a structure factors file

astiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >&g

Re: [ccp4bb] a challenge

iven some crystals can derive the best strategy to collect >>> data, >>> process the data optimally, derive phases using all available >>> information, build a model and refine it in such a way that it best >>> explains both data >>> and geometrical exp

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

biased so that the high peaks > are chosen more often... > It seem that the Patterson peaks are selected randomly.So I am very > confused. > Can you give me a short introduction about the 'mult' indicates and the > rule of peaks selection? > Thank you very much! > Best

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" > wrote: > >> I have never understood why Macs are so popular, although in thi

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

strikes me as a bit dangerous. >>> >>> --Bill Scott >>> >>> >>> >>> >>> >>> William G. Scott >>> Professor >>> Department 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, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582

Re: [ccp4bb] Off-topic: Best Scripting Language

*** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu <mailto:j-kell...@northwestern.edu> > *** -- Prof. George M. Sheldrick FR

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

du.au | >> > > LEGAL NOTICE > Unless expressly stated otherwise, information contained in this > message is confidential. If this message is not intended for you, > please inform postmas...@ccdc.cam.ac.uk and delete the message. > The Cambridge Crystallographic Data Centre is a company Limited > by Guarantee and a Registered Charity. > Registered in England No. 2155347 Registered Charity No. 800579 > Registered office 12 Union Road, Cambridge CB2 1EZ. > -- 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] Refmac and metal on a two-fold?

) from > the corresponding symmetry element. If for whatever reason the atom > shifts, the vdw will push it out. Why would such atoms shift varies - I > suspect in some cases it is due to hydrogen bonding restraints, in > others it could be due to noisy density. > > > >

[ccp4bb] [gsheldr: Re: [ccp4bb] phaser openmp]

-- 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 --- Begin Message --- In my experience, writing efficient multithreaded code is much harder than writing

Re: [ccp4bb] about .ins file for SHELXD

procedure involves > the elimination of the 'wrong' atoms'  which I don't fully understand, should > the following nums be bigger than the total num of atoms in one unit cell? > > Thanks in advance! > > Lu > -- 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] Crystalization in low PH

and compare the differences between > the crystals in regular PH and low PH. > > I was wondering how people set up the boxes in low PH, as usual buffers are > mostly less acidic. > > Regards > > Sam > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, Unive

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

guys opened my eyes about a series of issues that I should learn > about and approach, I'm most thankful for that. > Best regards, > Napo > > > > -- > Prof. Sergei V. Strelkov > Laboratory for Biocrystallography > Department of Ph

Re: [ccp4bb] atomic scattering factors in REFMAC

ement? It looks a bit strange, > because > the numbers of electrons are different. Or decreasing in number of > electrons is compensated with significant decrease in atom size (that can > have the same effect as Bf lowering)? With Bf=0 the difference in curves > is >

Re: [ccp4bb] Archiving Images for PDB Depositions

gt; to > > the pulldown menu! > > > > Best Regards, > > > > Jacob Keller > > > > -- > > *** > > Jacob Pearson Keller > > Northwestern University > > Medical Scientist Training Program > > email: j-kell...@northwestern.edu > > *** > > > > > P please don't print this e-mail unless you really need to > Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > Department of Biochemistry (B8) > Netherlands Cancer Institute, > Dept. B8, 1066 CX Amsterdam, The Netherlands > Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 > > > > -- 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] PDB header info wrong.

; > > > - -- > - -- > 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/ > > iD8DBQFOql4OUxlJ7aRr7hoRAurhAKCFuKzPjt9uGKlg38/PlIPvEYyK0QCfW3r5 > uOugyeB1TLn8WBjI5cHz66Q= > =72lY > -END PGP SIGNATURE- > -- 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] IUCr committees, depositing images

> > Dr. Martin Martinez-Ripoll > Research Professor > xmar...@iqfr.csic.es > Department of Crystallography & Structural Biology > www.xtal.iqfr.csic.es > Telf.: +34 917459550 > Consejo Su

Re: [ccp4bb] IUCr committees, depositing images

;> missing reflections.  I also heard this issue mentioned before but was > >>>>> always too lazy to actually pursue it. > >>>>> > >>>>> So. > >>>>> > >>>>> The role of the test set is to prevent overfittin

Re: [ccp4bb] Ice rings... [maps and missing reflections]

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] change of origin for reflections or map

thanks for your help, > > Klaas Decanniere -- 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] Ramachandran Restraints in refmac

el? > > best, > -- 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] Linux vs MacOS for crystallographic software

s Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > Johns Hopkins Malaria Research Institute > 615 North Wolfe Street, W8708 > Baltimore, MD 21205 > Office: +1-410-614-4742 > Lab: +1-410-614-4894 > Fax: +1-410-955-2926 > http://web.mac.com/bosch_lab/ > > > > > -- 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] Direct method solution at 1.15A

; 20sigma) > And a tightly bound phosphate (P peak around 22sigma) > Could I try and solve this directly or is it crazy idea? > If so what program should I try? > > thanks > Yuri > > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tam

Re: [ccp4bb] 64-bit CCP4

; 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] Windows 7 and Xtal Software

so clean? Was it > something about the punch cards? > > Jacob > > On Mon, Aug 29, 2011 at 12:29 PM, George M. Sheldrick > wrote: > > The current SHELX binaries (including the beta-test multi-CPU SHELXD) all > > appear to run fine under Windows 7. There is no nee

Re: [ccp4bb] Windows 7 and Xtal Software

web interfaces). > > -Nat -- 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] [CCP4]data processing I222 vs pointless I121

d orthorhombic > (Cell: 104.1 108.6 264.890 90 90) > The crystal system chosen for output is body-centred monoclinic > (Cell: 104.1 108.6 264.890 90 90) > > I couldn't see the difference between I222 and I121. May I ask do I need to go >

Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases

1 at 09:46:37AM +0200, George M. Sheldrick wrote: > Dear Jacob, > > Andrea Thorn and I will be demonstrating such a program (called AnoDe) at > the Software Fayre at the IUCr Meeting in Madrid and it is already available > from my beta-test site on email request. AnoDe requires only

Re: [ccp4bb] Map Using Both Bijvoet and Dispersive Differences with Model Phases

hwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: 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 or -3068 Fax. +49-551-39-22582

Re: [ccp4bb] Problem running shelxC/D/E

2697, USA > Tel: 949-824-4322(or -1953); Fax: 949-824-3280 > email: h...@uci.edu > -- 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] Milestones in Crystallography

ere some new scientific findings about the structure of > inclusion bodies... > So, news and milestones from the crystallography for a really hard PhD test > are > wellcome! > > Thanks in advance! > > Best regards, > > Lena -- Prof. George M. Sheldrick FRS Dept. Struc

Re: [ccp4bb] non-waters among structured solvent atoms

t; >>>>> Wolfram Tempel > >>>> > >>> > >>> > >>> > >>> -- > >>> Dr Stephen Graham > >>> 1851 Research Fellow > >>> Cambridge Institute for Medical Research > >>> Wellcome Trust/MRC Building > >>> Addenbrooke's Hospital, Hills Road > >>> Cambridge, CB2 0XY, UK > >>> Phone: +44 1223 762 638 > >>> > >> > >> > >> > >> -- > >> *** > >> Jacob Pearson Keller > >> Northwestern University > >> Medical Scientist Training Program > >> cel: 773.608.9185 > >> email: j-kell...@northwestern.edu > >> *** > >> > > > > > > -- > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: 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 or -3068 Fax. +49-551-39-22582

Re: [ccp4bb] low res. SAD phasing

inland > >>Tel. +358-9-191 58903 > >>Fax +358-9-191 59940 > >> > > > >-- > >-- > >Tim Gruene > >Institut fuer anorganische Chemie > >Tammannstr. 4 > >D-37077 Goettingen > > > >GPG Key ID = A46BEE1A > > > > Tommi

Re: [ccp4bb] Unit cell change - was Re: [ccp4bb] XDS question

>The following links are the images: > > > >http://www.facebook.com/photo.php?fbid=2127189780277&set=o.1363238963856 > >79&type=1&theater > > > >http://www.facebook.com/photo.php?fbid=2127189180262&set=o.1363238963856 > >79&type=1&theater >

Re: [ccp4bb] Anomalous substructure solution at data with 37% completeness

adequate. A better comparison would be with small molecule direct methods, where structures are frequently solved (e.g. with shelxd) with less than half the data by chemists impatient to see if they have synthesized the right compound. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry

Re: [ccp4bb] SHELXL/ BAVERAGE

Dear Fatima, Thanks. I am anyway planning to allow chain identifiers in the next version of SHELXL. 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

Re: [ccp4bb] I/sigmaI of >3.0 rule

Dear Boaz, You are quite correct, 'latter' and 'former' need to be switched in my email. Apologies to CCP4bb for the confusion caused! Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen,

Re: [ccp4bb] I/sigmaI of >3.0 rule

is much larger than the former, maybe you are including a lot of weak data. Similarly in calculating merging R-values, most programs replace negative intensities by zero, again avoiding the problems you describe. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, U

Re: [ccp4bb] I/sigmaI of >3.0 rule

different for centrosymmetric space groups: very weak AND very strong reflections (relative to the average in a resolution shell) are much more common! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39

Re: [ccp4bb] Teaching powerpoints

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] Do carbon scattering include hydrogen

(at very high resolution) they can be seen in the difference map. Adding the electrons to the C, N or O atoms is not a good idea. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39

Re: [ccp4bb] Mg2+ or water

that it is in German (like most of our teaching). 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 Tue, 21 Dec 2010, Ian Tickle wrote: > Note that the o

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

is probably the most serious known 'bug' in SHELXL, but is proving rather difficult to eliminate completely. 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] Fwd: [ccp4bb] Wyckoff positions and protein atoms

molecule crystallography. I agree that the use of orthogonal rather than crystal coordinates can obscur the situation, e.g. for an atom on a threefold axis. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

lies on the center of symmetry). Occupancies are often tied to free variables which would also complicate any changes to the code. And in any case, SHELX has been upwards compatible for the last 35 years and I wish it to remain that way. Best wishes, George Prof. George M. Sheldrick FRS Dept

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

s has an occupancy of 1.0) and this has caused considerable confusion in the small molecule world ever since; atoms are frequently encountered on special positions in inorganic and mineral structures. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tamma

Re: [ccp4bb] partial hydrogen refinement.

you can very easily see in a difference map (e.g. with COOT) if there is density near their expected positions. 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] relationship between B factors and Koff

years. One factor that can affect the results is that if the ligand isn't there, something else (e.g. water) probably is. 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. +4

Re: [ccp4bb] bruker smart and mosflm

x27;s book page 424. Unlike MOSFLM, SAINT can integrate non-merohedral twins handling the reflection overlap properly and can process phi scans for which the oscillation axis is not perpendicular to the incident beam. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, Universi

Re: [ccp4bb] limit for number of files for CAD...

I think that XPREP would also be suitable for the purpose, but is limited to 99 input files. 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, 4 Nov

Re: [ccp4bb] SHELX as model building

(e.g. S-SAD or a MR solution for a small fraction of the structure, as in Arcimboldo where it starts from a couple of alpha-helices) and the resolution of the native data is about 2.5A or better. For details of how it works, see Acta Cryst. D66 (2010) 479-485 (open access). George Prof. George M

Re: [ccp4bb] Bug in c_truncate?

Tim, Although I always like to advocate XPREP, that would not work because the .sca format - most unfortunately - does not know about free R flags. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551

Re: [ccp4bb] Against Method (R)

lding and correction, but the final refinement should be performed in reciprocal space. 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 Fr

Re: [ccp4bb] Against Method (R)

Not quite. I was trying to say that for good small molecule data, R1 is usally significantly less than Rmerge, but never less than the precision of the experimental data measured by 0.5*/ = 0.5*Rsigma (or the very similar 0.5*Rpim). George Prof. George M. Sheldrick FRS Dept. Structural

Re: [ccp4bb] Against Method (R)

). Rpim gives similar results to R(sigma), both attempt to measure the precision of the MERGED data, which are what one is refining against. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or

Re: [ccp4bb] molecule on symmetry axis

or example it allows hydrogens to be generated correctly and suppresses unwanted anti-bumping restraints. 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, 16

Re: [ccp4bb] molecule on symmetry axis

something that it would be nice to have in phenix or refmac too. 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, 15 Oct 2010, Jacqueline Vitali wrot

Re: [ccp4bb] Twinned data

roups. 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, 1 Oct 2010, Clayton, Gina Martyn wrote: > Hi there > > Just wondering if anyone has a

Re: [ccp4bb] Deposition of riding H

s, if AFIX 137 hydrogens are not deposited, they cannot be regenerated except by a full refinement against the experimental data. 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. +4

Re: [ccp4bb] Deposition of riding H

a files or libraries, and FORTRAN will always be FORTRAN, the deposition of these two files would be sufficient to define the refinement for posterity. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Te

Re: [ccp4bb] Deposition of riding H

involving hydrogens are useful. 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 Tue, 14 Sep 2010, Dr. Mark Mayer wrote: > Here's one for the communit

Re: [ccp4bb] Fd-3m with pdbset

g the space group symmetry using the symmetry operators, 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

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

rectly, 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 understan

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 Goettin

Re: [ccp4bb] Heavy atom sites?

le 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. Struc

Re: [ccp4bb] process data in R32

problem. I know that many 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

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] 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] attachments

troubled by viruses or large attachments. 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, 2 Jul 2010, Ed Pozharski wrote: > pine is quite handy if you

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

/ (it is a standard 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. +49-551-3

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 of

Re: [ccp4bb] Computing hardware

wondering 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 comp

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

odern 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 T

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 pla

Re: [ccp4bb] Charge flipping.

ution (say 0.9A) 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. +49-55

Re: [ccp4bb] problems with hydrogen names in PDB file from Shelx refinement

asily regenerate them, e.g. using MolProbity. This workaround also sidesteps the RCSB cheking the chirality of the CH2-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

Re: [ccp4bb] lossy compression of diffraction images

e data transfer rates could be rather slow. SHELXL and some of my other programs can still read these 'condensed data'. 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] software to represent raw reflections in hkl zones

would be necessary to apply it to your data. Although intended for - and widely used by - small molecule crystallographers this should work equally well for macromolecules. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen

Re: [ccp4bb] chiral volumes--2nd try

For CB_ILE, the chiral volume sign in the REFMAC monomer library is the same as used by SHELXL, not the opposite as stated in my last posting. Apologies! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel

Re: [ccp4bb] chiral volumes--2nd try

Note that the RTAB instuction in SHELXL can be used to print out chiral volumes without specifying the three bonded atoms, they are taken from the connectivity table. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D3707

Re: [ccp4bb] chiral volumes--2nd try

use other conventions (e.g. the Cahn-Ingold-Prelog rules). 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, 19 Apr 2010, Bernhard Rupp wrote: > &q

Re: [ccp4bb] Phasing statistics

orge 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, 14 Apr 2010, MARTYN SYMMONS wrote: > I agree this is very interesting - > > The 'real' F

Re: [ccp4bb] Phasing statistics

to calculate it at all. By chance a paper "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification" has just appeared as Open Access: Acta Cryst. D66 (2010) 479-485. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goetting

Re: [ccp4bb] R merge and R init

be given 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, 24 Mar 2010, Muhammed bashir Khan wrote: > Dear All; > > I have a crystal

Re: [ccp4bb] self rotation education

the self-rotation function was spectacular. 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, 22 Mar 2010, Eleanor Dodson wrote: > I absolutely ag

Re: [ccp4bb] anomalous difference fourier maps

ateful for all the support we get. In particular, we should not underestimate the unique role CCP4bb plays in crystallographic education. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or

Re: [ccp4bb] tls problem in C2221

Maybe it was a bit early to turn on TLS. Pseudomerohedral twinning of a P21 crystal with a and c approximately equal often looks like C2221 with an appropriate transformation of the axes, that could explain the high R-values. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry

Re: [ccp4bb] Distinguishing Between Na+ and H2O

(or two anions) that are close to each other should not have an occupancy sum greater than unity. 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 T

Re: [ccp4bb] reforigin on 2FKA

prefer. 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 Mon, 8 Feb 2010, Ian Tickle wrote: > > Yes, thanks! I wish I had spotted th

Re: [ccp4bb] reforigin on 2FKA

igins directly rather than the Cheshire groups so may be slightly easier to use. 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, 27 Jan 2010, Ian Tickle

Re: [ccp4bb] HKL-MTZ conversion

COMBAT routes; anyone who is using SAINT will also have SADABS and it only takes a few seconds to run. 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 O

Re: [ccp4bb] Help with MR in P21

Dear Michele, Your 'pseudo-translation' is too close to an origin, it cannot be real. The problem is probably your model, it wasn't derived from an NMR structure by any chance? It would seem to me that your structure would be very suitable for ACHIMBOLDO. Best wishes, George

Re: [ccp4bb] Lots of noise in structure

. water) on the noise peaks and refine their occupancies leads to very small values. Missing data can make this problem more severe! 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] H32 or R 3 2 :H

There is really no excuse for introducing another unnecessary incompatibility. 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 Tue, 15 Dec 2009, Eleanor

Re: [ccp4bb] Regarding "Open Source"

to 400!) and SHELXL-97 modified by Kay Diederichs (for multiple CPUs) became part of the standard distribution. I was also worried that rival versions of SHELX, all with different input requirements and bugs, would get into circulation and confuse users. CCP4 faces similar problems and may wel

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

Apologies for the typo, I meant to say 'Bernhard'. 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, 14 Nov 2009, George M. Sheldrick wrot

Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

people still active who really understand how it works. On the other hand, Berhard's impressive new book may solve that problem (if people still read books). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel

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