Re: [ccp4bb] reference for true multiplicity?

2013-05-14 Thread George Sheldrick
Dear Frank, We did extensive testing of this approach at the beginning of this millenium - see Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our idea. Best wishes, George On 05/14/2013 06:50 AM, Frank von Delft wrote: Hi, I'm meant to know this but I'm blanking, so I'll

Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

2013-05-15 Thread George Sheldrick
One day many years ago, my Ph.D. students all appeared wearing T-shirts with the logo We want more redundancy. They had clearly got the message about how to do sulfur SAD phasing, but were completely unaware of the usual meaning of the word in the UK! George -- Prof. George M. Sheldrick FRS

Re: [ccp4bb] shelx c/d/e question

2013-06-05 Thread George Sheldrick
Dear Olga, I always run SHELXC/D/E from hkl2map because of the nice graphical diagnostics while the programs are running. If you start hkl2map, give any project name and choose 'more options' you will be able to specify that you need more memory. From your comment I suspect that you are

Re: [ccp4bb] Off-topic: NMR and crystallography

2013-06-09 Thread George Sheldrick
The title of my PhD thesis was NMR of inorganic hydrides but I soon realized that I was out of my depth with the theory so switched to something easier to understand (gas phase electron diffraction). However this involved taking the (somewhat dangerous) samples by train to Durward

Re: [ccp4bb] OT: (a bit) shelx(pro)

2013-06-17 Thread George Sheldrick
Dear Peter, i am planning to produce a new pdb2ins containing several improvements, but until this is ready please continue to use the old shelxpro. Best wishes, George On 17.06.2013 16:57, Peter Moody wrote: At the risk of (more) people pointing at me and laughing... I used to use

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread George Sheldrick
The flexibility of CIF is indeed infinite. Even the names of the unit-cell dimsnsions are different in mmCIF and (small molecule) core CIF. One of the main reasons why I had to bring out a new version of SHELXL recently (SHELXL-2013 to replace SHELXL-97) was that in the meantime COMCIFS

Re: [ccp4bb] Why MAD didn't work but SAD works well

2013-08-20 Thread George Sheldrick
Dear Yafang, If radiation damage is not a major problem, MAD should give you more phase information than SAD, i.e. better maps, especially at low resolution. If SAD works but MAD doesn't, there are several possible explanations: 1. (most likely) your datasets are inconsistently indexed. This

Re: [ccp4bb] shelx anamalous data

2013-11-14 Thread George Sheldrick
I'm not sure why you want to do that. If you wish to look at a map or poly-Ala trace from SHELXE, just read the .pdb and then .phs files into Coot directly. If you want to use them to make pictures with PYMOL, use Tim Gruene's SHELX2map. For further information please go to the SHELX homepage

[ccp4bb] Fwd: Re: [ccp4bb] shelx anamalous data

2013-11-16 Thread George Sheldrick
(+) and I(-) SIGI(-) But as George says Why do you want it? That will change the way you proceed. Eleanor On 14 Nov 2013, at 21:08, George Sheldrick wrote: I'm not sure why you want to do that. If you wish to look at a map or poly-Ala trace from SHELXE, just read the .pdb and then .phs files

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

2013-12-17 Thread George Sheldrick
Dear Chang, As far as I know, most CCP4 programs are single-CPU and would need extensive changes to make them patallel. Examples of multiple-CPU programs are XDS, SHELXD, SHELXL and (in part) PHASER. Best wishes, George On 12/17/2013 06:51 AM, Chang Qing wrote: Dear all I just installed

Re: [ccp4bb] How to config CPU to run ccp4 with multi-processor

2013-12-18 Thread George Sheldrick
Adapting programs to make optimal use of modern multicore chips is non-trivial and depends very much on the algorithms employed, there is no magic bullet. First one needs to understand Amdahl's law. Assume we have a chip with four cores such as the widely used Intel i7, amd the program consists

Re: [ccp4bb] Sister CCPs

2014-02-12 Thread George Sheldrick
It would be so nice to have a 'sister CCP' for questions aboud wet-lab problems that have nothing to do with CCP4 or crystallographic computing, The is clearly a big need for it, and those of us who try to keep out of wet-labs would not have to wade though it all. George On 02/12/2014 03:05

Re: [ccp4bb] Sister CCPs

2014-02-14 Thread George Sheldrick
I think that more people read wikis than contribute to them, so this 'experiment' (see below) is a little biased. On the other hand, it is often easier to put a question to CCP4bb than to search for the answer in wikis and other documentation, however well organized they are. Kay: can you see

[ccp4bb] Biophysics faculty position at Milwaukee

2014-02-28 Thread George Sheldrick
Abbas Ourmazd who is physics professor at Milwaukee has asked me to post this job advert on CCP4bb: http://jobs.sciencecareers.org/job/325225/assistant-or-associate-professor-in-biophysics/ George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen,

Re: [ccp4bb] small molecule crystallography

2014-03-25 Thread George Sheldrick
Indexing involves storing all the reflection positions in orthogonal reciprocal space and then finding a reciprocal lattice that fits most of them. For a 10 degree frame all we know is that a reflection lies somewhere on a sort of 10 degree arc; only two of the three coordinates are precisely

Re: [ccp4bb] difference between polar angle and eulerian angle

2014-03-29 Thread George Sheldrick
There are good arguiments for using quaternions rather than Eulerian (or other) angles anyway, this is very well explained in the paper *Quaternions *in *molecular modeling*

Re: [ccp4bb] SAD Pattersons (previously space group problem)

2014-04-02 Thread George Sheldrick
Dear Chen, If you don't know how many sites to expect - and in some cases, e.g. an iodide soak, this is inevitable - I recommend trying different numbers (FIND N in shelxd) and choosing the one where the occupancy of peak N comes out as about 0.2. If it is higher you need a higher N and vice

Re: [ccp4bb] Confusion about space group nomenclature

2014-05-02 Thread George Sheldrick
In my program documentation I usually call these 65 the Sohnke space groups, as defined by the IUCr: http://reference.iucr.org/dictionary/Sohnke_groups George On 05/02/2014 02:35 PM, Jim Pflugrath wrote: After all this discussion, I think that Bernhard can now lay the claim that these 65

Re: [ccp4bb] correct pdb encoding for split-personality solvent HETATM?

2014-05-14 Thread George Sheldrick
Dear Alastair, As you point out, SHELXL allows atom names, RESIdue numbers and PARTs (=Altlocs) to be used in any combination. The only rule is that no two non-hydrogen atoms may have the same settings for all three. Other refinement programs may be more restrictive. Best wishes, George

Re: [ccp4bb] refine an ion atom with different status

2014-06-20 Thread George Sheldrick
I agree with Pavel. Even for accurate small molecule data with R-values below 3% the differences are hardly significant, the 'B-factors' compensate so well. The large majority of small molecule structures are refined with neutral atom scattering factors even if ions are present. The calculated

[ccp4bb] Fwd: Re: [ccp4bb] Shelxc failure

2014-06-20 Thread George Sheldrick
Dear Roberto, If you are using shelxc/d/e, it is best to read the XDS.ASCII.HKL file DIRECTLY into shelxc. This is what hkl2map does. When you run shelxe (from the command line or hkl2map), you usually need to try both hands of the heavy atom substructure. If the 'contrast' for one hand is

Re: [ccp4bb] [phenixbb] So what is unique?

2014-07-15 Thread George Sheldrick
I think that 'observed' goes back to whether it was possible to see a reflection (and estimate its intensity by eye) on the photographic FILM. In small molecule crystallography it is usually understood to mean F4sigma(F) (or I2sigma(I)). George On 07/15/2014 07:02 PM, Edward A. Berry wrote:

Re: [ccp4bb] aimless and anisotropic scaling (and the docs?)

2012-04-25 Thread George Sheldrick
I think that anything that irrevocably modifies the experimental data should be avoided whenever possible. Since anisotropic scaling is a relatively fast calculation and there are several ways of doing it, it is better to apply it locally when it is needed, e.g. in phasing (where it is applied

Re: [ccp4bb] ShelXL and Coot

2012-05-06 Thread George Sheldrick
You probably need to insert the space group name into the CRYST1 record. Tthe version of SHELXL that I am planning to release this summer already deduces the space group name from the LATT and SYMM cards and puts it there. If you read the .res file into Coot instead of the .pdb, Coot can

Re: [ccp4bb] Calculating ED Maps from structure factor files with no sigma

2012-05-23 Thread George Sheldrick
In SHELXL. a refinement program sometimes used by small molecule crystallographers, all Fourier map for at least the last 20 years were weighted by Ic^2/(Ic^2+sigma^2(I)), where Ic is the calculated squared structure factor and sigma(I) is the square root of 1/w. w is the weight assigned to a

Re: [ccp4bb] P321 space group reindex problem

2012-05-29 Thread George Sheldrick
Which programs require that the data be the 'standard' a.u.? None of mine require this. George On 05/29/2012 03:44 PM, Ian Tickle wrote: Mark, thanks for pointing that out, I see it now: In P321 the only possible alternate indexing is (-h, -k, l): this is a 2-fold || c which is an operator

Re: [ccp4bb] High Rfree values and using Bruker detector w/ iMosflm

2012-06-25 Thread George Sheldrick
Dear Annette, I suspect that a trivial error like confusing F and intensity is the cause of your problem. You would probably get a better response if you sent your message to the very informative Bruker mailing list or asked one of the Bruker applications scientists. If you wish to send me

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

2012-09-12 Thread George Sheldrick
It is the lack of compatibility between different versions mentioned by Ethan that really put me off learning PYTHON. In contrast, the FORTRAN-66 program SHELX76 still compiles and runs correctly with any modern FORTRAN compiler. The only significant 'new' features that I now use are dynamic

Re: [ccp4bb] Off topic

2012-09-15 Thread George Sheldrick
shelx .hkl files often have a blank line or a line filled out with zeros at the end as a terminator. This is useful if you wish to edit in extra information such as the cell dimensions after this line, but is not obligatory. However if you concatenate the files with cat or a text editor you

Re: [ccp4bb] coot, shelx res files and R32 (H32)

2012-11-19 Thread George Sheldrick
shelxl-2012 does include the space group in a way that Coot understands when it writes a .pdb file. This version is in the final beta-testing stage with a lot of new features (mainly for small molecules) and no known bugs, so I hope to release it soon. If anyone would like to try it now please

Re: [ccp4bb] The information of shelxc_fa.lst

2012-11-30 Thread George Sheldrick
That is a list of the strongest Patterson peaks, the ones marked with '*' are used as translation search vectors to kick-start the heavy atom location. x,y,z are the crystal coordinates of the peaks, height is the peak height, mult indicates how the peaks have coalesced because they are on

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

2012-12-07 Thread George Sheldrick
is as good as any and you clearly already know how to use it. The older shelxs has further Patterson options, as do many other programs such as the CCP4 program FFT. Best wishes, George On 12/07/2012 11:31 AM, ccp4...@hotmail.com wrote: Dear professor George Sheldrick, I am sorry to bother you

Re: [ccp4bb] archival memory?

2012-12-12 Thread George Sheldrick
Punched cards, stored in a sealed dry box, and perhaps irradiated to kill off any bacteria, should long outlive any magnetic or capacitive storage medium. If it is difficult to find a working card reader, they could always be read by eye, though that might be tedious. Their EBCDIC code is not

Re: [ccp4bb] 3D alignment of points (atoms)

2012-12-27 Thread George Sheldrick
A computationally elegant and probably faster approach is to use quaternions, proposed by MacKay in Acta Cryst. A40 165-166. For a recent description of this method see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958452/ George On 12/27/2012 09:09 PM, Dale Tronrud wrote: If you just

Re: [ccp4bb] a challenge

2013-01-12 Thread George Sheldrick
Dear James, I agree with Pavel that your example is not very realistic. In practice one would start from the heavy atom positions. As well as providing starting phases, they are useful in other ways. For example. shelxe (and probably most other tracing programs) adds them to a 'no-go' map so it

Re: [ccp4bb] a challenge

2013-01-12 Thread George Sheldrick
James, I had in fact just come to the conclusion that the indexing was consistent with 3dko for 'possible' but not for 'impossible', which I suppose was logical. George Woops! sorry folks. I made a mistake with the I(+)/I(-) entry. They had the wrong axis convention relative to 3dko and

Re: [ccp4bb] a challenge

2013-01-13 Thread George Sheldrick
I have now looked at James's two challenges to see what I could learn from them, and will try to give enough details so that less experienced readers of this list can repeat what I did and apply the experience thereby gained to solving their own structures. For those who are not interested

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

2013-01-28 Thread George Sheldrick
Dear Huw, It looks as though you have correctly diagnosed a problem with AMPLE. For expansion from borderline partial structures, I recommend the latest SHELXE (on my beta-test server since Jan. 20th) and experimenting with the -O and -F switches, e.g. -F0.9 -O100 -a30 However SHELXE is

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

2013-01-28 Thread George Sheldrick
Correct, shelxe does not use the free -R flags, and works just as well with the original unmerged unctruncated intensities. George Hi Ronan, On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote: Well spotted! We originally gave structure factors to SHELXE in our testing as for most of

[ccp4bb] SHELX-2013 release and homepage

2013-02-26 Thread George Sheldrick
As some of you have already discovered, there is a major new release of the whole of SHELX (the first since 1997) complete with a new homepage that should make downloads easier. To obtain the programs, please point your browser to: http://shelx.uni-ac.gwdg.de/SHELX/ and then 'register' (top

Re: [ccp4bb] SHELX-2013 release and homepage

2013-02-27 Thread George Sheldrick
' commands). (also see my blog article http://grauonline.de/wordpress/?p=71 ) Is it possible to build one for Mac 10.5.8? Thanks! Guangyu Zhu On 2/26/13 3:32 AM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: As some of you have already discovered, there is a major new release

Re: [ccp4bb] How to use SHELXE to perform phasing and density modification

2013-03-15 Thread George Sheldrick
Dear Wei, There is a new SHELX homepage with extensive documentation and downloading instructions at: http://shelx.uni-ac.gwdg.de/SHELX/ SHELXE requires reflection files name.hkl (native) and name_fa.hkl (data for phasing) and and the heavy atoms in SHELX format in name_fa.res. I recommend

Re: [ccp4bb] How to use SHELXE to perform phasing and density modification (correction)

2013-03-15 Thread George Sheldrick
or P6522, then you should run shelxe twice, once with and once without -i (which would invert the space group and atom coordinates). It is usually worth trying different solvent contents (-s). George On 03/15/2013 11:09 AM, George Sheldrick wrote: Dear Wei, There is a new SHELX homepage

Re: [ccp4bb] crystallization of synthetic peptides

2011-11-10 Thread George Sheldrick
As Mark says, structure solution of smallish peptides is not usually as easy as one might expect. A number of the small (say up to 50 residue) peptides in the PDB were solved by direct methods, but these require native data to 1.2A or (preferably) better. If sulfur is present in the molecule,

Re: [ccp4bb] Anomalous signal for chlorides

2011-11-26 Thread George Sheldrick
Dear Yuri, The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is designed for this and is very simple to use. It may be downloaded from the SHELX beta-test server (please email me if you require downloading intructions). George On 11/26/2011 06:05 AM, Yuri Pompeu wrote:

Re: [ccp4bb] shelxD

2011-12-06 Thread George Sheldrick
SHELXD does not use the solvent content. However since you know how many seleniums it found and presumably know how many methionines are in the sequence, you can use that to estimate the number of molecules is the asymmetric unit. Note that an N-terminal selenomethionine is often disordered

Re: [ccp4bb] shelxD: frogot to mention shelxe beta result

2011-12-06 Thread George Sheldrick
The pseudo-free CC in SHELXE is not a very decisive figure of merit. By far the best way is to run the autotracing (e.g. with -a5) and to look at the CC for the trace against the native data. A value of more than 25% is almost always solved. George On 12/06/2011 10:02 PM, Tiruttani

Re: [ccp4bb] New Faster-than-fast Fourier transform

2012-01-20 Thread George Sheldrick
From the rather non-technical inofrmation available so far, it seems to me that it is like leaving out all but the strongest reflections (or perhaps the strongest normalized structure factors). This is unlikely to improve the quality of structure refinement, the importance of using as much

Re: [ccp4bb] No diffraction

2012-01-26 Thread George Sheldrick
It depends a lot on which home source and which synchrotron, there are enormous differences. Goettingen is uniquely well placed because we can reach four synchrotrons in a few (3-7) hours by high speed train and in theory at least five more with a longer train journey, trains are very

Re: [ccp4bb] Lysozyme/Xenon derivatives Phenix.

2012-02-02 Thread George Sheldrick
Dear Brennan, Since you accidentally sent your request to the CCP4bb rather than the Phenix email list, I suggest that you try SHELXC/D/E, e.g. using Thomas Schneider's HKL2MAP, to see if it gets the same answers. These programs have solved lysozyme hundreds of times. HKL2MAP will also

Re: [ccp4bb] [ccp4]questions about SHELXD

2012-02-19 Thread George Sheldrick
Dear Lu Yu, Most readers of this list will only be familiar with the use of SHELXD to find heavy atom sites for experimental phasing, but it appears that you are using it for small molecule direct methods, which in fact is what the program was originally written for. For small molecule direct

Re: [ccp4bb] Matthews coeff. from model

2012-03-12 Thread George Sheldrick
for any such purposes. I got the number 140A^3/a.a. from George Sheldrick who told me where he got this number from, but I do not remember for sure - it could be Kevin Cowtan, but George may update my memory in order to pay proper credit. Cheers, Tim On 03/12/2012 08:48 PM, Bernhard Rupp

Re: [ccp4bb] unstable refinement error in SHELXL

2012-03-19 Thread George Sheldrick
Dear Lu Yu, SHELXL is usually very stable so there must be an error in your .ins file, but it is difficult fo us to guess what it is without seeing the full file. A common error that can cause such instability is caused by a long-standing bug in Coot, which sets some occupancies in the .ins

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

2012-03-20 Thread George Sheldrick
Dear Gerard, That will be an extremely useful facility. Is a 'regrading' of the monomer library planned, at least for common cofactors and crystallization additives? Best wishes, George On 03/19/2012 06:22 PM, Gerard Bricogne wrote: Dear all, The generation of reliable restraints

Re: [ccp4bb] correlated alternate confs - validation?

2014-07-23 Thread George Sheldrick
Dear Frances, I don't think that you can put the blame entirely on the 80 column limitation. The program SHELX76 was limited to 80 columns because the input came as punched cards. It introduced a simple concept, the /free variables/, that are frequently used to represent occupancies and can

Re: [ccp4bb] Twinning in space group Pc

2014-08-13 Thread George Sheldrick
Dear Kristof, Have you tried to solve it with the new SHELXT? You can force it to consider only chiral (Sohnke) space groups by putting -c on the command line. Best wishes, George On 13.08.2014 11:00, Kristof Van Hecke wrote: Dear, I’m struggling with the following (small molecule)

Re: [ccp4bb] Calculating anomalous Fourier maps

2014-08-29 Thread George Sheldrick
You might consider using AnoDe (J. Appl. Cryst. 44 (2011) 1285-1287). This program and its documentation are available via the SHELX homepage. You will need a PDB file name.pdb of the native structure and a file name_fa.hkl that contains the anomalous differences. You can use SHELXC or XPREP

Re: [ccp4bb] Space group numbers

2014-10-02 Thread George Sheldrick
The strange thing is that small molecule crystallographers do not suffer from this problem, because they don't use space group numbers! This is just as well, because instead of just 8 combinations of primitive orthorhombic space groups and settings, they have to consider 111 (if I have

Re: [ccp4bb] monitoring refmac refinement

2014-10-02 Thread George Sheldrick
Dear Alistair, Erratic behaviour is often caused by the antibumping restraints because they get switched off and on, and riding hydrogens and changes in the occupancies can affect their action. This probably applies to both programs. Any suggestions for improving the bulk solvent model in

Re: [ccp4bb] Space group numbers

2014-10-03 Thread George Sheldrick
Since this discussion doesn't want to end. I should point out (a) The IUCr has, in its wisdom, decided to use the */Hall space group symbols/* to settle the matter. See International Tables for Crystallography, Vol. B (2001), Chapter 1.4, Appendix 1.4.2//and /Acta Cryst./ (1981). A*37*,

Re: [ccp4bb] Space group numbers

2014-10-04 Thread George Sheldrick
Dear Ian, Kay et al., The omnipotent CheckCIF program that is used to check all small molecule structures submitted to /Acta Cryst./ and many other journals requires (a) the H-M space group name, (b) the Hall symbol and (c) the list of equivalent positions, and checks that *all three* are

[ccp4bb] SHELX for Macromolecules Course

2015-01-23 Thread George Sheldrick
Immediately after the DGK Meeting in Goettingen, there will be an IRTG Methods Course on Macromolecular Applications of SHELX there on the afternoon of Thursday March 19th. See: http://shelx.uni-ac.gwdg.de/SHELX/workshops.php for details. George -- Prof. George M. Sheldrick FRS Dept.

Re: [ccp4bb] extracting PHENIX structures

2015-01-26 Thread George Sheldrick
Dear George and Patrick, It is particularly tricky to do such a search for SHELX because there are different ways of referencing it for refinement (SHELX, SHELX-76, SHELXL, SHELXL-97, SHELXL-2014 etc.) and there are other ways of using SHELX, in particular SHELXD for finding the heavy atom

Re: [ccp4bb] .raw file from SAINT to pointless

2015-01-06 Thread George Sheldrick
Dear Georg, When you start SADABS, the first question is whether you rquire 'expert mode'. This mode asks more questions to set additional parameters. If you select expert mode, the second question is the maximum number of reflections. 200 is merely the default value. I would be

Re: [ccp4bb] .raw file from SAINT to pointless

2015-01-05 Thread George Sheldrick
Dear Georg, Since you collected your data on a Bruker machine and integrated them with SAINT you should simply scale the .raw files with the Bruker program SADABS and then read them into into XPREP. This can scale the two datasets together and produce either merged or unmerged but scaled

Re: [ccp4bb] Absorption correction in small molecule crystals

2015-03-03 Thread George Sheldrick
Dear Finke, SADABS and similar programs work best when given scans about several axes relative to the crystal. Scanning about a single axis can do more harm than good especially if the symmetry is low. SADABS can also do a face-indexed numerical absorption correction too, but this assumes

Re: [ccp4bb] Phaser going into infinite loop in Ample

2015-04-22 Thread George Sheldrick
Dear Dale, Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the same resolution requirements (2.1A or better) as AMPLE because both use SHELXE to expand the solution. It also employs PHASER to place a small fragment but it is often sufficient to let it search for just two or

Re: [ccp4bb] SHELX expired?

2015-04-18 Thread George Sheldrick
Dear Tom, Please go to the SHELX homepage (Google knows where that is) and 'register'. You will then immediately receive an email with downloading instructions (free for academic use). Sometimes this email lands in the trash folder. Best wishes, George On 04/18/2015 11:40 AM, Tom Wong

Re: [ccp4bb] SHELXL refinement with TYR on special position

2017-01-24 Thread George Sheldrick
Dear Francis, You need to put the atoms starting with CG into PART -1 to prevent them clashing, and reset the occupancies to 10.5 (i.e. fixed at 0.5). There must be another disorder component pointing somewhere else (also with half occupancy). SHELXPRO has been made obsolete by Anna

Re: [ccp4bb] Proper way to handle multiple conformations of ions/waters

2017-02-21 Thread George Sheldrick
Dear Paul, As you suggest, small molecule crystallographers are used to such complicated situations and often use SHELXL for the purpose. Since you fortunately have 1.0A data you could do the same, first using pdb2ins to convert your PDB file to a SHELXL .ins file. You will need to use PART

Re: [ccp4bb] Parallelization?

2017-02-09 Thread George Sheldrick
Dear Bernhard, After Kay showed me how to do it by making SHELXL parallel, I was able to make SHELXD, ANODE and SHELXT (my current small molecule direct methods program) highly parallel. I'm still working on SHELXE because it requires major changes. In principle chain tracing is difficult to

Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS

2016-10-26 Thread George Sheldrick
best wishes Phil On 25 Oct 2016, at 20:31, George Sheldrick<gshe...@shelx.uni-ac.gwdg.de> wrote: SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be dow

[ccp4bb] New version SHELXL 2016/6 and PDB2INS

2016-10-25 Thread George Sheldrick
SHELXL may be used to refine both small and macromolecular structures against X-ray or neutron diffraction data, including non-merohedral twins. A new version 2016/6 of SHELXL may now be downloaded from the SHELX server. It has been well tested by about 20 volunteers to whom I am very

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

2016-10-14 Thread George Sheldrick
Just for the record, the Fortran sources for all the SHELX programs are identical for Windows (32 or 64 bit), Linux (32 or 64 bit) and MacOSX (always 64 bit) except for one line that I need to comment out for Windows. I use the Intel ifort compiler for all these platforms. I pay the commercial

Re: [ccp4bb] SAD phasing

2016-12-28 Thread George Sheldrick
ch" resolution-extended data. Best wishes, George Sheldrick On 28.12.2016 11:43, 张士军 wrote: Dear Kay You mean after convert .phs to .mtz ,use the .mtz file refine the initial structure model? By the way , what's the difference between this density map with the density map modified af

Re: [ccp4bb] New version of SHELXE

2017-08-13 Thread George Sheldrick
A new version 2017-1 of SHELXE is available for downloading from the SHELX server. See /recent changes/ on the SHELX homepage at shelx.uni-goettingen.de for details. The most important changes (contributed by Isabel Uson) should extend the chain tracing to lower resolution. Since this requires

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

2017-04-29 Thread George Sheldrick
Dear Murpholino, I suspect that the pipelines in CCP4i and CCP4i2 do not include RIP phasing (perhaps they should) but you can also run the SHELX programs from a command line since you don't like black boxes. SHELXC reads XDS_ASCII.HKL files and has some special facilities for RIP, you can

Re: [ccp4bb] "reset" a structure before re-refinement

2017-08-17 Thread George Sheldrick
Dear Graeme, The WIGL instruction in SHELXL does exactly that, and has some useful options. http://shelx.uni-ac.gwdg.de/SHELX/shelxl_html.php#WIGL Best wishes, George On 08/17/2017 05:17 PM, Graeme Winter wrote: Dear All, Is there a protocol out there to gently perturb atomic positions so

Re: [ccp4bb] how to run shelx C/D/E using CCP4 GUI on windows

2017-05-09 Thread George Sheldrick
Just to confirm what Eleanor said: all SHELX programs prefer to be given intensities but can accept F if the intensities have been lost. Converting intensities to F (e.g. with ctruncate) and back again degrades the statistics for the weak reflections and is discouraged. The same applies to

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

2017-04-29 Thread George Sheldrick
Dear Murpholino, I must apologize, there was a mistake in may last email. The critical parameter is, as you correctly pointed out, DSCA not RIPW and it is necessary to try a range of values for DSCA. For this reason I am CCing this to CCP4bb. As you will be discovering, RIP phasing is not

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

2017-10-16 Thread George Sheldrick
Dear James. What small molecule programs report often looks like: R1 = 0.1550 for 17413 Fo > 4sig(Fo) and 0.2058 for all 23715 data R1(Free) = 0.2208 for 1938 Fo > 4sig(Fo) and 0.2766 for all 2635 data from a well-known small molecule program being (mis)used to refine a protein.

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

2017-09-12 Thread George Sheldrick
Over 50 years ago, a Toepler pump that I had glass-blown myself developed a crack that caused several kilos of mercury to hit tha ceiling and give me a shower. Fortunately I did not then know how poisonous it was and suffered no ill-effects George On 12.09.2017 19:46, James Holton wrote:

Re: [ccp4bb] New version of SHELXE

2017-08-28 Thread George Sheldrick
Dear Carlos, You are correct. I reinstalled CCP4 two days ago and also got version 0044 and that did not incude the new shelxe_2017-1. However the new shelxe is definitely on the shelx server. It is a single statically linked executable with no dependencies (!) so you can simply replace the

Re: [ccp4bb] coot shelxl problem

2017-11-02 Thread George Sheldrick
Dear Abhishek, Maybe Paul had forgotten that shelxl was designed to read 80 column punched cards. To check against overrun it was checking that column 80 is a blank. I may be able to fix this in the next version of shelxl. For the moment you will have to do some hand editing, e.g. using

Re: [ccp4bb] update 057

2018-05-10 Thread George Sheldrick
Dear Charles (and CCP4 users), I was delighted to see that CCP4 update 057 at last includes Anna Luebben's pdb2ins, which we had been requesting for months and is very useful for preparing the two input files needed to run shelxl. Unfortunately you were too modest to mention this in your

Re: [ccp4bb] Python3 and MTZ

2018-06-08 Thread George Sheldrick
This discussion has not convinced me to stop using Fortran. FORTRAN66 programs such as SHELX76 still compile and run unchanged with modern Fortran compilers, though I do use a few useful features introduced in FORTRAN77 and FORTRAN90 such as character handling and run-time memory allocation.

Re: [ccp4bb] [ccp4bb] Oxford University Press

2018-07-02 Thread George Sheldrick
Since neither I nor my university can afford Elsevier journals, I have no access to papers published in them. In view of their excessive profits, for some years I have not submitted papers to them and have declined all requests to referee for them. If everyone did that, they might reconsider

Re: [ccp4bb] Regarding symmetry notion in coot

2018-06-21 Thread George Sheldrick
For small molecules, programs such as SHELXT move the structure to be as near as possible to the center of the unit-cell, not the origin. Failure to do so may cause a 'checkCIF alert'. George On 06/21/2018 09:34 PM, John Berrisford wrote: From a PDB deposition point of view, I echo Paul’s

Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread George Sheldrick
A particularly useful command line option in SHELXT for such cases is -L15 to try all trigonal and hexagonal space groups. SHELXT is included in recent CCP4 distributions and is also available with documentation from shelx.uni-goettingen.de George On 02.08.2018 15:53, Aaron Finke wrote: Hi

Re: [ccp4bb] Oxford University Press

2018-07-05 Thread George Sheldrick
there are/were even more prolific candidates  Best, BR *From:*George Sheldrick *Sent:* Wednesday, July 4, 2018 16:17 *To:* b...@hofkristallamt.org; ccp4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Oxford University Press Dear Bernhard, I agree with you sentiments, but was wondering which 'poor Russian

Re: [ccp4bb] Oxford University Press

2018-07-04 Thread George Sheldrick
/wiki/Elsevier#cite_note-28> A complaint about Elsevier/RELX was made to the Competition and Markets Authority <https://en.wikipedia.org/wiki/Competition_and_Markets_Authority>.^[29] <https://en.wikipedia.org/wiki/Elsevier#cite_note-29> On 2 July 2018 at 08:01, Georg

[ccp4bb] New SHELX versions and email address

2018-03-13 Thread George Sheldrick
Here is another attempt from my old email address. I was not registered to use the email lists from my new address, but please use it in future! New versions of SHELXE, SHELXL and SHELXT and also Anna Luebben's program pdb2ins that provides a quick way of setting up a shelxl refinement given a

Re: [ccp4bb] According correct space group assignment...

2018-04-25 Thread George Sheldrick
Dear Rafal et al, With some help from Kay I think that I could find out what is happening here. SHELXT finds the space group Ibca and solves the structure easily with default parameters but has difficulty in assigning the elements because it was not expecting arsenic (!). The data are not very

Re: [ccp4bb] shelxe version 2019-1

2018-12-26 Thread George Sheldrick
SHELXE 2019-1 may now be downloaded from the shelx server at shelx.uni-goettingen.de. With default parameters this version traces structures with good resolution and phasing power faster, for difficult structures see 'recent changes' on the shelx homepage or the summary printed when the

Re: [ccp4bb] buying a cluster

2018-11-23 Thread George Sheldrick
To put the record straight, despite our efforts SHELXE is not currently multiply threaded, but ARCIMBOLDO is able to run several copies of SHELXE simultaneusly (which can be more effective). On the other hand SHELXL, SHELXD and SHELXT (widely used to solve small molecule structures) are

[ccp4bb] postdoc position for crystallographic methods development

2019-04-21 Thread George Sheldrick
. for sulphur-SAD phasing. Although shelxd is still used it has not been changed for decades and needs to be brought up to date. Anyone interested should contact me by email. George Sheldrick -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry University of Goettingen Tammannstr. 4s

Re: [ccp4bb] Combining MR and SIR phases

2019-07-23 Thread George Sheldrick
I'm afraid that I have to disagree with Eleanor, a very rare event. Both pure SIR and pure SAD give you only half of the necessary phase information. The initial map will in both cases be a double image. One then tries to improve it by density modification. For pure SAD one image is positive

Re: [ccp4bb] Shelx and debian 10

2019-10-08 Thread George Sheldrick
As explained in the attached email from Peter Keller, I was deliberately preparing the binary Linux SHELX distribution using older (2011) system libraries so that the programs would run on older systems that many users are still using. Unfortunately this means that they do not run on some

Re: [ccp4bb] refinement of 0.73A data in shelxl

2020-02-03 Thread George Sheldrick
Dear Matthias, That is very strange. First please repeat the shelxl refinement with the occupancy of the offending chlorine(s) in the .ins file changed from 11  (i.e. fixed at 1.0) to 1.0 (i.e. freely refined starting from 1.0). If that does not help I would be happy to look at it in

Re: [ccp4bb] Question about P3, H3 and R3 space groups

2020-07-22 Thread George Sheldrick
This is precisely why SHELX always used the coordinates of the general position (LATT+SYMM) to define the space group rather than a name or number. George On 22/07/20 14:15, Ian Tickle wrote: Hi David The problem is that the PDB incorrectly used the H lattice symbol (without consulting any

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