Re: [ccp4bb] Comparing two datasets

Hello Mirek, A very quick approach for that is offered by pointless: pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz or pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK You will obtain a table looking like that, taking into account to possible reindexing: Alternative indexing s

Re: [ccp4bb] R: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

significant. Best regards Vito -Messaggio originale- Da: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> Per conto di LEGRAND Pierre Inviato: mercoledì 10 giugno 2020 09:31 A: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Oggetto: Re: [ccp4bb] Heavy atom vs light a

Re: [ccp4bb] Heavy atom vs light atoms density

Dear Vito, Could you precise in what kind of maps are you experiencing these effects: 2FoFc refinement maps or experimental phasing ? I had this kind of effects long ago in experiemental phasing due to Fourier transform ripple effects. This could be due to scaling problems, low resolution trunca

Re: [ccp4bb] Interesting pattern on a crystallization drop

Dear Beatriz, Nice drops :-)) Could it be that there is a reaction going on in these drops ? The conditions are quite "exotic" with possibilities of coordination or oxydoreduction (Co2+/Co3+) or polymerization... Do you have reductants with the protein buffer ? Is the protein an enzyme or a metal

Re: [ccp4bb] Racemic crystallography and structure solving problem

Hi Prasum, In such case, with xia2 you could try to add the option: small_molecule=true. This will enable the consideration of centrosymmetric spacegourps. Or you can try in pointless the options: CHIRALITY NONCHIRAL or CENTROSYMMETRIC Your spacegroup could be P-1 (#2). Good luck, Pierre __

Re: [ccp4bb] Iron Oxidising state

Hi, Due to the absorbed X-ray dose and photoreduction process during datacollection, it is most probably Fe+2. See for example: J Biol Chem. 2013 Apr 5; 288(14): 9648–9661. doi: 10.1074/jbc.M112.438796

Re: [ccp4bb] new ContaMiner features

Dear Gérard, As being part of the group how has initially raised the issue to Stefan, I stand out to try clarifying a misinterpretation. In brief, because we are happy users of StarAniso, it happened that we have submitted an mtz that it had produced to the ContaMiner server. We were very surpr

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

It seems to me important here to remind that this wave-particle duality is not limited to photons. Electrons and neutrons of course, but also atoms and even molecules have to be considered. To illustrate this, and since it is Friday, shall I propose some nice reading for the week-end :

Re: [ccp4bb] self-rotation in the absence of NCS

Hi Peer, The first thing I would suggest is calculating the self-rotation again but using the FC from the refined model, for comparaison. Then, if you don't see the same supplementary peaks, you can try to play with the integration radius and resolution range. This could give you some hint on t

[ccp4bb] Probleme with D-peptide cif dictionary with refmac5.8

Dear all, A quick note to report the problems I have experienced (and a solution) with the refinement of a peptide containing both D- and L-amino-acids with refmac5.8 (Refmac_5.8.0073). This refinement was done with high resolution data, with hydrogens included in the model (important to rememb

[ccp4bb] Call for beamtime on PROXIMA, FIP and SWING beamlines

Dear all, We would like to draw your attention that the deadline for SOLEIL's (and French ESRF-CRG) next call for proposal is approaching: September 15th, 2014 – 23:59 (French time). Four beamlines relevant for the MX community are accessible through the SUNSET online proposal system (http://s

Re: [ccp4bb] pairwise CCano

Hello Tim :-) You can try to do this with sftools. It is also an interactive type of program input but you can easily calculate correlations. After converting xds files to mtz, you can try some thing like this : sftools << eof > sftools_1.log READ $mtz1 READ $mtz2 SELECT RESOL > 2.8 CORREL COL

[ccp4bb] RE : [ccp4bb] is there any version of xia2 or XDSME compatible with new XDS?

Hi, Sorry, I'm a bit late on this one. I have just uploaded a new version of xdsme (0.5.0.2) that works with the latest version of xds. We have tested it for a few days on the beamlines, but do not hesitate to report bugs (directly to me). You can catch it here: http://code.google.com/p/xdsme/

[ccp4bb] RE : [ccp4bb] Large unit cell, overlaps [OOPS sign error]

range. Pierre De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de LEGRAND Pierre Date d'envoi : mardi 17 juillet 2012 08:26 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] RE : [ccp4bb] Large unit cell, overlaps Hi Jason, To answer your initial question a

[ccp4bb] RE : [ccp4bb] Large unit cell, overlaps

Hi Jason, To answer your initial question about overlaps versus finer slicing, you can get a good description of the problem in Fig10 of Z. Dauter article "Data-collection strategies" (open access article here: http://journals.iucr.org/d/issues/1999/10/00/ba0020/ba0020.pdf). From the initial

[ccp4bb] RE : [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

, Cheers, Pierre De : Garib Murshudov [garib.murshu...@gmail.com] de la part de Garib N Murshudov [ga...@mrc-lmb.cam.ac.uk] Date d'envoi : vendredi 28 octobre 2011 17:49 À : LEGRAND Pierre Cc : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 c

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Dear Ed, Not in my case. I still do *restrained* refinement. I use: refi type REST - resi MLKF - meth CGMAT - bref MIXED ncyc 10 blim 0.1 200.0 With both: weight MATRIX 50 or weight AUTO it gives the same problem. I have also tested the latest refmac5 version (Refmac_5.6.0119) and late

[ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0

Hi Kenneth, I am experiencing exactly the same problem, in similar conditions: refinement with H at 0.84 A resolution. >From a bunch of tests made yesterday, I have found that it is linked to >incompatibilities between cif dictionaries definitions and H names in the >input PDB. For me, one si

Re: [ccp4bb] Problem with NCS detection in Parrot

Hi Florian, I have found that, in some cases, playing with -ncs-mask-filter-radius can help parrot to successfully detect and apply ncs averaging. In one recent case, with 8 molecules where NCS was not found without this option, values from 14 to 30 angstroms worked (but gave maps of variable q

[ccp4bb] Post-doctoral Position in biochemistry/structural biology at PROXIMA-1/SOLEIL.

Dear members, We are seeking a motivated young scientist with a background in structural biology and an interest in instrumentation and/or methodology. As a member of the PROXIMA 1 beamline team, your main scientific mission will be to contribute to a research program focused on the structural

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

Hi, I think there is something like that described in this paper: F. M. D. Vellieux "An enveloped cross rotation function" J. Appl. Cryst. (1995). 28, 834-836 If I remember correctly, the calculations where done using x-plor scripts. Pierre Proxima-1 Team Synchrotron-SOLEIL Message d'or