Re: [ccp4bb] Negative CCanom

...since he was not using XDS... Oooops! My bad! I just recognized the phenomenon and assumed it to be from XDS. That explains the different column names. I'll keep my eyes open next time. Cheers, Jose. Jose Antonio Cuesta-Seijo, PhD Carlsberg Laboratory Gamle

Re: [ccp4bb] Negative CCanom

Going back to the original discussion on XDS producing negative CCanom, I am not sure that this is the result of some crystal artifact. I just checked many datasets from the last years and in all cases virtually for every every resolution shell, XDS reports a negative CC anom. Please note that

Re: [ccp4bb] Cleaved peptide density!

Hi all, late to the discussion as usual... Related to the issue of "why does my single point mutant appear to have residual activity", what do people here make of this warning from 1989? http://pubs.acs.org/doi/pdf/10.1021/ar00163a001 Some highlights: "Substitution of the Ser68 codon with a codo

Re: [ccp4bb] Poor resolution

Dera Prerana, Without more information, we cannot help. What have you done, what have you not done, 3.0Å where, etc... Except to say that 3.0Å is not poor at all, often that's all you can get and that's fine. What type of biological or chemical question are you trying to answer ? (we need more

Re: [ccp4bb] Cis-peptide bond checking

Dear all, The version of Refmac that I currently use through ccp4i has "If following features are found in coordinate file then make restraints to maintain them:" activated by default for cis-peptides. I usually deactivate it during refinement, but this means that if one does nothing and moving

Re: [ccp4bb] chloride or water

At the risk of derailing the discussion, can it be that the blob is actually an accumulation of many Fourier ripples? (on top of bulk solvent, I guess). The “chloride” seems to be about 3.5Å away from a lot of atoms, with nothing closer. This is mostly based on intuition and the fact that in my e

Re: [ccp4bb] Free Reflections as Percent and not a Number

Hi all, I'd like to challenge the notion that a "jiggle" to an RMSD of 0.2Å will actually move your atoms by anywhere close to 0.2Å, hence affecting at least the reflections at 2Å. Well, it will, but think of what happens to two atoms that were at their ideal distance then then are 0.4Å furthe

Re: [ccp4bb] making sure related molecules occupy the same space

Correction: that won’t fix any origin issues, only cell and assymetric unit. Jose Antonio Cuesta-Seijo, PhD Carlsberg Laboratory Gamle Carlsberg Vej 10 DK-1799 Copenhagen V Denmark Tlf +45 3327 5332 Email josea.cuesta.se...@carlsberglab.dk

Re: [ccp4bb] making sure related molecules occupy the same space

Depends on what you are trying to do, but if all you want to do is to move your solutions into whichever unit cell / origin / assymetric unit best matches your reference, a quick workaround is this: 1) Load your molecule in Pymol, let it generate a healthy number of symmetry mates for each chain

[ccp4bb] Compounded problems for molecular replacement

Hi all, I am dealing with a molecular replacement problem for a 60KDa protein composed of 2 rigid domains joined by a flexible linker which can move relative to each other. Sequence identity for my best model is 46% evenly spread, so in principle this should be a tractable problem. Then the

Re: [ccp4bb] How to identify unknow heavy atom??

Shameless self plug: http://scripts.iucr.org/cgi-bin/paper?fw5057 That was done with a crappy crystal in a relatively weak beamline. With a good crystal one can get cleaner data. Cheers. Jose. Jose Antonio Cuesta-Seijo, PhD Carlsberg Laborat

[ccp4bb] TCEP resistant disulfide

Has anyone worked with, or seen an example of, a solvent accessible disulfide that cannot be reduced with TCEP? Alternatively solvent accessible disulfides that resist reduction with DTT but can be reduced with TCEP? Thanks in advance, Jose. Jose Antonio