Dear all Personally I feel that we really have an obligation to make the raw images available, even if it is painful to do so in terms of data storage. It is the only way of truly allowing others to reproduce our experiments, which is a basic requirement for all published scientific work crystallographic or non-crystallographic. I also hope it would allow structures to be improved as future tools develop, for errors to be corrected and perhaps one day to apply new methods (for example to deal more appropriately with twinned structures). Now people have developed ways to routinely share vast quantities of data (music movies etc) then it should not be beyond our community to release image data. Helen Berman from the pdb mentioned that the pdb could store unmerged reflection data which is great, however, I still feel that we should make our images available so everything can be reprocessed if someone wishes to. In regards to the 2hr0 structure Piet Gros and colleagues made the comment that the issue could be resolved with the release of the images - no mention of that request is made in the reply.
James Richard Baxter <[EMAIL PROTECTED]> wrote:> > Dear All, > > Without passing any judgement on the veracity of C3b structure 2hr0, I > note that the Ca RMSD of this structure with C3 structure 2a73 was > unusually low, compared to the RMSD of 2a73 to the related entries 2a74 > and 2i07 by the same group, bovine C3 structure 2b39 and C3b and C3c > structures 2ice and 2icef. If one took a high resolution structure as a > molecular replacement solution of a new structure at lower resolution > this might be expected, but not vice versa? > > As to whether the structures problem arise from malfeasance or neglect, > I do not understand why the journal did not require the raw images be > made available given the evidence presented against the published data, > isn't that what is done in other fields when such issues are raised? > Isn't it more practical to make the availability of raw data upon > request a requirement of publication more practical than trying to set > up a vast repository of images when submission to that repository is > still a matter of choice? > > I have several questions regarding the reply that I would like to hear > an answer to, perhaps Todd can help obtain them: > > 1. Could the statement "Statistical disorder resulting in apparent > 'gaps' in the lattice has been observed for other proteins" not be > referenced by citation to numerous deposited structures if they indeed > exist? > > 2. I was not convinced that the Z-scores of the PHASER solutions were > significant, shouldn't they be greater than 6.0? It didn't look like > density at 0.7 sigma was contiguous over the main chain. > > 3. Can the domain suggested to fill the void in the asymmetric unit be a > "contaminant" when it must be present in stoichiometric ratio in order > to provide lattice contacts? Why not present a SDS/PAGE gel of a > redissolved crystal, surely that domain would show up. > > 3. I don't understand why the statement "Bulk-solvent modelling is > contentious, making many refinements necessary to constrain parameters > to obtain acceptable values" was considered an acceptable response to > the question of the low resolution data. Whether one chooses to include > low-resolution data with bulk solvent modelling or to truncate the low > res data is a separate issue from the physical effect of solvent on > intensities at low resolution. > > One point in the reply that seemed reasonable is the issue of B-factor > variation, because the deposited C3 structures do exhibit a wide range > in the average <B>, also resolution, and whether TLS refinement was used > and how heavily restraints were set. However, that does not really > address the issue of seemingly random coil without other contacts having > such great contours at 2.5 sigma. > > I would look forward to learning from people with more experience on > these matters. > > sincerely, > > Richard Baxter > > On Thu, 2007-08-16 at 10:11, Green, Todd wrote: >> Hello all, >> >> I started to write a response to this thread yesterday. I thought the >> title was great even the content of Eleanor's email was very helpful. >> What I didn't like was the indictment in the next to last paragraph. >> This has been followed up with the word fabrication by others. No one >> knows definitively if this was fabricated. You have your suspicions, >> but you don't "know." Fabrication suggests malicious wrong-doing. I >> actually don't think this was the case. I'm probably a bit biased >> because the work comes from an office down the hall from my own. I'd >> like to think that if the structure is wrong that it could be chalked >> up to inexperience rather than malice. To me, this scenario of >> inexperience seems like one that could become more and more prevalent >> as our field opens up to more and more scientists doing structural >> work who are not dedicated crystallographers. >> >> Having said that, I think Eleanor started an extremely useful thread >> as a way of avoiding the pitfalls of crystallography whether you are a >> novice or an expert. There's no question that this board is the best >> way to advance one's knowledge of crystallography. I actually gave a >> homework assignment that was simply to sign up for the ccp4bb. >> >> In reference to the previously mentioned work, I'd also like to hear >> discussion concurring or not the response letter some of which seems >> plausible to me. >> >> I hope I don't ruffle anyones feathers by my email, but I just thought >> that it should be said. >> >> Cheers- >> Todd >> >> >> -----Original Message----- >> From: CCP4 bulletin board on behalf of Randy J. Read >> Sent: Thu 8/16/2007 8:22 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] The importance of USING our validation tools >> >> On Aug 16 2007, Eleanor Dodson wrote: >> >> >The weighting in REFMAC is a function of SigmA ( plotted in log >> file). >> >For this example it will be nearly 1 for all resolutions ranges so >> the >> >weights are pretty constant. There is also a contribution from the >> >"experimental" sigma, which in this case seems to be proportional to >> |F| >> >> Originally I expected that the publication of our Brief Communication >> in >> Nature would stimulate a lot of discussion on the bulletin board, but >> clearly it hasn't. One reason is probably that we couldn't be as >> forthright >> as we wished to be. For its own good reasons, Nature did not allow us >> to >> use the word "fabricated". Nor were we allowed to discuss other >> structures >> from the same group, if they weren't published in Nature. >> > -- > Richard Baxter <[EMAIL PROTECTED]> -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
