Hardware: Say I do a lot of screening on Beamline A (many hours used), collect a low resolution anomalous dataset on Beamline B, which helps me to solve the structure, then I collect a high resolution native dataset on Beamline C (in just a few minutes) for refinement and model building. Many people deposit just the data from C and acknowledge beamline C and perhaps B. Beamline A is almost always ignored. I think all three beamlines contributed directly to the paper should be cited. There is no other way for the beamline A to assess its impact if it isn't cited.
Software: How many of you have ever cited FFTW, CBFLib, etc when those libraries were used behind the scenes by the other programs? Should you be expected to cite them? How far down the dependency chain should that citation list go? I don't think the license should be the determining factor on what gets cited or not. It is a nice suggestion for pipelines to generate a list of relevant citations for the given dataset which includes references to all the software used. But if the pipeline itself was published, and cites all those packages, users should not need to cite the individual packages again. We certainly do not want a situation in which the list of references is 10x longer than the rest of the paper. Just like we do not include all the citations from the papers we cite, we shouldn't be expecting authors to include all the software/libraries used vicariously. Are we perhaps abusing the citation system as a way of "tipping" the hardware/software people? We need a better way of measuring impact, and then using impact for funding applications rather than citations. If I cite XIA2, there should be a mechanism for XDS or MOSFLM to see an increase in their impact due to the XIA2 citations -- because it's 2015. I do not think it is a good idea to *politely* force users of XIA2 to cite all the other programs as well. http://article-level-metrics.plos.org/ /Michel -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Graeme Winter Sent: November 6, 2015 3:42 AM To: [email protected] Subject: Re: [ccp4bb] A polite reminder to xia2 users Dear All, Slightly ignorant and certainly oblique question perhaps, but are there still journals out there which limit the number of references allowed? This used to be a “reason” people would use for not properly citing all of the resources they used in arriving at the results included in the manuscript. In real life, particularly with the move to electronic publication, there should be no excuses or reasons for incomplete citations or citations in supplementary materials (I feel). I guess it should be possible for e.g. processing software to identify the beamline from the correctly populated image header (*) and make for the user’s convenience some kind of mmCIF file (perhaps) with the appropriate citations for beamline and software for *that* data set – though this would require some infrastructure to exist in a public place (PDB?) where this was stored so the software developers could access it to get the right info. This sounds like something we were all discussing in 2006 ☹ Also, I guess people should know where their data came from & be capable of correctly acknowledging this, but it sounds like this is not the case perhaps? *should* pipeline developers be doing more here? Cheerio Graeme ===== (*) no a given I know… From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Marjolein Thunnissen Sent: 06 November 2015 09:12 To: ccp4bb Subject: Re: [ccp4bb] A polite reminder to xia2 users Hi All, This is slightly OT for the list as such but it is of interest of the current thread. I would like to argue that just as important it is to reference to the software in an adequate way, it is also important to give due to the hardware, i.e. the beam lines on which most of the data is collected. Most beamlines have now publications that describe them, it is very important to us that these will be referenced to. This will make it easier for us in the long end to keep them in the best state possible so that you can obtain the best data possible. best regards Marjolein Thunnissen [cid:[email protected]] Dr. Marjolein Thunnissen Science Coordinator Structural Biology Chair Special Interest Group 1 (MX) ECA MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/> On 05 Nov 2015, at 20:32, Tim Gruene <[email protected]<mailto:[email protected]>> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jacob, I tend to follow the authors' suggestion. When you start refmac, even without any options, it says: Main reference "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 The same is true for many other programs. Best, Tim On Thursday, November 05, 2015 04:22:24 PM Keller, Jacob wrote: I have a general question about this: many programs in CCP4 have interdependencies, so does one have to ferret out and cite all dependencies? For example, I recently was looking up the citation for Refmac, and was astonished to see the list below. Now, are we really supposed to cite all nine of these for each time Refmac is used/mentioned (provided those features were used)? I certainly understand the reasoning for accumulating citations for continued funding, but, well...really? JPK Refmac "Application of Maximum Likelihood Refinement" G. Murshudov, A.Vagin and E.Dodson, (1996) in the Refinement of Protein structures, Proceedings of Daresbury Study Weekend. "Refinement of Macromolecular Structures by the Maximum-Likelihood method" G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) in Acta Cryst. D53, 240-255. "Incorporation of Prior Phase Information Strengthen Maximum-Likelihood Structure Refinemen" N.J.Pannu, G.N.Murshudov, E.J.Dodson and R.J.ReadA (1998) Acta Cryst. section D54, 1285-1294. "Efficient anisotropic refinement of Macromolecular structures using FFT" G.N.Murshudov, A.Lebedev, A.A.Vagin, K.S.Wilson and E.J.Dodson (1999) Acta Cryst. section D55, 247-255. "Use of TLS parameters to model anisotropic displacements in macromolecular refinement" M. Winn, M. Isupov and G.N.Murshudov (2000) Acta Cryst. 2001:D57 122-133 "Fisher's information matrix in maximum likelihood molecular refinement." Steiner R, Lebedev, A, Murshudov GN. Acta Cryst. 2003 D59: 2114-2124 "Macromolecular TLS refinement in REFMAC at moderate resolutions," Winn MD, Murshudov GN, Papiz MZ. Method in Enzymology, 2003:374 300-321 "Direct incorporation of experimental phase information in model refinement" Skubak P, Murshudov GN, Pannu NS. Acta Cryst. 2004 D60: 2196-2201 "REFMAC5 dictionary: organisation of prior chemical knowledge and guidelines for its use." Vagin, AA, Steiner, RS, Lebedev, AA, Potterton, L, McNicholas, S, Long, F and Murshudov, GN. Acta Cryst. 2004 D60: 2284-2295 -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Graeme Winter Sent: Thursday, November 05, 2015 9:07 AM To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] A polite reminder to xia2 users Dear xia2 users on the CCP4bb, While we of course welcome any recognition of the use of xia2 in structure depositions and publications, we would like to gently remind users that xia2 uses other software *on your behalf* for example but not limited to XDS, pointless, aimless, mosflm, DIALS, CCP4. Please could you also include the citations for these packages in your publications and depositions, so that the software used on your behalf gets appropriate recognition :) This is made slightly easier for you as xia2 writes out appropriate citations for the packages it has used as illustrated here http://xia2.blogspot.co.uk/2015/11/xia2-citing-software-xia2-has-used.html If you have found xia2 *and* XDS useful (say) in a PDB deposition where the processing was performed with xia2 -3d, then appropriate text could be REMARK 200 INTENSITY-INTEGRATION SOFTWARE : xia2/XDS REMARK 200 DATA SCALING SOFTWARE : xia2/XSCALE or REMARK 200 INTENSITY-INTEGRATION SOFTWARE : xia2/MOSFLM REMARK 200 DATA SCALING SOFTWARE : xia2/AIMLESS since this would recognise the contributions of the program authors while making it clear that the "blame" for any poor choices made in the processing belonged to xia2. We appreciate in some cases (not limited to Diamond Light Source) the MTZ file from your data may appear "by magic" and you may not have run the software yourself - even in this case it should be straightforward to find out from the log file, which should be looked at, which packages were used. We appreciate your help with this, it makes our relationship with other program authors *much* easier. Thanks & best wishes Graeme - -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5754 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFWO67VUxlJ7aRr7hoRAnpmAJ9okhimWn+jf5v3VAKjd1uTi2xQEQCeLOfw FroobO8eSH1TBOsXBqlPaRs= =Fvm3 -----END PGP SIGNATURE----- -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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