Dear Phil,
I suppose the license for software used to analyse ITC does not ask for a
citation? That's sometimes the case for software that comes with a commercial
product.
Where positions depend on citations, the software license should be like the
'Creative Commons' with the addition that 'appropriate credit' means 'citing
upon publication'. It would then be illegal to use that program and not cite
it.
Cheers,
Tim
On Friday, November 06, 2015 08:08:54 PM Phil Evans wrote:
> That is a problem: journals have their own policies, despite modern online
> methods. While we all like to be cited, one of my colleagues was recently
> complaining about a 50 reference limit, and was wondering why they were
> expected to reference papers for a dozen or so crystallographic programs,
> while all the biochemical and cell biological methods could be considered
> as “standard” and not need references (no reference for software used to
> analyse ITC or mass spec data for example): not to mention beamlines and
> synchrotrons, which just get an acknowledgement.
>
> Phil
>
> > On 6 Nov 2015, at 18:42, Graeme Winter <[log in to unmask]>
> > wrote:
> >
> > 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:[log in to unmask]] 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:image001.png@01D11875.0BBFE260]
> >
> >
> >
> >
> > 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
> > <[log in to unmask]<mailto:[log in to unmask]>> 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:[log in to unmask]] On Behalf Of
> > Graeme Winter Sent: Thursday, November 05, 2015 9:07 AM
> > To: [log in to unmask]<mailto:[log in to unmask]>
> > 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
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> > =Fvm3
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> >
> >
> >
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--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
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