It would also be good if all CCP4 program contributors could check
that their program is (i) listed on that page and (ii) all references
are given - including the preferred citation (maybe in bold if there
more than one).
Some notable absentees are POINTLESS, AIMLESS and MOLREP (I'm sure
there are many more).
Clemens
On Thu, Nov 05, 2015 at 08:31:11PM +0000, Keller, Jacob wrote:
> Okay, makes sense. I googled "refmac citation" and got to the page I mentioned before. Maybe change that page to reflect author preferences?
>
> http://www.ccp4.ac.uk/html/REFERENCES.html
>
> JPK
>
> -----Original Message-----
> From: Tim Gruene [mailto:[log in to unmask]]
> Sent: Thursday, November 05, 2015 2:33 PM
> To: Keller, Jacob
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] A polite reminder to xia2 users
>
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>
> 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]
> > 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
>
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