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
-----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]
> 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-----
|