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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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