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Jacob Personally I tend to use last general reference for each given program. Don't know if this is a general rule for others, or if xia2 is up to date in this regard. Best wishes Graeme > On 5 Nov 2015, at 17:44, Keller, Jacob <[log in to unmask]> wrote: > > Yes it seems there are some typos, like "refinemen[sic]." > > But the general question remains: should authors really cite all of these papers when Refmac is used? What's the best practice? > > JPK > > -----Original Message----- > From: Steiner, Roberto [mailto:[log in to unmask]] > Sent: Thursday, November 05, 2015 11:42 AM > To: Keller, Jacob > Cc: <[log in to unmask]> > Subject: Re: [ccp4bb] A polite reminder to xia2 users > > shocking ! it should have been Steiner, RA (not Steiner R or Steiner, RS,) > > plus the most recent one is missing from the list….! > > REFMAC5 for the refinement of macromolecular crystal structures. > Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. > Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. > > > Cheers > Roberto (A.) > > > >> On 5 Nov 2015, at 16:22, Keller, Jacob <[log in to unmask]> 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 >> >> -- >> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. >> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. >> Diamond Light Source Limited (company no. 4375679). Registered in >> England and Wales with its registered office at Diamond House, Harwell >> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United >> Kingdom > > > Roberto A. Steiner, PhD > Randall Division of Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London > > [log in to unmask] > Phone 0044 20 78488216 > Fax 0044 20 78486435 > > Room 3.10A > New Hunt's House > Guy's Campus > SE1 1UL > London > -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom