For ‘standard refinement’ I typically cite the most recent general paper. In the case of Refmac:
> 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. With best wishes RAS > On 5 Nov 2015, at 17:40, Keller, Jacob <kell...@janelia.hhmi.org> 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:roberto.stei...@kcl.ac.uk] > Sent: Thursday, November 05, 2015 11:42 AM > To: Keller, Jacob > Cc: <CCP4BB@JISCMAIL.AC.UK> > 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 <kell...@janelia.hhmi.org> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Graeme Winter >> Sent: Thursday, November 05, 2015 9:07 AM >> To: CCP4BB@JISCMAIL.AC.UK >> 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 > > roberto.stei...@kcl.ac.uk > Phone 0044 20 78488216 > Fax 0044 20 78486435 > > Room 3.10A > New Hunt's House > Guy's Campus > SE1 1UL > London > Roberto A. Steiner, PhD Randall Division of Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London roberto.stei...@kcl.ac.uk Phone 0044 20 78488216 Fax 0044 20 78486435 Room 3.10A New Hunt's House Guy's Campus SE1 1UL London
