Re: [ccp4bb] A polite reminder to xia2 users
Dear All, Slightly ignorant and certainly oblique question perhaps, but are there still journals out there which limit the number of references allowed? This used to be a “reason” people would use for not properly citing all of the resources they used in arriving at the results included in the manuscript. In real life, particularly with the move to electronic publication, there should be no excuses or reasons for incomplete citations or citations in supplementary materials (I feel). I guess it should be possible for e.g. processing software to identify the beamline from the correctly populated image header (*) and make for the user’s convenience some kind of mmCIF file (perhaps) with the appropriate citations for beamline and software for *that* data set – though this would require some infrastructure to exist in a public place (PDB?) where this was stored so the software developers could access it to get the right info. This sounds like something we were all discussing in 2006 ☹ Also, I guess people should know where their data came from & be capable of correctly acknowledging this, but it sounds like this is not the case perhaps? *should* pipeline developers be doing more here? Cheerio Graeme = (*) no a given I know… From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marjolein Thunnissen Sent: 06 November 2015 09:12 To: ccp4bb Subject: Re: [ccp4bb] A polite reminder to xia2 users Hi All, This is slightly OT for the list as such but it is of interest of the current thread. I would like to argue that just as important it is to reference to the software in an adequate way, it is also important to give due to the hardware, i.e. the beam lines on which most of the data is collected. Most beamlines have now publications that describe them, it is very important to us that these will be referenced to. This will make it easier for us in the long end to keep them in the best state possible so that you can obtain the best data possible. best regards Marjolein Thunnissen [cid:image001.png@01D11875.0BBFE260] Dr. Marjolein Thunnissen Science Coordinator Structural Biology Chair Special Interest Group 1 (MX) ECA MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/> On 05 Nov 2015, at 20:32, Tim Gruene <tim.gru...@psi.ch<mailto:tim.gru...@psi.ch>> wrote: -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." Va
Re: [ccp4bb] A polite reminder to xia2 users
Perfect segue to bring us back to the origin of this thread. Graeme was reminding the users of Xia2 that Xia2 was using other software for data analysis and that other software to be credited as well. Indeed, when we extract "Xia2 has been used for PDB files reported in X high-impact publications (with IF>Y)", we give all credit to Xia2 and none to the programs used by Xia2 - exactly the point Graeme was making. One (hopefully) practical thought: many of us cite what is recommended by the authors of the software we site, as already suggested in this thread by several colleagues. At the same time, the end users sometimes (in most cases?) are not aware that wrappers use other software underneath. Perhaps the authors of the wrappers could provide the citation of the program(s) used by the said wrappers, and recommend those citations to be used in publications? Just as individual programs provide recommended references. It may not work in all cases but may in some. Best, N. Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Mark J van Raaij [mjvanra...@cnb.csic.es] Sent: Friday, November 06, 2015 5:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] A polite reminder to xia2 users The PDB files should note the programs and beamlines used, I am sure software developers are already using PDB statistics in funding applications? From the PDB database, with a bit of work, one could extract data like “Xia2 has been used for PDB files reported in X high-impact publications (with IF>Y)" or similar. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij > On 6 Nov 2015, at 12:08, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > > That is a problem: journals have their own policies, despite modern online > methods. While we all like to be cited, one of my colleagues was recently > complaining about a 50 reference limit, and was wondering why they were > expected to reference papers for a dozen or so crystallographic programs, > while all the biochemical and cell biological methods could be considered as > “standard” and not need references (no reference for software used to analyse > ITC or mass spec data for example): not to mention beamlines and > synchrotrons, which just get an acknowledgement. > > Phil > >> On 6 Nov 2015, at 18:42, Graeme Winter <graeme.win...@diamond.ac.uk> wrote: >> >> Dear All, >> >> Slightly ignorant and certainly oblique question perhaps, but are there >> still journals out there which limit the number of references allowed? This >> used to be a “reason” people would use for not properly citing all of the >> resources they used in arriving at the results included in the manuscript. >> In real life, particularly with the move to electronic publication, there >> should be no excuses or reasons for incomplete citations or citations in >> supplementary materials (I feel). >> >> I guess it should be possible for e.g. processing software to identify the >> beamline from the correctly populated image header (*) and make for the >> user’s convenience some kind of mmCIF file (perhaps) with the appropriate >> citations for beamline and software for *that* data set – though this would >> require some infrastructure to exist in a public place (PDB?) where this was >> stored so the software developers could access it to get the right info. >> This sounds like something we were all discussing in 2006 ☹ >> >> Also, I guess people should know where their data came from & be capable of >> correctly acknowledging this, but it sounds like this is not the case >> perhaps? *should* pipeline developers be doing more here? >> >> Cheerio Graeme >> >> = >> >> (*) no a given I know… >> >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Marjolein Thunnissen >> Sent: 06 November 2015 09:12 >> To: ccp4bb >> Subject: Re: [ccp4bb] A polite reminder to xia2 users >> >> Hi All, >> >> This is slightly OT for the list as such but it is of interest of the >> current thread. >> >> I would like to argue that just as important it is to reference to the >> software in an adequate way, it is also important to give due to the >> hardware, i.e. the beam lines on which most of the data is collected. Most >> beamlines have now publications
Re: [ccp4bb] A polite reminder to xia2 users
Hardware: Say I do a lot of screening on Beamline A (many hours used), collect a low resolution anomalous dataset on Beamline B, which helps me to solve the structure, then I collect a high resolution native dataset on Beamline C (in just a few minutes) for refinement and model building. Many people deposit just the data from C and acknowledge beamline C and perhaps B. Beamline A is almost always ignored. I think all three beamlines contributed directly to the paper should be cited. There is no other way for the beamline A to assess its impact if it isn't cited. Software: How many of you have ever cited FFTW, CBFLib, etc when those libraries were used behind the scenes by the other programs? Should you be expected to cite them? How far down the dependency chain should that citation list go? I don't think the license should be the determining factor on what gets cited or not. It is a nice suggestion for pipelines to generate a list of relevant citations for the given dataset which includes references to all the software used. But if the pipeline itself was published, and cites all those packages, users should not need to cite the individual packages again. We certainly do not want a situation in which the list of references is 10x longer than the rest of the paper. Just like we do not include all the citations from the papers we cite, we shouldn't be expecting authors to include all the software/libraries used vicariously. Are we perhaps abusing the citation system as a way of "tipping" the hardware/software people? We need a better way of measuring impact, and then using impact for funding applications rather than citations. If I cite XIA2, there should be a mechanism for XDS or MOSFLM to see an increase in their impact due to the XIA2 citations -- because it's 2015. I do not think it is a good idea to *politely* force users of XIA2 to cite all the other programs as well. http://article-level-metrics.plos.org/ /Michel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme Winter Sent: November 6, 2015 3:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] A polite reminder to xia2 users Dear All, Slightly ignorant and certainly oblique question perhaps, but are there still journals out there which limit the number of references allowed? This used to be a “reason” people would use for not properly citing all of the resources they used in arriving at the results included in the manuscript. In real life, particularly with the move to electronic publication, there should be no excuses or reasons for incomplete citations or citations in supplementary materials (I feel). I guess it should be possible for e.g. processing software to identify the beamline from the correctly populated image header (*) and make for the user’s convenience some kind of mmCIF file (perhaps) with the appropriate citations for beamline and software for *that* data set – though this would require some infrastructure to exist in a public place (PDB?) where this was stored so the software developers could access it to get the right info. This sounds like something we were all discussing in 2006 ☹ Also, I guess people should know where their data came from & be capable of correctly acknowledging this, but it sounds like this is not the case perhaps? *should* pipeline developers be doing more here? Cheerio Graeme = (*) no a given I know… From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marjolein Thunnissen Sent: 06 November 2015 09:12 To: ccp4bb Subject: Re: [ccp4bb] A polite reminder to xia2 users Hi All, This is slightly OT for the list as such but it is of interest of the current thread. I would like to argue that just as important it is to reference to the software in an adequate way, it is also important to give due to the hardware, i.e. the beam lines on which most of the data is collected. Most beamlines have now publications that describe them, it is very important to us that these will be referenced to. This will make it easier for us in the long end to keep them in the best state possible so that you can obtain the best data possible. best regards Marjolein Thunnissen [cid:image001.png@01D11875.0BBFE260] Dr. Marjolein Thunnissen Science Coordinator Structural Biology Chair Special Interest Group 1 (MX) ECA MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/> On 05 Nov 2015, at 20:32, Tim Gruene <tim.gru...@psi.ch<mailto:tim.gru...@psi.ch>> wrote: -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.S
Re: [ccp4bb] A polite reminder to xia2 users
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 &g
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 confi
Re: [ccp4bb] A polite reminder to xia2 users
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 >
