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:[log in to unmask]] 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 <[log in to unmask]<mailto:[log in to unmask]>> wrote:
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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]<mailto:[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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