Re: [ccp4bb] atomic scattering factors in REFMAC
Just for the record, except for charge density studies most small molecule
structures are refined with neutral atom scattering factors even when ions such
as Cl- are present. For example SHELX uses "4 Gaussian plus const:
International
Tables for Crystallography (1992)". Users rarely input ionic scattering factors
rather than using the default neutral atom scattering factors, possibly they are
afraid of a Category A Alert from CheckCIF if they have a charged crystal. In
practice, the difference between ionic and neutral atom scattering factors is
mostly absorbed by the displacement parameters (B-values) and the R-factors are
very similar. The main reason why routine small molecule R-values are rarely
much
less than 2% is the assumption that the scattering factors are spherically
symmetrical, i.e. bonding and lone-pair electrons are ignored. This could be
addressed by the inclusion of invarioms (precalculated aspherical scattering
factors that depend on the local chemical environment of an atom) in Refmac and
Phenix Refine.
George
On Wed, Nov 02, 2011 at 08:39:51PM -0700, Pavel Afonine wrote:
> Continuing on the subject, as far as I know there are at least three flavors
> of
> form-factors currently used in refinement programs:
>
> "4 gaussian plus const":
> International Tables for Crystallography (1992)
>
> "5 gaussian plus const":
> D. Waasmaier & A. Kirfel. Acta Cryst. (1995). A51, 416-431. "New analytical
> scattering-factor functions for free atoms and ions"
>
> "n-gaussian" (n determined dynamically)
> Grosse-Kunstleve RW, Sauter NK & Adams PD. Newsletter of the IUCr Commission
> on
> Crystallographic Computing 2004, 3:22-31. "cctbx news"
>
> All three are available in PHENIX (the 3rd is used by default), and I presume
> the first one is used in CNS and Refmac, if I remember correctly (the authors
> of respective programs please correct me).
>
> Pavel
>
> On Wed, Nov 2, 2011 at 7:17 PM, Ivan Shabalin wrote:
>
> Hi James!
>
> Thank you very much for the gnuplot-ish version of ${CLIBD}/atomsf.lib!!
> It
> works very nice and is very useful for education!
>
> As I understand, the form factor is the Fourier transform of electron
> charge density. It is plotted as f(electrons) vs sin(tetta)/lambda and is
> approximated as 5 Gaussian (Cromer and Mann) in REFMAC. And you made
> reverse Fourier transform of the approximation and plotted the electron
> density distribution in the real space.
>
> So, can I ask, what unit is x? Is it angstrom?
> And what is Y? is it e/A3 (electron density)?
>
> I found, that at Bf=20, density profiles look almost the same for ions and
> atoms (Mg2+ and Mg, Cl- and Cl). Does that means, there is no sense to
> specify atomic charge in refmac refinement? It looks a bit strange,
> because
> the numbers of electrons are different. Or decreasing in number of
> electrons is compensated with significant decrease in atom size (that can
> have the same effect as Bf lowering)? With Bf=0 the difference in curves
> is
> significant.
>
> With best regards,
> Ivan Shabalin
>
>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
Re: [ccp4bb] atomic scattering factors in REFMAC
Dear all, Just as a historic reminder, I feel necessary to mention a key article on refinement, written by R.Aragwal (1978) in Acta Cryst A, where he used 1- and 2-gaussian atomic factors (obviously, less precise that 4 gaussians + constant but allowed him at that moment to accelerate as much as possible the calculations). With best regards, Sacha Urzhumtsev De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Pavel Afonine Envoyé : jeudi 3 novembre 2011 04:40 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] atomic scattering factors in REFMAC Continuing on the subject, as far as I know there are at least three flavors of form-factors currently used in refinement programs: "4 gaussian plus const": International Tables for Crystallography (1992) "5 gaussian plus const": D. Waasmaier & A. Kirfel. Acta Cryst. (1995). A51, 416-431. "New analytical scattering-factor functions for free atoms and ions" "n-gaussian" (n determined dynamically) Grosse-Kunstleve RW, Sauter NK & Adams PD. Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3:22-31. "cctbx news" All three are available in PHENIX (the 3rd is used by default), and I presume the first one is used in CNS and Refmac, if I remember correctly (the authors of respective programs please correct me). Pavel
Re: [ccp4bb] atomic scattering factors in REFMAC
James - you are fantastic!
This is so educational..
Eleanor
On 11/02/2011 02:36 AM, James Holton wrote:
On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin wrote:
Does that mean, that with Bf>10 we cannot distinguish Mg and water by electron
density peak profile? Even if oxygen in water has twice as much bigger radius than
Mg2+?
Yup. Pretty much.
An "Mg+2" with B=10 is almost exactly the same density profile as a
single point electron (atom type "Ano") with occ=9.72 and B=12.7. You
can also fit "water" (an "O" with two "H" atoms on top of it) to Mg+2,
and get a pretty good fit with occ=1 and B=15 for the "water". If you
want to play around with this, I have placed a gnuplot-ish version of
${CLIBD}/atomsf.lib at:
http://bl831.als.lbl.gov/~jamesh/pickup/all_atomff.gnuplot
in gnuplot you can type:
load 'all_atomff.gnuplot'
plot Mg_plus_2_ff(x,20), O_ff(x,15)+2*H_ff(x,15)
and stuff like that.
-James Holton
MAD Scientist
Re: [ccp4bb] atomic scattering factors in REFMAC
James, this doesn't take the effect of resolution cut-offs into
account, right? You appear to be assuming that you have data to
atomic resolution (~ 1 A) or better. The integral of the scattering
factor should be confined to the experimental resolution range,
otherwise it's not going to be very realistic, in fact the calculated
profile is not going to show the observed resolution dependence (and
where the density can go negative). See slides 13 & 14 here
http://www.cse.scitech.ac.uk/events/CCP4_2011/talks/tickle.pdf for the
resolution-dependent version.
Cheers
-- Ian
On Wed, Nov 2, 2011 at 2:36 AM, James Holton wrote:
> On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin wrote:
>> Does that mean, that with Bf>10 we cannot distinguish Mg and water by
>> electron density peak profile? Even if oxygen in water has twice as much
>> bigger radius than Mg2+?
>
> Yup. Pretty much.
>
> An "Mg+2" with B=10 is almost exactly the same density profile as a
> single point electron (atom type "Ano") with occ=9.72 and B=12.7. You
> can also fit "water" (an "O" with two "H" atoms on top of it) to Mg+2,
> and get a pretty good fit with occ=1 and B=15 for the "water". If you
> want to play around with this, I have placed a gnuplot-ish version of
> ${CLIBD}/atomsf.lib at:
>
> http://bl831.als.lbl.gov/~jamesh/pickup/all_atomff.gnuplot
>
> in gnuplot you can type:
> load 'all_atomff.gnuplot'
> plot Mg_plus_2_ff(x,20), O_ff(x,15)+2*H_ff(x,15)
>
> and stuff like that.
>
> -James Holton
> MAD Scientist
>
[ccp4bb] Installation of CCP4 under Windows 7
does not seem to create anything "runnable" - please any experience here? I downloaded the latest Windows package "all users" - type. Installed under admin (as it would not let me otherwise). Now as a user I cannot start the interface no matter what I try. There is no ccp4.setup file ... Jan -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 390 Fax: +420 296 809 410
[ccp4bb] off-topic: Topology diagram
Dear all Does anyone know what tools can get a topology diagram ? Thanks! Zhang Qi lysudiezhang1985 via foxmail
Re: [ccp4bb] off-topic: Topology diagram
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Zhang Qi, I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein which quickly takes you to e.g. pdbsum. Tim On 11/03/2011 01:48 PM, lysudiezhang1985 wrote: > Dear all > > Does anyone know what tools can get a topology diagram ? Thanks! > > Zhang Qi > > > > > lysudiezhang1985 via foxmail - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOspHrUxlJ7aRr7hoRAl96AJ96OykVMr0a68Xm5HtvJ4ifvkUbPgCcDqP2 ru9oCeO1ZG0u++KJMCnrivs= =trrx -END PGP SIGNATURE-
Re: [ccp4bb] Installation of CCP4 under Windows 7
Hmm, works fine for me. Maybe disable user account control? Jacob On Thu, Nov 3, 2011 at 7:54 AM, Jan Dohnalek wrote: > does not seem to create anything "runnable" - please any experience here? > > I downloaded the latest Windows package "all users" - type. Installed under > admin (as it would not let me otherwise). > Now as a user I cannot start the interface no matter what I try. There is no > ccp4.setup file ... > > Jan > > > -- > Jan Dohnalek, Ph.D > Institute of Macromolecular Chemistry > Academy of Sciences of the Czech Republic > Heyrovskeho nam. 2 > 16206 Praha 6 > Czech Republic > > Tel: +420 296 809 390 > Fax: +420 296 809 410 > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Installation of CCP4 under Windows 7
I have slightly different problem. I have windows 7 Enterprise. I don't get any shortcuts on my desktop after installation.I work with admin account. If I try to execute /ccp4-6.2.0/ccp4i/bin/ccp4i.tcl I get the following error. please see attachment.I installed " ActiveTcl8.4.19.5.294332-win32-ix86-threaded" which was available on CCP4 website. Still it didnt helpI would greatly appreciate if you could me help me in solving this problem. ThanksRaj > Date: Thu, 3 Nov 2011 08:35:48 -0500 > From: j-kell...@fsm.northwestern.edu > Subject: Re: [ccp4bb] Installation of CCP4 under Windows 7 > To: CCP4BB@JISCMAIL.AC.UK > > Hmm, works fine for me. Maybe disable user account control? > > Jacob > > On Thu, Nov 3, 2011 at 7:54 AM, Jan Dohnalek wrote: > > does not seem to create anything "runnable" - please any experience here? > > > > I downloaded the latest Windows package "all users" - type. Installed under > > admin (as it would not let me otherwise). > > Now as a user I cannot start the interface no matter what I try. There is no > > ccp4.setup file ... > > > > Jan > > > > > > -- > > Jan Dohnalek, Ph.D > > Institute of Macromolecular Chemistry > > Academy of Sciences of the Czech Republic > > Heyrovskeho nam. 2 > > 16206 Praha 6 > > Czech Republic > > > > Tel: +420 296 809 390 > > Fax: +420 296 809 410 > > > > > > -- > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > *** <>
Re: [ccp4bb] atomic scattering factors in REFMAC
Yes, in my gnuplot "form factor" functions, "x" is the real-space
distance from the center of the atom in Angstrom and the "return value"
is electron density in electrons/A^3.
I did not realize the gnuplot file would be so interesting! If anyone
wants the reciprocal-space version (which is simpler), it is here:
http://bl831.als.lbl.gov/~jamesh/pickup/all_atomsf.gnuplot
Where the "s" value is sin(theta)/lambda and the return value is simply
"electrons". This is because the structure factor is defined as the
ratio of the scattering to the atom (or any other object) to the
scattering from a single point electron at the origin (Debye & Scherrer,
Phys Z. 1918; Hartree, Philo Mag. 1925).
The incorporation of a B factor is formally a convolution in real space
(blurring function), which translates into a simple multiplication in
reciprocal space. The funky (4*pi/B)**1.5 factors in the real-space
functions arise because the total number of electrons must not change
when you apply a B factor. This is why the peak height goes down with
increasing B, and you also rapidly loose any "atomic radius" information
as the width of the B-factor Gaussian becomes large when compared to the
width of the relevant Ee_ff(x,0) function.
Ian has also pointed out that none of this considers the mechanics of
how you actually calculate maps, where things like "series termination
error" come into play. But perhaps that is a topic for a new thread?
-James Holton
MAD Scientist
On 11/2/2011 7:17 PM, Ivan Shabalin wrote:
Hi James!
Thank you very much for the gnuplot-ish version of ${CLIBD}/atomsf.lib!! It
works very nice and is very useful for education!
As I understand, the form factor is the Fourier transform of electron charge
density. It is plotted as f(electrons) vs sin(tetta)/lambda and is approximated
as 5 Gaussian (Cromer and Mann) in REFMAC. And you made reverse Fourier
transform of the approximation and plotted the electron density distribution in
the real space.
So, can I ask, what unit is x? Is it angstrom?
And what is Y? is it e/A3 (electron density)?
I found, that at Bf=20, density profiles look almost the same for ions and
atoms (Mg2+ and Mg, Cl- and Cl). Does that means, there is no sense to specify
atomic charge in refmac refinement? It looks a bit strange, because the numbers
of electrons are different. Or decreasing in number of electrons is compensated
with significant decrease in atom size (that can have the same effect as Bf
lowering)? With Bf=0 the difference in curves is significant.
With best regards,
Ivan Shabalin
Re: [ccp4bb] Archiving Images for PDB Depositions
I tried looking for such "evil symmetry problem" examples some time ago, only to find that primitive monoclinic with a 90-degree beta angle is much more rare than one might think by looking at the PDB. About 1/3 of them are in the wrong space group. Indeed, there are at least 366 PDB entries that claim "P2-ish", but POINTLESS thinks the space group of the deposited data is higher (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned data, but at least 286 of these entries do not mention twinning. Of these, 40 explicitly list NCS operators (not sure if the others used NCS?), and 35 of those were both solved by molecular replacement an explicitly say the free-R set was picked at random. These are: Now, I'm sure there is an explanation for each and every one of these. But in the hands of a novice, such cases could easily result in a completely wrong structure giving a perfectly reasonable Rfree. This would happen if you started with, say, a wrong MR solution, but picked your random Rfree set in PG2 and then applied "NCS". Then each of your "free" hkls would actually be NCS-restrained to be the same as a member of the working set. However, I'm sure everyone who reads the CCP4BB already knew that. Perhaps because a discerning peer-reviewer, PDB annotator or some clever feature in our modern bullet-proof crystallographic software caught such a mistake for them. (Ahem) Of course, what Graeme is asking for is the opposite of this: data that would appear as "nearly" PG222, but was actually lower symmetry. Unfortunately, there is no way to identify such cases from deposited Fs alone, as they will have been overmerged. In fact, I did once see a talk where someone managed to hammer an NCS 7-fold into a crystallographic 2-fold by doing some aggressive "outlier rejection" in scaling. Can't remember if that ever got published... -James Holton MAD Scientist On 11/2/2011 1:33 AM, Graeme Winter wrote: Hi Ed, Ok, I'll bite: I would be very interested to see any data sets which initially were thought to be e.g. PG222 and scale OK ish with that but turn out in hindsight to be say PG2. Trying to automatically spot this or at least warn inside xia2 would be really handy. Any pseudosymmetric examples interesting. Also any which are pseudocentred - index OK in C2 (say) but should really be P2 (with the same cell) as the "missing" reflections are in fact present but are just rather weaker due to NCS. I have one example of each from the JCSG but more would be great, especially in cases where the structure was solved& deposited. There we go. Now the matter of actually getting these here is slightly harder but if anyone has an example I will work something out. Please get in touch off-list... I will respond to the BB in a week or so to feed back on how responses to this go :o) Best wishes, Graeme
Re: [ccp4bb] Archiving Images for PDB Depositions
Hi James, scary ... I was just looking at exactly the same thing (P21 with beta~90), using the same tool (POINTLESS). Currently I'm going through the structures for which images can be found ... I haven't gone far through that list yet (in fact actually only the first one), but this first case should indeed be in a higher spacegroup (P 2 21 21). As you say (and that's what Graeme looks for): finding 'over-merged' datasets can be a bit more tricky ... once the damage is done. I have the hunch that it might happen even more often though: we tend to look for the highest symmetry that still gives a good indexing score, right? Otherwise we would all go for P1 ... Some other interesting groups for under-merging: * orthorhombic with a==b or a==c or b==c (maybe tetragonal?) * trigonal (P 3 etc) when it should be P 6 * monoclinic with beta==120 A few cases for each of those too ... all easy to check in ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx and then (if structure factors are deposited) running POINTLESS on it (great program Phil!). Cheers Clemens On Thu, Nov 03, 2011 at 12:00:33PM -0700, James Holton wrote: > I tried looking for such "evil symmetry problem" examples some time > ago, only to find that primitive monoclinic with a 90-degree beta > angle is much more rare than one might think by looking at the PDB. > About 1/3 of them are in the wrong space group. > > Indeed, there are at least 366 PDB entries that claim "P2-ish", but > POINTLESS thinks the space group of the deposited data is higher > (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned > data, but at least 286 of these entries do not mention twinning. Of > these, 40 explicitly list NCS operators (not sure if the others used > NCS?), and 35 of those were both solved by molecular replacement an > explicitly say the free-R set was picked at random. These are: > > Now, I'm sure there is an explanation for each and every one of > these. But in the hands of a novice, such cases could easily result > in a completely wrong structure giving a perfectly reasonable Rfree. > This would happen if you started with, say, a wrong MR solution, but > picked your random Rfree set in PG2 and then applied "NCS". Then > each of your "free" hkls would actually be NCS-restrained to be the > same as a member of the working set. However, I'm sure everyone who > reads the CCP4BB already knew that. Perhaps because a discerning > peer-reviewer, PDB annotator or some clever feature in our modern > bullet-proof crystallographic software caught such a mistake for > them. (Ahem) > > Of course, what Graeme is asking for is the opposite of this: data > that would appear as "nearly" PG222, but was actually lower > symmetry. Unfortunately, there is no way to identify such cases > from deposited Fs alone, as they will have been overmerged. In > fact, I did once see a talk where someone managed to hammer an NCS > 7-fold into a crystallographic 2-fold by doing some aggressive > "outlier rejection" in scaling. Can't remember if that ever got > published... > > -James Holton > MAD Scientist > > On 11/2/2011 1:33 AM, Graeme Winter wrote: > >Hi Ed, > > > >Ok, I'll bite: I would be very interested to see any data sets which > >initially were thought to be e.g. PG222 and scale OK ish with that but > >turn out in hindsight to be say PG2. Trying to automatically spot this > >or at least warn inside xia2 would be really handy. Any > >pseudosymmetric examples interesting. > > > >Also any which are pseudocentred - index OK in C2 (say) but should > >really be P2 (with the same cell) as the "missing" reflections are in > >fact present but are just rather weaker due to NCS. > > > >I have one example of each from the JCSG but more would be great, > >especially in cases where the structure was solved& deposited. > > > >There we go. > > > >Now the matter of actually getting these here is slightly harder but > >if anyone has an example I will work something out. Please get in > >touch off-list... I will respond to the BB in a week or so to feed > >back on how responses to this go :o) > > > >Best wishes, > > > >Graeme -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Archiving Images for PDB Depositions
not sure I follow this thread, but this table might be interesting : http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf from: Detection and correction of underassigned rotational symmetry prior to structure deposition B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Sauter Acta Cryst. (2010). D66, 503-513[ doi:10.1107/S0907444910001502 ]
Re: [ccp4bb] Archiving Images for PDB Depositions
On Thu, Nov 03, 2011 at 04:13:44PM -0400, Bryan Lepore wrote: > not sure I follow this thread, but this table might be interesting : > > http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf > > from: > > Detection and correction of underassigned rotational symmetry prior to > structure deposition > B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Sauter > Acta Cryst. (2010). D66, 503-513[ doi:10.1107/S0907444910001502 ] Oh yes, that is relevant and very interesting. As far as I understand it, the detection of higher symmetry is based on the atomic coordinates and not structure factors though (please correct me if I'm wrong here). At least some of the cases for which the deposited structure factors strongly suggest a higher symmetry don't seem to be detected using that papers approach (I can't find them listed in the supplemental). Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Archiving Images for PDB Depositions
God bess the symmetry, we are saved from the over-interpreting symmetry (except probably of very exotic cases) by the very high Rsym factors around 40% 50% if the symmetry is wrong. Even wild rejection of outliers, cannot reform "acceptable" Rmerge. In my personal repository, 1QZV is a manifest of that. In 4.4 angstrom resolution, wrong interpretation of 90.2 angle monoclinic angle as 90 degrees orthorhombic supported by two molecules in the monoclinic asymmetric was corrected in the middle of the first data collection. Habitual on-fly processing of the data (integration and repetitive scaling after every several frames with HKL) detected that about half-through the data R factor in orthorhombic space group jumped to 40% from about 7%. Reindexing solved the problem on the spot. I still keep the raw data. Needless to say that before about a decade we would make precession photographs (I still own precession camera) and would not make such a mistake. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 3, 2011, at 21:42, Clemens Vonrhein wrote: Hi James, scary ... I was just looking at exactly the same thing (P21 with beta~90), using the same tool (POINTLESS). Currently I'm going through the structures for which images can be found ... I haven't gone far through that list yet (in fact actually only the first one), but this first case should indeed be in a higher spacegroup (P 2 21 21). As you say (and that's what Graeme looks for): finding 'over-merged' datasets can be a bit more tricky ... once the damage is done. I have the hunch that it might happen even more often though: we tend to look for the highest symmetry that still gives a good indexing score, right? Otherwise we would all go for P1 ... Some other interesting groups for under-merging: * orthorhombic with a==b or a==c or b==c (maybe tetragonal?) * trigonal (P 3 etc) when it should be P 6 * monoclinic with beta==120 A few cases for each of those too ... all easy to check in ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx and then (if structure factors are deposited) running POINTLESS on it (great program Phil!). Cheers Clemens On Thu, Nov 03, 2011 at 12:00:33PM -0700, James Holton wrote: I tried looking for such "evil symmetry problem" examples some time ago, only to find that primitive monoclinic with a 90-degree beta angle is much more rare than one might think by looking at the PDB. About 1/3 of them are in the wrong space group. Indeed, there are at least 366 PDB entries that claim "P2-ish", but POINTLESS thinks the space group of the deposited data is higher (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned data, but at least 286 of these entries do not mention twinning. Of these, 40 explicitly list NCS operators (not sure if the others used NCS?), and 35 of those were both solved by molecular replacement an explicitly say the free-R set was picked at random. These are: Now, I'm sure there is an explanation for each and every one of these. But in the hands of a novice, such cases could easily result in a completely wrong structure giving a perfectly reasonable Rfree. This would happen if you started with, say, a wrong MR solution, but picked your random Rfree set in PG2 and then applied "NCS". Then each of your "free" hkls would actually be NCS-restrained to be the same as a member of the working set. However, I'm sure everyone who reads the CCP4BB already knew that. Perhaps because a discerning peer-reviewer, PDB annotator or some clever feature in our modern bullet-proof crystallographic software caught such a mistake for them. (Ahem) Of course, what Graeme is asking for is the opposite of this: data that would appear as "nearly" PG222, but was actually lower symmetry. Unfortunately, there is no way to identify such cases from deposited Fs alone, as they will have been overmerged. In fact, I did once see a talk where someone managed to hammer an NCS 7-fold into a crystallographic 2-fold by doing some aggressive "outlier rejection" in scaling. Can't remember if that ever got published... -James Holton MAD Scientist On 11/2/2011 1:33 AM, Graeme Winter wrote: Hi Ed, Ok, I'll bite: I would be very interested to see any data sets which initially were thought to be e.g. PG222 and scale OK ish with that but turn out in hindsight to be say PG2. Trying to automatically spot this or at least warn inside xia2 would be really handy. Any pseudosymmetric examples interesting. Also any which are pseudocentred - index OK in C2 (say) but should really be P2 (with the same cell) as the "missing" reflections are in fact present but are just rather weaker due to NCS. I have one example of each from the JCSG but more would be great, especially in ca
Re: [ccp4bb] Archiving Images for PDB Depositions
Clemens, In the past, we have used TRACER (free domain) for higher symmetry or we interpreted manually Niggly values :-) TRACER is gone long time ago. Niggly values are not displayed anymore, so we trust auto indexing of DENZO which, assuming all experimental parameters are properly set ( we do this by using a standard crystal such as lysozyme) is extremely sensitive in defining Bravais system. I have no experience with POINTLESS, but assume that it is also doing an excellent work. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 3, 2011, at 22:27 , Clemens Vonrhein wrote: > On Thu, Nov 03, 2011 at 04:13:44PM -0400, Bryan Lepore wrote: >> not sure I follow this thread, but this table might be interesting : >> >> http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf >> >> from: >> >> Detection and correction of underassigned rotational symmetry prior to >> structure deposition >> B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Sauter >> Acta Cryst. (2010). D66, 503-513[ doi:10.1107/S0907444910001502 ] > > Oh yes, that is relevant and very interesting. As far as I understand > it, the detection of higher symmetry is based on the atomic > coordinates and not structure factors though (please correct me if I'm > wrong here). > > At least some of the cases for which the deposited structure factors > strongly suggest a higher symmetry don't seem to be detected using > that papers approach (I can't find them listed in the supplemental). > > Cheers > > Clemens > > -- > > *** > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * > * Global Phasing Ltd. > * Sheraton House, Castle Park > * Cambridge CB3 0AX, UK > *-- > * BUSTER Development Group (http://www.globalphasing.com) > ***
Re: [ccp4bb] off-topic: Topology diagram
That lmgtfy.com is as almost as cool as HHpred. Thanks for a very useful piece of information! Petr On Nov 3, 2011, at 2:06 PM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Zhang Qi, > > I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein > which quickly takes you to e.g. pdbsum. > > Tim > > On 11/03/2011 01:48 PM, lysudiezhang1985 wrote: >> Dear all >> >> Does anyone know what tools can get a topology diagram ? Thanks! >> >> Zhang Qi >> >> >> >> >> lysudiezhang1985 via foxmail > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFOspHrUxlJ7aRr7hoRAl96AJ96OykVMr0a68Xm5HtvJ4ifvkUbPgCcDqP2 > ru9oCeO1ZG0u++KJMCnrivs= > =trrx > -END PGP SIGNATURE-
