[ccp4bb] B-factor statistics around an ion - Summary
Dear all,
I received a few replies to my request, all but Pavel's privately.
Those included suggestions of using moleman2, pymol, baverage (from ccp4).
Several required manual intervention like visual selection of the
responding atoms, which made them less appealing to me.
I used Robbie Joosten's suggestion who pointed out that the PDB updated
all PDB entries to contain link records and that these link records
match the atom description on the ATOM/HETATM cards.
As my perl script had a bug I could not resolve within an acceptable
period of time I wrote a c++ program which makes use of the STL map to
create per-Atom statistics of the atoms within the link record.
I attach the program in case anyone is interested. It is not debugged
and utterly slow (21s for 50PDB files), but it served my purpose.
Thanks to everyone who responded.
Best,
Tim
On 01/23/2014 01:36 PM, Tim Gruene wrote:
Dear all,
could anyone suggest a way to get the average B-factor from a PDB-file
of those atoms a specific ion binds to (e.g. as judged by header LINK
records or a distance interval)?
I would like to get this number for all K-ions from a set of
PDB-files, and I hope there is a quicker way than using coot to click
on the surrounding atoms and transfer the numbers into a chart.
Best,
Tim
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
#include iostream
#include fstream
#include vector
#include map
#include string
class KData {
public:
double BK_;
double enviB_;
int numenvi_;
KData() : BK_(0.0),
enviB_(0.0), numenvi_(0) {
}
};
void printKs(const std::mapstd::string, std::vectorstd::string Ks) {
std::mapstd::string, std::vectorstd::string ::const_iterator it;
for (it = Ks.begin(); it != Ks.end(); ++it) {
std::cout K: it-first :\n;
std::vectorstd::string::const_iterator it2;
for (it2 = it-second.begin(); it2 != it-second.end(); ++it2) {
std::cout --- *it2 \n;
}
}
}
void printData (const std::mapstd::string, KData data) {
std::mapstd::string, KData::const_iterator it;
for (it = data.begin(); it != data.end(); ++it) {
std::cout # --- \ it-first \:
number of LINKed atoms:
it-second.numenvi_ ;
B/ average B:\n
it-second.BK_
it-second.enviB_ / it-second.numenvi_ \n;
}
}
void checkline(const std::string line,
const std::mapstd::string, std::vectorstd::string Ks,
std::mapstd::string, KData data) {
std::mapstd::string, std::vectorstd::string ::const_iterator it;
for (it = Ks.begin(); it != Ks.end(); ++it) {
if (line.find(it-first) != std::string::npos) {
std::string B(line.substr(60, 6));
double b(std::stod(B));
data[it-first].BK_ = b;
}
std::vectorstd::string::const_iterator it2;
for (it2 = it-second.begin(); it2 != it-second.end(); ++it2) {
if (line.find(*it2) != std::string::npos) {
std::string B(line.substr(60, 6));
double b(std::stod(B));
data[it-first].enviB_ += b;
++(data[it-first].numenvi_);
}
}
}
}
int main(int argc, char* argv[]) {
std::mapstd::string, std::vectorstd::string Kenvi;
std::mapstd::string, KData data;
if (argc 2) {
std::cout *** Error: please provide one of more PDB filenames.\n;
}
char* line;
int linewidth(100);
line = new char[linewidth + 1];
for (int i = 1; i argc; ++i) {
std::ifstream inp(argv[i]);
if (!inp.is_open()) {
std::cout --- Cannot open file argv[i] \n;
}
// extract link records
while (true) {
inp.getline(line, linewidth);
if (!inp.good()) break;
std::string myline(line);
// break on CRYST1
if (myline.substr(0, 6) == CRYST1) {
break;
}
if (myline.substr(0, 4) == LINK) {
std::string atom1 = myline.substr(12, 14);
std::string atom2 = myline.substr(42, 14);
if (atom1.find( K) != std::string::npos) {
Kenvi[atom1].push_back(atom2);
} else if (atom2.find( K) != std::string::npos) {
Kenvi[atom2].push_back(atom1);
}
}
}
// map is set, find atoms
while (true) {
inp.getline(line, linewidth);
if (!inp.good()) break;
std::string myline(line);
if (myline.substr(0, 6) == ATOM ||
myline.substr (0, 6) == HETATM) {
// check each line against map content to extract K-values
checkline (myline, Kenvi, data);
}
}
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
In the case of F1-ATPase they are not biologically independent copies in the a.u. though, rather subunits of a biological complex... (but perhaps I interpreted the question to narrowly) Mark J van Raaij Lab 20B 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 28 Jan 2014, at 05:38, Frank von Delft wrote: F1 ATPase. Got some Nobel glamour too. Sent from tiny silly touch screen - Reply message - From: Aaron Thompson aaron.a.thomp...@gmail.com Date: Tue, Jan 28, 2014 01:10 Subject: [ccp4bb] Examples of multiple ASU copies with different conformations To: CCP4BB@JISCMAIL.AC.UK The structure of kappa opioid receptor fused with T4 lysozyme (4DJH) contains two copies in the ASU – each copy displays a different orientation between the receptor and lysozyme. On Mon, Jan 27, 2014 at 10:08 AM, Shane Caldwell shane.caldwel...@gmail.com wrote: Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University
[ccp4bb] AW: [ccp4bb] Examples of multiple ASU copies with different conformations
Dear Shane, Human antithrombin III (code 1ath) is a dimer of an active and latent conformation. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Shane Caldwell Gesendet: Montag, 27. Januar 2014 19:09 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Examples of multiple ASU copies with different conformations Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
Dear Shane, To add a bit of detail to Frank von Delft's suggestion, perhaps the best example is the structure of the yeast F1-ATPase that has 3 copies in the asu, from David Mueller's lab in Chicago. Two of these are very similar, but the third is rather different and shows a (physiologically relevant) phosphate binding site that is not found in the other two copies. I would not describe the differences as dramatic though. The paper is: Kabaleeswaran et al., EMBO J 25, 5433 (2006) PDB ID 2HLD Best wishes, Andrew Leslie On 27 Jan 2014, at 18:08, Shane Caldwell shane.caldwel...@gmail.com wrote: Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
Hi there,
another nice kinase example might be IRAK-4. there are several pdbs,
the one I have in mind is 2OIB. The alphaC helix that takes on
different conformations in active and inactive conformations in
kinases ('in' and 'out') is in four different positions in the four
different copies per asu. A side note is that in this particular
kinase, the helix-out conformation is the active conformation.
Baerbel
On Mon, Jan 27, 2014 at 10:08 AM, Shane Caldwell shane.caldwel...@gmail.com
wrote:
Hi ccp4bb,
I'm putting together a talk for some peers that highlights strengths and
weaknesses of structural models for the outsider. For one point, I'd like
to find some examples of proteins that show very different conformations
between different copies in the ASU. One example I know of is
c-Abl (1OPL),
which crystallizes with both autoinhibited and active forms in the ASU,
with dramatically different domain organization. I'd like to find some
additional examples - can anyone suggest some other structures that have
multiple copies with large structural variations?
Thanks in advance!
Shane Caldwell
McGill University
--
Bärbel Blaum, Ph.D.
Interfakultäres Institut für Biochemie (IFIB)
Hoppe-Seyler-Strasse 4
D-72076 Tübingen
Germany
+49 70 71 29 73 375
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
If you are including two copies in a single biological complex, then the two halves of the reverse transcriptase heterodimer have dramatically different domain organizations (OK, one copy is truncated - losing one whole domain out of five; PDB codes ad nauseam). Indeed one stretch of sequence at the end of domain 4 is extended in one copy and alpha helical in the other.
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
Dear Shane, the others have already given very good examples of high impact biology structures; I would still like to add the structure PDB:1J49 (Razeto et al. (2002). JMB 318, 109). Its a structure of a D-Lactate dehydrogenase, a two-domain enzyme, where one ASU subunit adopts an open and the other one a closed conformation - a very interesting case imho. Regards, Fabio Date:Mon, 27 Jan 2014 13:08:33 -0500 From:Shane Caldwell shane.caldwel...@gmail.com Subject: Examples of multiple ASU copies with different conformations Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University -- Dr. rer. nat. Fabio Dall'Antonia European Molecular Biology Laboratory c/o DESY Notkestraße 85, Bldg. 25a D-22603 Hamburg phone: +49 (0)40 89902-178 fax:+49 (0)40 89902-149 e-mail: fabio.dallanto...@embl-hamburg.de
[ccp4bb] Lysis of E coli
Dear All, Does anyone have experience with the FreezerMill for lysing E coli? see: http://www.spexsampleprep.com/products_by_category.aspx?cat=2 It seems to be more for tissues, but perhaps it could also be used for lysing reasnoble quantities of E coli - the reason for asking is that I have to decide whether it would be useful for us and if so, to support its purchase. Greetings, Mark Mark J van Raaij Lab 20B 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
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
Hi Shane, One example that comes to mind is aquaporin-z. Two protomers were found in the ASU, one contained the water channel in an open conformation while the other in a closed conformation. The structural differences are not “large” but the functional implication is. Here is the primary citation Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z. Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JD 3rd, Stroud RM. PLoS Biol. 2003 Dec;1(3):E72. Epub 2003 Dec 22. Kind regards Tamir —— gon...@hhmi.org On Jan 27, 2014, at 1:08 PM, Shane Caldwell shane.caldwel...@gmail.com wrote: Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University
Re: [ccp4bb] Lysis of E coli
We do not have experience with this product. We use a BeadBeater. Can handle up to 25-30 g of wet packed cells in the medium beater jar. The large jar will handle maybe 3-5x that, but I've never had to go to that scale. ___ Roger Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 01/28/2014 08:21 AM, Mark J van Raaij wrote: Dear All, Does anyone have experience with the FreezerMill for lysing E coli? see: http://www.spexsampleprep.com/products_by_category.aspx?cat=2 It seems to be more for tissues, but perhaps it could also be used for lysing reasnoble quantities of E coli - the reason for asking is that I have to decide whether it would be useful for us and if so, to support its purchase. Greetings, Mark Mark J van Raaij Lab 20B 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
Re: [ccp4bb] Examples of multiple ASU copies with different conformations
Another interesting example might be a structure of Mad2, protein essential in the process of chromosome segregation. Protein has 2 different secondary structure topologies and both of them are part of the AU in 2V64. There are other X-ray structures where only one of the conformations is captured in the crystal. Good luck, Nikolina Nikolina Sekulic, PhD Research Associate Department of Biochemistry and Biophysics University of Pennsylvania Stellar-Chance Laboratory 912 422 Curie Blvd, Philadelphia cell: 312-437-9095 lab: 215-898-4476 e-mail: seku...@mail.med.upenn.edu On Tue, Jan 28, 2014 at 8:26 AM, tamir gonen tgonen...@gmail.com wrote: Hi Shane, One example that comes to mind is aquaporin-z. Two protomers were found in the ASU, one contained the water channel in an open conformation while the other in a closed conformation. The structural differences are not large but the functional implication is. Here is the primary citation Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z. http://www.ncbi.nlm.nih.gov/pubmed/14691544 *Savage* DF, Egea PF, Robles-Colmenares Y, O'Connell JD 3rd, *Stroud* RM. PLoS Biol. *2003* Dec;1(3):E72. Epub *2003* Dec 22. Kind regards Tamir gon...@hhmi.org On Jan 27, 2014, at 1:08 PM, Shane Caldwell shane.caldwel...@gmail.com wrote: Hi ccp4bb, I'm putting together a talk for some peers that highlights strengths and weaknesses of structural models for the outsider. For one point, I'd like to find some examples of proteins that show very different conformations between different copies in the ASU. One example I know of is c-Abl (1OPL), which crystallizes with both autoinhibited and active forms in the ASU, with dramatically different domain organization. I'd like to find some additional examples - can anyone suggest some other structures that have multiple copies with large structural variations? Thanks in advance! Shane Caldwell McGill University
[ccp4bb] making high res image in pymol
Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
Re: [ccp4bb] making high res image in pymol
CCP4MG? On 28 Jan 2014, at 15:27, A K wrote: Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] Call for Speakers, 2014 ACA Meeting, Industrial Research from Young Scientists
The Industrial Special Interest Group and Young Scientists Special Interest Group of the American Crystallographic Association will be hosting a scientific session on Sunday, May 25, 2014 during the ACA Meeting in Albuquerque, New Mexico which will highlight research by young scientists (undergraduate, graduate, post-doc) that is done in industry or in collaboration with industry. We encourage young scientists in this area to submit an abstract for consideration for a talk during this session. A brief description of the session is highlighted below,1.2.1 Industrial Research from Young ScientistsOrganizers: George Lountos, Pete Wood An industrial environment can provide invaluable research and career experience for students and other young scientists. At the same time a short or long term research placement can provide an industrial partner with the opportunity to have very focussed research carried out in an otherwise time-stretched setting. This session will showcase research being performed by young scientists at any level (undergraduate, post-graduate or early post-doctoral) either within industry or funded by industry. The deadline for abstract submission is January 31, 2014. Abstracts may be submitted online at http://www.amercrystalassn.org/2014-abstractsYoung scientists wishing to present at the meeting are also encouraged to apply for a Travel Grant. http://www.amercrystalassn.org/2014-young-scientistsIf you have any questions, feel free to contact the session organizers, Pete Wood (w...@ccdc.cam.ac.uk) or George Lountos (lount...@mail.nih.gov)Thanks,George
Re: [ccp4bb] making high res image in pymol
Hi Alex - I'm not surprised you're having memory issues. I just tried this test with one of my molecules. Simply generating and displaying the symmetry mates in a 250 A radius required 4 G of memory, and the raytracing would have needed a lot more (I only have 8 G on this computer, so I didn't finish that job). Unless you're running your job on a server-scale computer with 32 G or more of memory, I think you'll have trouble with so many molecules. However, that's with cartoon rendering. I assume you're trying to show unit cell packing, and the molecules will be so tiny that it doesn't matter what they look like. Use ribbon rendering instead, and the memory demands are greatly reduced. I was able to raytrace a 2000 x 2000 pixel image (which should be more than adequate for a poster - that's 10 x 10 inches at 200 dpi) in 40 seconds with peak memory usage under 2 G. This is with the Fink compiled version of Pymol - version 1.6.9.0. Hope that helps, Matt On 1/28/14 10:27 AM, A K wrote: Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] making high res image in pymol
Hi Alex - You can also try reducing the value of `hash_max`http://www.pymolwiki.org/index.php/Hash_max (e.g. `set hash_max, 50`). The default value is 130; a lower number reduces the memory PyMOL tries to obtain for ray tracing. The trace will take longer, but hopefully will get you through without crashing. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.eduhttp://kong.med.nyu.edu/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of A K [alek6...@gmail.com] Sent: Tuesday, January 28, 2014 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
[ccp4bb] twinning fun
Dear all, I recently collected several datasets for a protein that needs experimental phasing. The crystals are hexagonal plates, and (automatic) data processing suggests with high confidence that the space group is P622. This is where the fun begins. For some datasets (processed in P622), the intensity distributions are normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is no twinning (twinning fractions 0.05). However, for other datasets (same cell dimensions), the intensity distributions are not normal (eg Z-scores 10). Given that twinning is not possible in P622, this suggests to me that the real space group could be P6 with (near) perfect twinning. If I now process the normal L-test P622 datasets in P6, the twin-law based tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), suggesting all my data is twinned. Does this make sense (ie can one have twinning with normal intensity distributions)? If it does, would the normal L-test datasets have a higher probability of being solvable? Is there any strategy for experimental phasing of (near) perfect twins? SAD would be more suitable than SIR/MIR? (I also have potential heavy atom derivatives). Thanks for any insights! Bert
Re: [ccp4bb] making high res image in pymol
Hi Alex, If you don't mind forgoing the ray tracing, you may try the draw command to specifically set the resolution (and antialiasing) to your needs, and then save the image. Yong -- Yong Wang, Ph.D. Research Advisor, Discovery Chemistry Research Eli Lilly Company Phone: 317-655-9145 Lilly Corporate Center DC 0403 Fax: 317-651-6333 Indianapolis, IN 46285 wang_y...@lilly.com CONFIDENTIALITY NOTICE: This e-mail message from Eli Lilly and Company (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of A K Sent: Tuesday, January 28, 2014 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex
Re: [ccp4bb] twinning fun
Dear Bert Van-Den-Berg, as far as I understand this, if you have true P622, process the data in P6 and then test for twinning, both the Britton-test and H-test will indicate perfect merohedral twinning. This is because the Britton-test checks for a sudden increase of negative intensities after de-twinning, which happens only at twin fractions close to 0.5 if the intensities used for de-twinning are the same. But this is true if they are related by crystallographic symmetry. The H-test relates the absolute difference to the sum of the presumably twinned intensities, which gives 0 for intensities related by crystallographic symmetry, again resulting in twin fractions close to 0.5. In other words, intensities related by crystallographic symmetry would indicate perfect twinning in both of these tests. A better test for perfect merohedral twinning would be the ratio of I^2/I^2 which should be 2 for untwinned and 1.5 for perfectly twinned data, tested in the higher space group. These values are reported by data processing programs like XDS. Please, be aware that these ratios have rather strange values if you have an unusually high background (loop fiber diffraction, ice rings, etc.) or extremely weak data. For a really good discussion of twin tests, see Yeates, Methods. Enzymol. 276, 344-358, 1997. Best regards, Dirk. Am 28.01.14 18:26, schrieb Bert Van-Den-Berg: Dear all, I recently collected several datasets for a protein that needs experimental phasing. The crystals are hexagonal plates, and (automatic) data processing suggests with high confidence that the space group is P622. This is where the fun begins. For some datasets (processed in P622), the intensity distributions are normal, and the L-test (aimless, xtriage) and Z-scores (xtriage) suggest that there is no twinning (twinning fractions 0.05). However, for other datasets (same cell dimensions), the intensity distributions are not normal (eg Z-scores 10). Given that twinning is not possible in P622, this suggests to me that the real space group could be P6 with (near) perfect twinning. If I now process the normal L-test P622 datasets in P6, the twin-law based tests (britton and H-test in xtriage) give high twin fractions (0.45- 0.5), suggesting all my data is twinned. Does this make sense (ie can one have twinning with normal intensity distributions)? If it does, would the normal L-test datasets have a higher probability of being solvable? Is there any strategy for experimental phasing of (near) perfect twins? SAD would be more suitable than SIR/MIR? (I also have potential heavy atom derivatives). Thanks for any insights! Bert -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Call for abstracts - Exciting Structures - ACA 2014
Dear Crystallographers, Your are invited to submit your abstract for the Exciting Structures session at the upcoming ACA meeting (Albuquerque May 24-28. 2014). The focus of this session is to provide young scientists an opportunity to present highly relevant structures of biological macromolecules, which may fall outside the scope of the other structural biology sessions. Oral presentations will be chosen from contributed abstracts. Abstract submission deadline: January 31. You can submit your abstract at http://www.amercrystalassn.org/2014-abstracts. Younger scientists (Students and Post-Docs) are encouraged to apply for a Travel Grant (see http://www.amercrystalassn.org/2014-young-scientistsIf). Cheers, Daouda
