Re: [ccp4bb] idiffdisp fails from CCP4 gui in ccp4-6.2.0
Hi Boaz, I get the same thing when I try to run it from the command line. Well as a workaround I used mosflm instead... Best Sabine On 08/09/2011 11:33 PM, Boaz Shaanan wrote: Hi Sabine, What happens if you try to run it from command line? Just curious. It's a useful program (though not as good as ipdisp in some options). I hope it'll be fixed soon. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sabine Schneider [sabine.schnei...@mytum.de] Sent: Tuesday, August 09, 2011 3:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] idiffdisp fails from CCP4 gui in ccp4-6.2.0 Hello everyone, I installed new ccp4 about two weeks ago. When I try to open idiffdisp from the CCP4 gui it fails with: Impossible to load Diffraction Image library /usr/local/share/Xray/ccp4new/ccp4-6.2.0/lib/libDiffractionImage.so!!!. if I look into /ccp4-6.2.0/lib it looks like that lrwxrwxrwx 1 13003 10602 29 2011-07-26 16:33 lib_DiffractionImage.so - lib_DiffractionImage.so.0.0.0 lrwxrwxrwx 1 13003 10602 28 2011-07-26 16:33 libDiffractionImage.so - libDiffractionImage.so.0.0.0 lrwxrwxrwx 1 13003 10602 29 2011-07-26 16:33 lib_DiffractionImage.so.0 - lib_DiffractionImage.so.0.0.0 lrwxrwxrwx 1 13003 10602 28 2011-07-26 16:33 libDiffractionImage.so.0 - libDiffractionImage.so.0.0.0 -rwxr-xr-x 1 13003 10602 7708504 2011-06-16 23:09 lib_DiffractionImage.so.0.0.0 -rwxr-xr-x 1 13003 10602 7678200 2011-06-16 23:09 libDiffractionImage.so.0.0.0 Anyone an idea what's going on, or how I can fix that problem? Thanks for your help! Sabine -- -- Dr. Sabine Schneider Technische Universität Munich Department of Chemistry Chair of Biochemistry Lichtenbergstr. 4 D-85747 Garching Germany Tel.: +49 (0) 89 289 12891 Fax: +49 (0) 89 289 13363 http://www.biochemie.ch.tum.de/index.php?id=919
[ccp4bb] MOLREP no output!
Dear all, I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb file although the last contrast value written in the log file is 3.13! Are there certain criteria which have to be fulfilled before it gives a pdb file or is it a bug? Thanks for your help! Eric
[ccp4bb] Cavity is waiting unknown ligand
Dear All, I have inside cavity in my protein structure with some conserved residues. We do not know function or ligand for that domain. How I could find ligand candidates which fit to this cavity? Maybe somehow with pdbe? Thank you, Heidi
Re: [ccp4bb] Cavity is waiting unknown ligand
Hi Heidi You can try hunting for similar structural motifs which are likely to be involved in ligand binding or function: http://www.russelllab.org/cgi-bin/tools/pints.pl You can then try fitting suggested ligands to the cavity. good luck Alex On 10.08.2011 13:46, Heidi Tuominen wrote: Dear All, I have inside cavity in my protein structure with some conserved residues. We do not know function or ligand for that domain. How I could find ligand candidates which fit to this cavity? Maybe somehow with pdbe? Thank you, Heidi -- -- Alexander V. Shkumatov, Ph.D. Biological Small Angle Scattering Group EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178 Building 25A Notkestraße 85 fax: +49 40 89902 149 22603 Hamburg, Germany email: ashku...@embl-hamburg.de --
[ccp4bb] aimless ccp4 GUI fails
Dear colleagues,
I am trying to install the ccp4 GUI for aimless (both Ubuntu 10.04 LTS and
SuSE SLES 11.0 on 64bit machines):
- I downloaded aimless-0.0.16.linux from ftp.mrc-lmb.cam.ac.uk/pub/pre/ (I
also tried aimless-0.014.linux64), in addition, I downloaded
aimless_ccp4i_0.8.tar.gz.
- All files are located in $CCP4/bin
- renamed the binary aimless
- ran CCP4 6.2.0 GUI - System Administration - Install/uninstall Tasks -
pointed the package directory to the aimless tar.gz file
- Task successfully installed
- when I now click Data Reduction - Symmetry, Scale, Merge (Aimless) button,
the following error message appears:
***
can't read array(DIR_XYZIN): no such element in array
can't read array(DIR_XYZIN): no such element in array
while executing
if { $array($file_dir) == } {
if { [GetCurrentProject] != } {
set array($file_dir) [GetCurrentProject]
} else {
set array($...
(procedure CreateInputFileLine line 18)
invoked from within
CreateInputFileLine line Enter input reference PDB file name (XYZIN)
Reference PDB XYZIN DIR_XYZIN
(procedure aimless_task_window line 122)
invoked from within
aimless_task_window aimless_PROJECT
(eval body line 1)
invoked from within
eval $cmd
(procedure RunTask line 109)
invoked from within
RunTask aimless
invoked from within
.module.menu.action.canvas.frame.t.f_14 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_14
(command bound to event)
**
When I close the error message and click the aimless button again, the task
window appears but only with a small size and it cannot be resized. Also, the
options tabs cannot be expanded.
Did I make a mistake or is this a bug?
Cheers,
Uli
---
dr ulrich gohlke
staff scientist - macromolecular structure and interaction
max-delbrück-center for molecular medicine (mdc)
+49 30 9406 - 2725 (w)
+49 30 9406 - 2548 (fax)
ulrich.goh...@mdc-berlin.de
http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
Re: [ccp4bb] aimless ccp4 GUI fails
You also need to install the updated task for pointless, from the same ftp site
ftp.../pub/pre/pointless_ccp4i_1.4.tar.gz
sorry about this, but I had to change that to make the pointless/aimless task
work
Phil
On 10 Aug 2011, at 14:11, Ulrich Gohlke wrote:
Dear colleagues,
I am trying to install the ccp4 GUI for aimless (both Ubuntu 10.04 LTS and
SuSE SLES 11.0 on 64bit machines):
- I downloaded aimless-0.0.16.linux from ftp.mrc-lmb.cam.ac.uk/pub/pre/ (I
also tried aimless-0.014.linux64), in addition, I downloaded
aimless_ccp4i_0.8.tar.gz.
- All files are located in $CCP4/bin
- renamed the binary aimless
- ran CCP4 6.2.0 GUI - System Administration - Install/uninstall Tasks -
pointed the package directory to the aimless tar.gz file
- Task successfully installed
- when I now click Data Reduction - Symmetry, Scale, Merge (Aimless) button,
the following error message appears:
***
can't read array(DIR_XYZIN): no such element in array
can't read array(DIR_XYZIN): no such element in array
while executing
if { $array($file_dir) == } {
if { [GetCurrentProject] != } {
set array($file_dir) [GetCurrentProject]
} else {
set array($...
(procedure CreateInputFileLine line 18)
invoked from within
CreateInputFileLine line Enter input reference PDB file name (XYZIN)
Reference PDB XYZIN DIR_XYZIN
(procedure aimless_task_window line 122)
invoked from within
aimless_task_window aimless_PROJECT
(eval body line 1)
invoked from within
eval $cmd
(procedure RunTask line 109)
invoked from within
RunTask aimless
invoked from within
.module.menu.action.canvas.frame.t.f_14 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_14
(command bound to event)
**
When I close the error message and click the aimless button again, the task
window appears but only with a small size and it cannot be resized. Also,
the options tabs cannot be expanded.
Did I make a mistake or is this a bug?
Cheers,
Uli
---
dr ulrich gohlke
staff scientist - macromolecular structure and interaction
max-delbrück-center for molecular medicine (mdc)
+49 30 9406 - 2725 (w)
+49 30 9406 - 2548 (fax)
ulrich.goh...@mdc-berlin.de
http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structure_and_interaction/
[ccp4bb] protein segments from pdb
Dear all, how do you extract segments from a pdb file, so that from an input pdb file you get output like this: 10-103, 120-174, 200-240 or, better yet: A: 10-103, 120-174, 200-240 B: 10-104, 120-174, 199-241 if the N terminus is missing and there are two gaps in the structure. I tend to open the pdb file with PyMOL and click on the ends, but a script/command would be much quicker. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] protein segments from pdb
If you mean what I think you mean, then use the SUMMarise option of pdbcur. That gives output like: Chain A has 505 residues in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730 0 residues have alternative conformations Composition: ALA 23 ARG 23 ASN 36 ASP 24 CYS 34 CYH 0 GLN 21 GLU 30 GLY 38 HIS 11 ILE 29 LEU 44 LYS 32 MET 8 PHE 17 PRO 21 SER 36 THR 28 TRP 5 TYR 13 VAL 26 HEM 0 WAT 0 SUL 0 END 0 DUM 0 Other 6 HTH Martyn On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote: Dear all, how do you extract segments from a pdb file, so that from an input pdb file you get output like this: 10-103, 120-174, 200-240 or, better yet: A: 10-103, 120-174, 200-240 B: 10-104, 120-174, 199-241 if the N terminus is missing and there are two gaps in the structure. I tend to open the pdb file with PyMOL and click on the ends, but a script/command would be much quicker. Thanks. Andreas -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] protein segments from pdb
I see that my questions was highly ambiguous/unclear. Martyn saw through it anyway. pdbcur does what I want. Andreas On 10/08/2011 5:32, Martyn Winn wrote: If you mean what I think you mean, then use the SUMMarise option of pdbcur. That gives output like: Chain A has 505 residues in 7 spans: 1-305 307-500 711-711 716-716 719-719 721-722 730-730 0 residues have alternative conformations Composition: ALA 23 ARG 23 ASN 36 ASP 24 CYS 34 CYH 0 GLN 21 GLU 30 GLY 38 HIS 11 ILE 29 LEU 44 LYS 32 MET 8 PHE 17 PRO 21 SER 36 THR 28 TRP 5 TYR 13 VAL 26 HEM 0 WAT 0 SUL 0 END 0 DUM 0 Other 6 HTH Martyn On Wed, 2011-08-10 at 17:24 +0100, Andreas Förster wrote: Dear all, how do you extract segments from a pdb file, so that from an input pdb file you get output like this: 10-103, 120-174, 200-240 or, better yet: A: 10-103, 120-174, 200-240 B: 10-104, 120-174, 199-241 if the N terminus is missing and there are two gaps in the structure. I tend to open the pdb file with PyMOL and click on the ends, but a script/command would be much quicker. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] Monomer_lib_cif from PDB (Sketcher)
Dear CCP4 users, I just wonder if this problem can be solved using Sketcher. When i use Sketcher (PC or linux) in the CCP4 GUI to generate the monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of this ligand change (see V3Oand the attached files are used. Any comment is highly appreciated. stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) V3OAc.pdb Description: Protein Databank data V3O_bondlist.cif Description: CIF chemical test V3O_libcheck.pdb Description: Protein Databank data V3O_mon_lib.cif Description: CIF chemical test
Re: [ccp4bb] Monomer_lib_cif from PDB (Sketcher)
On 10/08/11 18:42, Dr. STEPHEN SIN-YIN, CHUI wrote: Dear CCP4 users, I just wonder if this problem can be solved using Sketcher. When i use Sketcher (PC or linux) in the CCP4 GUI to generate the monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of this ligand change (see V3Oand the attached files are used. Any comment is highly appreciated. Hello Stephen, You just need to minimize the ligand (V30_libcheck.pdb). My understanding is that that is what typically happens for you when using Sketcher. Without the log files and/or button-press-tracking it is hard to know why this hasn't happened already. So just feed it into Refmac or your favourite other minimizer and it will turn out much closer to how you expect (I expect). (As an aside, I believe that the CCDC take a dim view of distributing work derived from their database.) Paul.
[ccp4bb] Improved EM-related resources at PDBe
Hi all, The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve its services to the scientific community. As part of our recent website update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved. EMDB (http://emdatabank.org) contains over 1000 maps and is expected to grow 5-10 fold over the next 10 years. The data held in EMDB form a treasure trove of information on the state of, and trends in, the 3DEM field. Examples of interesting information that can be mined from the archive are trends in the resolution obtained using different techniques and comparisons of the relative popularity of microscopes and software packages. A new service (http://pdbe.org/emstats) has been developed at PDBe to mine the database for such information and present the results as interactive charts. The charts are generated dynamically and represent the current state of the information in the database. The charts are active, i.e. when clicked, a query is sent to the database and the results are shown below the charts. Clearly, the current set of charts represents only a fraction of the interesting information that can be extracted from the database and we invite the 3DEM community as well as the wider structural biology community to engage with us in expanding this service. Atlas pages for EMDB entries can now be accessed directly using URLs of the type: pdbe.org/emd-, where is the 4-digit numerical EMDB accession code. For example, http://pdbe.org/emd-1831 takes you to the entry Pig Gastric H,K-ATPase with bound BeF and SCH28080 by Abe, Tani and Fujiyoshi. The look and feel of the EMDB atlas pages (served at both EMDataBank sites, PDBe and RCSB) have also been improved - for instance, empty boxes are not shown so as to create a cleaner and more concise look and an enhanced version of the OpenAstexViewer can be accessed from an entry's visualisation page. The viewer can overlay fitted PDB models on maps (for an example, see http://pdbe.org/emd-1180) and use symmetry information to generate symmetry-related copies of models. (See also: http://www.emdatabank.org/improved_3d_viewing.html) We hope that you will find the EM resources at PDBe useful. As always, we welcome constructive criticism, comments, suggestions, bug reports, etc. through the feedback button at the top of any PDBe web page. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Another paper structure retracted
Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer G?_1 ?_2 Structure, Volume 16, Issue 7 http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y_acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa243dc98e395b6ac590d, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Another paper structure retracted
On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Another paper structure retracted
CC alone wouldn't be totally sufficient. CC is scale independent. For example, if you compare two very weak densities, say visible at below 0.1 sigma, and If these densities are similar enough then you will still get good CC. Therefore it's good to use CC and map values together. This is exactly why phenix comprehensive validation prints you a list of map CC and 2mFo-DFc and mFo-DFc map values per atom or per residue (depending on resolution). It's good to use bias-free maps for this. There is no need to mention how to obtain those maps - there are plenty of literature on this subject. Pavel. On Wed, Aug 10, 2011 at 2:35 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Another paper structure retracted
For some ideas on this see my presentation to the last CCP4 study weekend (with some further ideas in Acta D, to be published): http://www.cse.scitech.ac.uk/events/CCP4_2011/talks/tickle.pdf Cheers -- Ian On Wed, Aug 10, 2011 at 10:35 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Another paper structure retracted
Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y_acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa243dc98e395b6ac590d, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] Another paper structure retracted
I've made a quick look at the model and the paper - and it doesn't need more than a quick look. The description of the model in the paper sounds great. The problems in the model are clear. My favorite is the quote Trp-477 of PTH1R makes several van der Waals contacts with Trp-339 and Lys-337 of G-beta-1 They are contacts all right. The distances between the 477:CH2 and 337:CE is 2.75 A and between 477:NE1 and 339:CH2 is 2.26 A. There are many more. In general the geometry of this entire model is terrible. In Table 1 the bond length rmsd is listed at 1.64 A and the bond angles are 0.0078 deg! Perhaps one is to presume the numbers should be swapped. In any case, the values I calculate for the model are 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists the (swapped) values from the paper and then reports hundreds of outliers. The tools proposed by the Validation Task Force should cause a model like this to pop out clearly. Even the old tools show this model is quite unreliable. We just have to use them. Dale Tronrud On 08/10/11 14:35, Jacob Keller wrote: On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Another paper structure retracted
Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable but not quite as bad. Sorry, Dale Tronrud On 08/10/11 15:45, Dale Tronrud wrote: I've made a quick look at the model and the paper - and it doesn't need more than a quick look. The description of the model in the paper sounds great. The problems in the model are clear. My favorite is the quote Trp-477 of PTH1R makes several van der Waals contacts with Trp-339 and Lys-337 of G-beta-1 They are contacts all right. The distances between the 477:CH2 and 337:CE is 2.75 A and between 477:NE1 and 339:CH2 is 2.26 A. There are many more. In general the geometry of this entire model is terrible. In Table 1 the bond length rmsd is listed at 1.64 A and the bond angles are 0.0078 deg! Perhaps one is to presume the numbers should be swapped. In any case, the values I calculate for the model are 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists the (swapped) values from the paper and then reports hundreds of outliers. The tools proposed by the Validation Task Force should cause a model like this to pop out clearly. Even the old tools show this model is quite unreliable. We just have to use them. Dale Tronrud On 08/10/11 14:35, Jacob Keller wrote: On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Another paper structure retracted
The paper with this structure was published in the year 2008, following which, the PI and coPIs who co-authored the paper would have submitted grants using this information as preliminary data. It is possible some of these grant applications may even have got funded at the expense of other grants that had the good data. This is the not the first instance, there have been papers/structures that have been retracted after ten years of publication. Is there any thing the funding agencies can do? Sridhar On 8/10/2011 3:50 PM, Dale Tronrud wrote: Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable but not quite as bad. Sorry, Dale Tronrud On 08/10/11 15:45, Dale Tronrud wrote: I've made a quick look at the model and the paper - and it doesn't need more than a quick look. The description of the model in the paper sounds great. The problems in the model are clear. My favorite is the quote Trp-477 of PTH1R makes several van der Waals contacts with Trp-339 and Lys-337 of G-beta-1 They are contacts all right. The distances between the 477:CH2 and 337:CE is 2.75 A and between 477:NE1 and 339:CH2 is 2.26 A. There are many more. In general the geometry of this entire model is terrible. In Table 1 the bond length rmsd is listed at 1.64 A and the bond angles are 0.0078 deg! Perhaps one is to presume the numbers should be swapped. In any case, the values I calculate for the model are 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists the (swapped) values from the paper and then reports hundreds of outliers. The tools proposed by the Validation Task Force should cause a model like this to pop out clearly. Even the old tools show this model is quite unreliable. We just have to use them. Dale Tronrud On 08/10/11 14:35, Jacob Keller wrote: On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schullerdj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu attachment: sprasad.vcf
Re: [ccp4bb] Another paper structure retracted
I Agree with the idea of adding crystallographer reviewers. But accessing to data is not feasible unless there is a good way to protect authors. For example, the editor should agree to publish the paper swiftly in advance before the data become accessible to reviewers. In any case, the flaw of this structure is very clear in the table. Nian On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y_acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa243dc98e395b6ac590d, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] Another paper structure retracted
the editor should agree to publish the paper swiftly in advance before the data become accessible to reviewers. This seems to miss the point - how is the reviewer then supposed to judge the map? BR Nian On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7 http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%2362 69%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y _acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa24 3dc98e395b6ac590d , 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 tel:%2B1%20604%20827%204267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] Another paper structure retracted
On Wednesday, 10 August 2011, Nian Huang wrote: I Agree with the idea of adding crystallographer reviewers. But accessing to data is not feasible unless there is a good way to protect authors. Disagree. The data supporting a paper's claims should always be made available to the reviewers. How else can you be assured of a valid review? The only exception to this I can think of would be human subjects/ privacy issues, but that must be a rarity in crystallographic papers. Ethan For example, the editor should agree to publish the paper swiftly in advance before the data become accessible to reviewers. In any case, the flaw of this structure is very clear in the table. Nian On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y_acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa243dc98e395b6ac590d, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] Another paper structure retracted
The reviewers who wish to get access to raw data should reveal their identity by signing the report! -Sankar On Thu, Aug 11, 2011 at 10:28 AM, Ethan Merritt merr...@u.washington.eduwrote: On Wednesday, 10 August 2011, Nian Huang wrote: I Agree with the idea of adding crystallographer reviewers. But accessing to data is not feasible unless there is a good way to protect authors. Disagree. The data supporting a paper's claims should always be made available to the reviewers. How else can you be assured of a valid review? The only exception to this I can think of would be human subjects/ privacy issues, but that must be a rarity in crystallographic papers. Ethan For example, the editor should agree to publish the paper swiftly in advance before the data become accessible to reviewers. In any case, the flaw of this structure is very clear in the table. Nian On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: Just another example of where it would have been good for the reviewers to get access to the data during the review process... and where at least one of the reviewers *should* be a protein crystallographer... Filip Van Petegem On Wed, Aug 10, 2011 at 2:01 PM, David Schuller dj...@cornell.edu wrote: Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7 http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%236269%232008%23999839992%23693753%23FLA%23_cdi=6269_pubType=Jview=c_auth=y_acct=C22719_version=1_urlVersion=0_userid=492137md5=9dc4b8953d3fa243dc98e395b6ac590d , 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
