Re: [ccp4bb] Potential Space Group Issue
Well you could have a monoclinic space group with beta = 90....0001, which for everyone would mean 90.0 degrees. You could also have beta = exactly 90 by pure chance. Normally the R-sym values should tell you which of the two possibilities is the correct one. If you obtain (an example) R-sym = 0.045 for P2(1) and R-sym = 0.052 for P2(1)2(1)2(1), then the orthorhombic space group is most likely the correct one. And a definitive proof is solving the structure in P2(1)2(1)2(1). Fred. Message du 08/07/11 05:31 De : Raji Edayathumangalam A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Potential Space Group Issue Hello Everyone, I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the correct space group is. The current unit cell in p212121 is 98.123 101.095 211.201 90.000 90.000 90.000 I fed the reflection data into Xtriage to look for twinning and pseudotranslational NCS and there is no indication for either issue in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically absent as they should be for p212121. However, my colleague who is also working on the same dataset recently reprocessed the data in P21. Here's the cell in p21: 98.010 100.940 210.470 90.00 90.04 90.00 p21 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% deviation of beta angle from ideal lattice for p212121). I don't think so but I could be wrong. Could someone please clarify? Also, what kind of twinning and twinning operators can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Unexplained density near cobalt
Are the imidazole rings of the histidines distorted? If they are, it could be water/hydroxide. If not, it is probably a cobalt ion side show. Cheers, Rob Meijers EMBL Hamburg --- On Thu, 7/7/11, Artem Evdokimov artem.evdoki...@gmail.com wrote: From: Artem Evdokimov artem.evdoki...@gmail.com Subject: Re: [ccp4bb] Unexplained density near cobalt To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, July 7, 2011, 9:39 PM Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion) depending on the chemical environment... Artem On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian mach...@med.unc.edu wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM
Re: [ccp4bb] Crystallographic Computing School - Mieres, Spain
Dear all We still have a few places available, so we have decided to extend the registration deadline - so if anyone wants to come who hasn't registered already, you still have an opportunity to do so. http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011 Unfortunately we have no more bursaries! On 2 Mar 2011, at 18:24, harry powell wrote: Dear all The registration website is now live - see http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011 We had to change venue at a late stage, so although we are still calling it the Mieres School, it is now going to take place in Oviedo, about 20km up the road. On 8 Jan 2011, at 11:33, harry powell wrote: Dear all Those of you who attended the CCP4 Study Weekend at Warwick University this week (either in vivo or in silico), and who stayed to the end will remember Roberto Steiner's suggestion that some of the younger members of the audience may wish to become involved in software development themselves. The IUCr Commission on Crystallographic Computing (CompComm) will be holding a Computing School immediately before the Madrid IUCr General Assembly and Congress this August that is intended to expose younger members of the Crystallographic community to the knowledge and experience of senior developers across the whole science. CCP4BB readers will possibly be most interested in those developers in macromolecular crystallography; the following people in this field have accepted our invitations to speak - Paul Emsley Ralf Grosse-Kunstleve Garib Murshudov George Sheldrick Tom Terwilliger There are many other speakers who will concentrate on their own specialities (e.g. powder diffraction, small-molecule crystallography), but who will offer food for thought for all. The School is intended for prospective (or current...) developers, not to help those people who just want to run the programs better. Registration will be open to all, but priority will be given to postgrads and postdocs; we hope to have a number of bursaries available for applicants from less economically favoured regions. We are still finalising items such as the registration fee, but I expect to be able to make the website live by the end of January with more comprehensive details. Watch this space... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH Treasurer British Crystallographic Association Chairman ECA SIG9 (Crystallographic Computing) Acting Chairman IUCr Commission on Crystallographic Computing Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011
[ccp4bb] Postdoctoral position in protein crystallography in Durham (UK)
Applications are invited for a Wellcome Trust postdoctoral position for two years at the Biophysical Sciences Institute at Durham University. The aim of the project is to investigate the structure and function of phospholipases from the opportunistic pathogen Pseudomonas aeruginosa. The successful applicant will be part of a team that uses a combination of biophysical and structural methods to establish the molecular basis of activity. The primary technique employed will be protein crystallography. Protein purification and crystallisation conditions have been already been established. The post-holder will be responsible for sample preparation, crystallisation and data collections at the synchrotron with the ultimate goal of solving the crystal structure of the target proteins and their complexes with substrates and inhibitors. Further information can be found here: http://www.dur.ac.uk/jobs/, informal enquiries should be directed to ehmke.p...@durham.ac.uk. -- Dr. Ehmke Pohl Reader in Protein Crystallography Biophysical Sciences Institute Durham University Durham DH1 3LE United Kingdom tel: +44 (0)191 334 3619 e-mail: ehmke.p...@durham.ac.uk --
[ccp4bb] Postdoc and PhD student opportunities in multidisciplinary ribosome research
RiboCORE http://www.icm.uu.se/ribocore/, a newly established center for multidisciplinary ribosome studies at Uppsala University, Sweden, is looking for a number of outstanding postdoctoral fellows with an interest for multidisciplinary research and PhD degrees in for example structural biology, molecular biology, single molecule biophysics, biochemistry, genetics, microscopy and image analysis, microbiology or computational chemistry. Excellent skills in spoken and written English is an absolute requirement. If you are interested, please send an email to riboc...@icm.uu.se including a brief statement of research interests and a CV including list of publications before 1 Aug 2011. We also recruit several PhD students. For more information and application procedures see the following link: http://www.personalavd.uu.se/ledigaplatser/1609PhD.html Best regards /Maria Maria Selmer, PhD, docent Assistant Professor Cell and Molecular Biology, Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden Telephone: +46-(0)18-4714177 Fax: +46-(0)18-536971
Re: [ccp4bb] Potential Space Group Issue
Raji, Assuming that the real space group is P212121, in P21 you will still get a solution except for the extra NCS which will closely resemble the extra 2-fold screw. Then you can probably tell if there are any significant differences between NCS-related copies that justify lower symmetry space group. It's not impossible, as Fred points out, that P21 is the true space group, but I think most people here would agree it may be less likely. Did your colleague actually try going orthorhombic? One possibility is that symmetry breakdown results from lattice distortion upon cryocooling. I would expect that shifts/rotations are small and naturally the effect on the refinement is resolution-dependent. I am sure there are more examples in the literature, but this one should hit close to the hills of Waltham: http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040099 which is PDB ID 2PZV - check out that P1 with beta=89.98. Colonel Pybus could tell you more (if the brass lets him, of course :), but what I recall is that most of the time and at lower resolution KSI can be processed in C2221 without problems. With that particular dataset (and the goal was to get as high resolution as possible to discern minute changes in hydrogen bonds) it processed fine too, except that R-values stayed a little too high (lower 20s?) for authors comfort. But they do go down significantly in P1. However, you are at much lower resolution. My own unpublished example was at 2.4A, processed fine in C2221, gave a clear MR solution, but then stayed in R~40% zone and had every loop missing in electron density. Turned out to be P21 with NCS resembling higher symmetry just enough to confuse denzo (and me). I guess the message is that everything is P1 and higher symmetry is just a dream within a dream so you can experience a drop at any time :) Cheers, Ed. On Thu, 2011-07-07 at 23:30 -0400, Raji Edayathumangalam wrote: Hello Everyone, I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the correct space group is. The current unit cell in p212121 is 98.123 101.095 211.201 90.00090.00090.000 I fed the reflection data into Xtriage to look for twinning and pseudotranslational NCS and there is no indication for either issue in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically absent as they should be for p212121. However, my colleague who is also working on the same dataset recently reprocessed the data in P21. Here's the cell in p21: 98.010 100.940 210.470 90.00 90.04 90.00 p21 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% deviation of beta angle from ideal lattice for p212121). I don't think so but I could be wrong. Could someone please clarify? Also, what kind of twinning and twinning operators can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] rosetta/ubuntu
Hi, everyone on board. I want to try mr_rosetta for my project, but I had problem installing rosetta on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling of rosetta 3.2 failed with the message: KeyError: Unknown version number 4.5 for compiler 'gcc' . I want to know whether anybody had any experience install rosetta in ubuntu? Or do I need to change to a different linux distribution? If so, what linux distribution is best for running most of the main stream crystallography software? thanks in advance. Harry
Re: [ccp4bb] rosetta/ubuntu
On 8 Jul 2011, at 14:21, Harry Xu wrote: I want to try mr_rosetta for my project, but I had problem installing rosetta on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling of rosetta 3.2 failed with the message: KeyError: Unknown version number 4.5 for compiler 'gcc' . There's a good summary of the problem and a proposed solution here: http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104 I haven't tried this myself, but I've done something similar to get it working with Intel compilers on an SGI ICE cluster. Basically, Rosetta uses SCons to compile itself. SCons has, among its many configuration files, one that lists the compiler versions it is prepared to use and any compiler-specific options that go with them. gcc 4.5 is relatively new and not in the config files included with rosetta. Editing the files and adding 4.5 as an acceptable compiler should fix the problem. Note that the author of the blog post also has a fix for a piece of code that gcc v4.5 rejects on syntactical grounds. Regards, Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] rosetta/ubuntu
Hi Harry,
Recently I successfully compiled rosetta 3.2.1 with gcc 4.5 following these
hints:
***
from http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104
Rosetta 3.2 with Ubuntu 11.04
Rosetta is a very useful program for the prediction of protein structure,
folding and interactions be that docking with proteins or ligands.
However, the current version of Rosetta (3.2.1) uses SCons to compile itself on
your system. This is usually fine except that these use gcc libraries 4.1 and
before.
Ubunutu 11.04 considers anything before gcc v4.4 to be obsolete and you can't
install them (even with apt-get).
As a result, a small amount of hacking is required.
First get SCons. Open a new terminal window.
sudo apt-get install scons
Check that the file tree has been updated
sudo apt-get update
Now you can unzip your Rosetta download to wherever you like. I personally put
new software into /opt
Change your terminal window to the correct path. So in my case
cd /opt/rosetta
Now in a perfect world, and according to the installation instructions you
should be able to type:
scons bin mode=release
And Rosetta will install and compile itself. However, amongst a load of other
errors you'll see the root of the problem
KeyError: Unknown version number 4.5 for compiler 'gcc'
Now, the first thing I tried was to specify a fixed gcc version for SCons to run
scons bin mode=release cxx=gcc cxx_ver=4.4
But this doesn't work as gcc v4.4 is still too new. And any version before 4.4
isnt supported by Ubuntu.
The solution
This isnt a short or elegant solution, but it is a solution that got Rosetta to
install for me. If you have any troubles yourself I recommend you head on over
to the Rosetta forums.
Install zlib
Install zlib (developer version) to ensure all your necessary libraries are
installed
sudo apt-get install zlib1g-dev
sudo apt-get update
basic.settings
In /rosetta_path/tools/build there is the file basic.settings
At line 203, I needed to add
gcc, 4.5 : {
appends : {
version : [ 4, 5 ],
flags : {
compile : [ -param inline-unit-growth=1000,
-param large-function-growth=5 ],
},
},
},
I didnt change line 329 but you can for completeness if you so wish.
options.settings
In /rosetta_path/tools/build there is the file options.settings
Line 11 and 12 now read
cxx : {
gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5, *
],
So as to include v4.4 and 4.5
util.cc
Finally and most importantly, in /rosetta_path/src/core/conformation/symmetry
open util.cc. At line 357 there is an if statement. What we need to do is
change the else argument so that the reference is correct (I've commented out
the old line)
#ifdef WIN32
pose::PDBInfoOP pdb_info_src (new pose::PDBInfo( pose.pdb_info() ));
#else
/// pose::PDBInfoOP pdb_info_src = new pose::PDBInfo::PDBInfo( pose.pdb_info()
);
pose::PDBInfoOP pdb_info_src = new pose::PDBInfo( pose.pdb_info() );
#endif
Apparently this is required as the new versions of gcc are fussier about their
name references than older versions.
After which we can now go back to the terminal and type:
scons bin mode=release cxx=gcc cxx_ver=4.5
After some amount of processing time (~30mins on my dual core 2.8 GHz), you
should be greeted with the final lines
Install file:
build/src/release/linux/2.6/64/x86/gcc/4.5/super_aln.linuxgccrelease as
bin/super_aln.linuxgccrelease
scons: done building targets.
Credit goes to those on the Rosetta forums for help.
qrsh -cwd ./scons.py bin mode=release cxx=gcc cxx_ver=4.5 extras=static -j16
doesn't work
the working solution:
qlogin
module load gcc/4.5.0
/scons.py bin mode=release cxx=gcc cxx_ver=4.5 -j16
exit
***
Best wishes,
Alex
On 8 Jul 2011, at 15:21, Harry Xu wrote:
Hi, everyone on board.
I want to try mr_rosetta for my project, but I had problem installing rosetta
on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling
of rosetta 3.2 failed with the message: KeyError: Unknown version number 4.5
for compiler 'gcc' .
I want to know whether anybody had any experience install rosetta in ubuntu?
Or do I need to change to a different linux distribution? If so, what linux
distribution is best for running most of the main stream crystallography
software?
thanks in advance.
Harry
--
Alex Batyuk
Lab of Prof. Dr. A. Plueckthun
Biochemistry Institute
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland
Phone: +41 44 635 5574
[ccp4bb] EMBO Practical Course on Computational structural biology - from data to structure to function
Hi all, From 14-18 November, an EMBO Practical Course on Computational structural biology - from data to structure to function will be held at the EBI in Cambridge (UK). The course is organised by James Watson, Rosemary Wilson, Gerard Kleywegt, Victor Lamzin, Christine Orengo and Gert Vriend. The course will address computational aspects of protein structure determination, validation and analysis. Students will learn to critically examine and validate data from the Protein Data Bank and use a variety of analysis tools to identify similarities that can help identify function. The course will also provide an introductory session to homology modelling for use with proteins less amenable to structure determination. Finally, the importance of protein structure to drug development will be illustrated with a day focussing on protein interactions, small molecules, chemoinformatics and docking. The course is aimed at PhD students and post-docs working on the collection and analysis of protein structure data. The goal is to provide them with insight into the protein structure determination process, how to critically assess the quality of data from models and also provide expertise in the analysis of protein structure data with a view to predicting protein function. Registration for the course is now open. For more information, surf to: http://www.ebi.ac.uk/training/handson/course_110912_structures.html --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Senior Scientist- X-Ray Crystallography Technology
Important: Do *NOT* reply to this e-mail to apply for this position. Only applications processed through the apply link will be accepted. Any direct replies to this e-mail will be ignored. Passionate About Science We're passionate and rigorous about our science. For more than 30 years, Genentech has been at the forefront of the biotechnology industry, using innovative science to develop breakthrough medicines that improve the lives of people with serious or life-threatening diseases. The following opportunity exists in our South San Francisco, CA, headquarters: Senior Scientist- X-Ray Crystallography Technology Responsibilities: Genentech has an opportunity for an outstanding X-ray crystallographer to join the Genentech Structural Biology Department as a Senior Scientist (Technology). The department encompasses protein expression, purification, crystallography, and NMR spectroscopy, and collaborates with scientists and project teams throughout the Research organization. Primary job responsibilities include being an integral member of project teams, creatively applying crystallography to structure-based drug design, and providing strategic and managerial oversight of protein expression, purification and crystallography approaches for projects at all stages of the drug discovery pipeline. In addition to participation on project teams, the successful candidate will be expected carry out innovative research resulting in co- and lead-authored publications on structures of therapeutic and biological importance. Requirements: This position requires a PhD in Structural Biology, Biophysics, Biochemistry or related discipline, relevant post doctoral experience and at least five years of additional experience as an independent scientific investigator or group leader. The candidate must have experience with successfully managing external resource and/or leading multi-disciplinary project teams and a strong publication record in top tier journals is required. Technical expertise in solving X-ray crystal structures including hand-on operation of relevant data collection devices and software packages is required along with an established track record as an effective manager. The ideal candidate is a skillful speaker at high profile internal and external forums. The successful candidate will show evidence of sustained productivity, creativity and independent contributions to science; and must also be highly organized, motivated, work independently in a collaborative team-oriented setting, and have strong managerial and communication skills. The applicant must be passionate about applying structural biology to the pursuit of drug discovery including using structure-based drug design and carrying out cutting edge research on protein complexes of importance to human diseases. Demonstrated scientific leadership resulting in significant achievements either in a collaborative academic setting or in the context of multi-disciplinary projects team in a biotech/pharmaceutical setting is a must. Passionate About Our People We recognize that our people are our most important asset. It's why we foster an inclusive environment that encourages diversity and offer competitive healthcare and benefits to help you bring the best to the business and to your personal life. Join us as we continue to tackle medicine's most challenging problems and live a life inspired. To apply for this job, visit https://roche.taleo.net/careersection/test/jobapply.ftl?lang=enjob=0037 7162src=JB-11480. Now a member of the Roche Group, Genentech has multiple medicines on the market for cancer and other serious illnesses. We are an equal opportunity employer.
Re: [ccp4bb] Unexplained density near cobalt
Hi MM, Co in its +2 oxidation state typically forms a tetrahedrally coordinated species in high pH environment; and pentagonally coordinated species with five ligands at low pH. A Co ion in its +3 oxidation state forms a octahedrally coordinated species with six ligands. Co +3 is unusual in biological molecules. However it is seen in crystal structures, sometimes with partial occupancy and is a likely product of radiation damage caused by the X-ray beam. In the past I have found that Co+2 is prone to oxidation in the beam if the crystallizing condition has a pH lower than 6.5. Here is a article you might enjoy. Comparison of solution and crystal properties of Co(II)-substituted human carbonic anhydrase II. Avvaru BS, Arenas DJ, Tu C, Tanner DB, McKenna R, Silverman DN. Cheers Balu
[ccp4bb] Beta test versions of Mosflm iMosflm
Dear all New versions of ipmosflm (7.0.8) and the matched iMosflm (1.0.6) are now available for beta testing. http://www.mrc-lmb.cam.ac.uk/harry/mosflm/betas/index.html The changes in ipmosflm are of particular relevance to processing very weak Pilatus images (with background pixel values of zero), but will also have some beneficial effect for any fine sliced data and result in both more stable detector parameter refinement and improved intensity estimates. The new version is strongly recommended when trying to measure small anomalous differences. The major change in iMosflm has eliminated the gradual slowing down of the rate of data processing when dealing with large datasets (500 images) that is observed with iMosflm 1.0.5. Again, this is a particular issue with fine sliced Pilatus datasets. We would welcome any feedback on the performance of the new release. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH http://www.iucr.org/resources/commissions/crystallographic-computing/schools/mieres2011
[ccp4bb] Off Topic: PDB validation server
Hi all, I am putting the finishing touches on a structure and as a good little crystallographer I am running it through Molprobity and PDB validation to make sure everything clears before deposition. Everything was looking alright until I threw the file into the PDB validation server and suddenly there are a significant number of solvents that violate the 3.5 angstrom rule. Concerned that something had gone wrong I put an older file that I had run through the server in April. I was shocked to discover that the file with only one questionable solvent in April now has 173 of them. I know that the PDB updated its validation server in May as described in their news link but it seemed to indicate an increase in output options rather than a change in criteria. Is anyone aware of what changes were made to the validation server in regards to the preferred geometrical and stereochemical features? Thanks for your time, Katherine
Re: [ccp4bb] Potential Space Group Issue
Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original email and NOT 00h, 00k, 00l. Note the correction especially if you are a first-year graduate student trying to learn stuff from these emails :) Raji On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam r...@brandeis.eduwrote: Hello Everyone, I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the correct space group is. The current unit cell in p212121 is 98.123 101.095 211.20190.000 90.00090.000 I fed the reflection data into Xtriage to look for twinning and pseudotranslational NCS and there is no indication for either issue in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically absent as they should be for p212121. However, my colleague who is also working on the same dataset recently reprocessed the data in P21. Here's the cell in p21: 98.010 100.940 210.470 90.00 90.04 90.00 p21 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% deviation of beta angle from ideal lattice for p212121). I don't think so but I could be wrong. Could someone please clarify? Also, what kind of twinning and twinning operators can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Potential Space Group Issue
I'd say its very likely to be orthorhombic. Refinement should tell you.its the best way to determine the space group anyway. Why do you doubt its orthorhombic? Is Vm reasonable? It could be monoclinic and merohedrally winned with the beta angle very close to 90 degrees, but my money is on orthorhombic. if refinement fails I would try monoclinic plus/minus twinning. As for the operators, xx.triage will tell you and xx.refine will apply them for you during refinement;-) Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji Edayathumangalam [r...@brandeis.edu] Sent: Friday, July 08, 2011 3:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Potential Space Group Issue Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original email and NOT 00h, 00k, 00l. Note the correction especially if you are a first-year graduate student trying to learn stuff from these emails :) Raji On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam r...@brandeis.edumailto:r...@brandeis.edu wrote: Hello Everyone, I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the correct space group is. The current unit cell in p212121 is 98.123 101.095 211.20190.000 90.00090.000 I fed the reflection data into Xtriage to look for twinning and pseudotranslational NCS and there is no indication for either issue in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically absent as they should be for p212121. However, my colleague who is also working on the same dataset recently reprocessed the data in P21. Here's the cell in p21: 98.010 100.940 210.470 90.00 90.04 90.00 p21 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% deviation of beta angle from ideal lattice for p212121). I don't think so but I could be wrong. Could someone please clarify? Also, what kind of twinning and twinning operators can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Potential Space Group Issue
Hi, yes, that would be my preferred strategy: often (but not always), sampling space by trying plausible options saves you more time than thinking hard first... and then still ending up trying -:) All the best, Pavel. On Fri, Jul 8, 2011 at 1:07 PM, Van Den Berg, Bert lambertus.vandenb...@umassmed.edu wrote: I'd say its very likely to be orthorhombic. Refinement should tell you.its the best way to determine the space group anyway. Why do you doubt its orthorhombic? Is Vm reasonable? It could be monoclinic and merohedrally winned with the beta angle very close to 90 degrees, but my money is on orthorhombic. if refinement fails I would try monoclinic plus/minus twinning. As for the operators, xx.triage will tell you and xx.refine will apply them for you during refinement;-) Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji Edayathumangalam [r...@brandeis.edu] Sent: Friday, July 08, 2011 3:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Potential Space Group Issue Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original email and NOT 00h, 00k, 00l. Note the correction especially if you are a first-year graduate student trying to learn stuff from these emails :) Raji On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumangalam r...@brandeis.edu mailto:r...@brandeis.edu wrote: Hello Everyone, I have a 3.1 Ang dataset for which I'd like to get to the bottom of what the correct space group is. The current unit cell in p212121 is 98.123 101.095 211.20190.000 90.00090.000 I fed the reflection data into Xtriage to look for twinning and pseudotranslational NCS and there is no indication for either issue in the Xtriage output. Also, all odd 00h, 00k, 00l reflections are systematically absent as they should be for p212121. However, my colleague who is also working on the same dataset recently reprocessed the data in P21. Here's the cell in p21: 98.010 100.940 210.470 90.00 90.04 90.00 p21 I am not sure if BETA=90.04 is significant enough to treat as p21 (0.04% deviation of beta angle from ideal lattice for p212121). I don't think so but I could be wrong. Could someone please clarify? Also, what kind of twinning and twinning operators can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
[ccp4bb] Position for a crystallographer at the Pfizer Connecticut location
We are looking for an enthusiastic crystallographer to join our structural biology and biophysics group at the Pfizer Connecticut location. The successful candidate for this position will join Groton Structural Biology and Biophysics (SBB), a multi-disciplinary group with well-established expertise in molecular biology, protein biochemistry, biological mass spectrometry, NMR, biophysics, crystallography computational sciences. Our mission is to provide integrated molecular insights into drug target mechanism and target-ligand interactions to impact discovery efforts across important therapeutic areas, such as Immunology Autoimmune Diseases, Inflammation Remodeling, Neuroscience, Cardiovascular, Metabolic Endocrine Diseases and Oncology. As a Principal Scientist - Protein Crystallography, you will apply expert knowledge to determine the atomic structures of novel drug target proteins and protein-ligand complexes by protein crystallographic methods and extract novel and relevant structural insights to drive drug discovery efforts. You will need to collaborate with other scientists in our multidisciplinary SBB teams to deliver high impact results from the laboratory, and partner with scientists across Medicinal Chemistry, Biology and other platform lines to impact project decisions. You will also use your deep knowledge in protein crystallography and other related techniques to drive the development of cutting-edge technologies and external collaborations in structural sciences. Responsibilities Primary Duties: - Determine the atomic structures of novel drug target proteins and protein-ligand complexes using protein crystallographic methods - Expert analysis of relevant data and literature to extract novel structural insights and drive drug discovery efforts. - Contribute to the design and execution of other experiments (e.g. construct design, purification, crystallization) and laboratory duties (e.g. synchrotron trips) when needed - Mentor junior scientists and contribute to vigorous experimental design and execution as well as high level of scientific engagement Qualifications Training Education: - Doctoral degree or equivalent in Biochemistry, Chemistry or related field - Postdoctoral or industry training in Protein Crystallography - Established track record in solving novel protein structures and applying innovative methods throughout the gene-to-structure process Prior Experience: - 3-5 years of additional research experience (after postdoctoral training) in using structural information to impact drug discovery efforts, preferably in an industrial setting and through collaborative efforts Please submit your application online via the link, https://jobs.pfizer.com/psc/recruit/EMPLOYEE/EMPL/S/WEBLIB_HRS_HROI.HRS_ ISCRIPT.FieldFormula.IScript_JobBoard?PostingId=88951 With best wishes, Ravi Ravi G Kurumbail Pfizer Global Research Development Research Fellow Mailstop: 8118W-235 Groton, CT email:ravi.g.kurumb...@pfizer.com
Re: [ccp4bb] Off Topic: PDB validation server
Hi again, I have an update. The nice people at the PDB have gotten in touch and they think it might be a bug. They are looking into it. Thank you for all the off-board replies and I hope you all have a wonderful weekend. Katherine On Fri, Jul 8, 2011 at 1:13 PM, Katherine Sippel katherine.sip...@gmail.com wrote: Hi all, I am putting the finishing touches on a structure and as a good little crystallographer I am running it through Molprobity and PDB validation to make sure everything clears before deposition. Everything was looking alright until I threw the file into the PDB validation server and suddenly there are a significant number of solvents that violate the 3.5 angstrom rule. Concerned that something had gone wrong I put an older file that I had run through the server in April. I was shocked to discover that the file with only one questionable solvent in April now has 173 of them. I know that the PDB updated its validation server in May as described in their news link but it seemed to indicate an increase in output options rather than a change in criteria. Is anyone aware of what changes were made to the validation server in regards to the preferred geometrical and stereochemical features? Thanks for your time, Katherine
[ccp4bb] peptide docking
Hi all, As I'm a newbie in peptide docking, I was wondering what programs/servers people would suggest for generating the peptide PDB (keeping all the proper stereochemistry)? Is it possible to extract a file from the PDB database? All comments will be much appreciated!
[ccp4bb] How to rebuild a molecular only
Dear All, There are 8 moleculars in an asymmetry unit, but only one molecular should be rebulit, what can I do ? Thanks a lot! Wei Feng
