[ccp4bb] Sunhats for plants
Hi all, Plants suffer from DNA damage caused by ultraviolet light in the same way that humans do. Unlike us though, they cant put on a sunhat (or move to England) to avoid the suns rays. Read more about how plants sense UV-B light and turn on a suite of genes to protect their DNA against its deleterious effects in the latest installment of Quips (QUite Interesting Pdb Structures; pdbe.org/quips) at: http://pdbe.org/quips?story=Sunhats The accompanying mini-tutorial shows you how PDBeFold can be used to compare and superimpose structures of proteins even if their sequences show circular permutation. If you have an interesting structure whose story you would like to tell (with our help) in the form of a Quips article, please contact us at p...@ebi.ac.uk --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] MR solution
Phaser no longer fixes the space group after the first translation function. Phaser carries the space group with each potential solution. If the solution is clear at the end, so will the space group be clear. In practice, we found that the space group was not correct after the first translation function only when there was pseudocentring present. Any pseudocentring is accounted for by the new translational NCS correction factors in Phaser, and with these corrections, the space group is clear (in our test cases) after the first translation function. So any issues with space group determination have been addressed in two ways, and space group determination should be very robust from Phaser-2.5.0 onwards. Airlie On Jul 9 2012, David Schuller wrote: Scaling should be the same in P222 vs. P212121. The only difference is the exclusion of systematic absences. You may have run into some quirk of Phaser in the way it handles multiple space groups vs. a single one. On 07/09/12 14:06, Shya Biswas wrote: Hi all, I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1 and c=93.5 however I do not get a right MR solution with this. So I went back and scaled it in p222 space group and asked phaser to find the right spacegroup solution for it, this time phaser gave me the right solution and in p212121 space group. By right solution I mean the molecule is a dimer and has to be oriented in a particular way, which I get only when I use p222 scaled data. I am puzzled and would like to know if anyone can explain this. thanks, Shya
Re: [ccp4bb] MR solution
If there is such a quirk then it's not one we know about. We would definitely appreciate being sent whatever is needed to reproduce the behaviour. Dimers in orthorhombic space groups can lead to translational NCS, which is handled much better in the latest versions of Phaser. Is it possible Phaser was updated between the two attempts? Best wishes Randy Read On 9 Jul 2012, at 21:17, David Schuller wrote: > Scaling should be the same in P222 vs. P212121. The only difference is the > exclusion of systematic absences. You may have run into some quirk of Phaser > in the way it handles multiple space groups vs. a single one. > > > On 07/09/12 14:06, Shya Biswas wrote: >> Hi all, >> >> I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1 >> and c=93.5 however I do not get a right MR solution with this. So I went >> back and scaled it in p222 space group and asked phaser to find the right >> spacegroup solution for it, this time phaser gave me the right solution and >> in p212121 space group. By right solution I mean the molecule is a dimer and >> has to be oriented in a particular way, which I get only when I use p222 >> scaled data. I am puzzled and would like to know if anyone can explain this. >> >> thanks, >> Shya > > > -- > === > All Things Serve the Beam > === >David J. Schuller >modern man in a post-modern world >MacCHESS, Cornell University >schul...@cornell.edu
Re: [ccp4bb] SOMoRe
On Jul 9 2012, James Stroud wrote: On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote: Dear Fulvio, http://lmgtfy.com/?q=somore+molecular+replacement should help you out, especially the but last paragraph of the first link provided. Not Found The requested URL /~djamrog/somore.html was not found on this server. Wayback to the rescue http://web.archive.org/web/20041204143913/http://www.caam.rice.edu/~djamrog/somore.html
Re: [ccp4bb] MR solution
Scaling should be the same in P222 vs. P212121. The only difference is the exclusion of systematic absences. You may have run into some quirk of Phaser in the way it handles multiple space groups vs. a single one. On 07/09/12 14:06, Shya Biswas wrote: Hi all, I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1 and c=93.5 however I do not get a right MR solution with this. So I went back and scaled it in p222 space group and asked phaser to find the right spacegroup solution for it, this time phaser gave me the right solution and in p212121 space group. By right solution I mean the molecule is a dimer and has to be oriented in a particular way, which I get only when I use p222 scaled data. I am puzzled and would like to know if anyone can explain this. thanks, Shya -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] SOMoRe
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, I was actually referring to the email address but just noticed that the domain 'xtal.biochem.wisc.edu' also does not exist anymore. The modification date 2005 is also not very encouraging for finding a working copy of somore... Maybe the TO might consider using EPMR, another 6D MR program. The web site http://www.epmr.info/ seems a lot more up to date ;-) Cheers, Tim On 07/09/12 19:40, James Stroud wrote: > > On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote: > >> Dear Fulvio, >> >> http://lmgtfy.com/?q=somore+molecular+replacement >> >> should help you out, especially the but last paragraph of the >> first link provided. > > > Not Found > > The requested URL /~djamrog/somore.html was not found on this > server. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP+yadUxlJ7aRr7hoRAnaeAJ9J7dsw4tAgxwsGKd6sxoZGQIVElQCdF3VW 8JafLd1kTx3vi+qyGuv2dWw= =JYWD -END PGP SIGNATURE-
[ccp4bb] MR solution
Hi all, I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1 and c=93.5 however I do not get a right MR solution with this. So I went back and scaled it in p222 space group and asked phaser to find the right spacegroup solution for it, this time phaser gave me the right solution and in p212121 space group. By right solution I mean the molecule is a dimer and has to be oriented in a particular way, which I get only when I use p222 scaled data. I am puzzled and would like to know if anyone can explain this. thanks, Shya
Re: [ccp4bb] SOMoRe
On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote: > Dear Fulvio, > > http://lmgtfy.com/?q=somore+molecular+replacement > > should help you out, especially the but last paragraph of the first > link provided. Not Found The requested URL /~djamrog/somore.html was not found on this server.
Re: [ccp4bb] SOMoRe
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Fulvio, http://lmgtfy.com/?q=somore+molecular+replacement should help you out, especially the but last paragraph of the first link provided. Best, Tim On 07/09/12 17:57, fulvio saccoccia wrote: > Dear ccp4 users, does anyone know where to download SOMoRe for > molecular replacement? > > Thanks in advance > > Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza > University of Rome Italy > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP+w62UxlJ7aRr7hoRAm8kAKDawaelsLYbZtX0Ob9i6Ef+AXRAcgCfbvKc SqHBoY6moII3spKHtA8267o= =JDzX -END PGP SIGNATURE-
[ccp4bb] SOMoRe
Dear ccp4 users, does anyone know where to download SOMoRe for molecular replacement? Thanks in advance Fulvio Saccoccia PhD student Dept. of Biochemical Sciences Sapienza University of Rome Italy
Re: [ccp4bb] Rfactors stuck very high
Dear Garib, I have run the jellybody refinement and whilst it has not reduced the Rfactors I am going to see whether I can see anything usable in the new maps. many thanks james Dr James Garnett Centre for Structural Biology Division of Molecular Biosciences Level 5 Sir Ernst Chain Building South Kensington Campus Imperial College London London SW7 2AZ Tel: +44 (0) 207 594 5464 Fax: +44 (0) 207 594 3057 From: Garib N Murshudov [ga...@mrc-lmb.cam.ac.uk] Sent: 09 July 2012 12:07 To: Garnett, James A Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfactors stuck very high Dear James It seems that at this stage you may not be able to distinguish between these space groups. As I see they are subgroup of each other (more precisely P1 < C2 < I222 with the cell parameters you have) and it would not be easy to find out the exact space group at this stage. Highest space group may be more likely than others in the absence of other evidences. It seems that the problem is that the model is sufficiently far and refinement programs struggle to converge. We had some good results for this type of cases when we used jelly body refinement in refmac with 40-100 cycles and sigma set to 0.01. Phenix may have similar tricks. After that you can try either shelxe or arpwarp or one after another. Although at 2.3A they may not produce results as spectacular as in presentations, they may give you improved maps to work with. regards Garib On 8 Jul 2012, at 22:11, James Garnett wrote: Dear all, I have some troublesome data to ~2.3A and I hope someone can help. My data indexes and scales equally well in I222, C2 and P1 I222 a=46.3 b=76.3 c=81.1 C2 a=111.3 b=46.3 c=76.3 beta=133.2 (reset in I2 a=76.3 b=46.3 c=81.1 beta=90.1) C2 a=94.5 b=76.3 c=46.3 beta=119.6 (reset in I2 a=46.3 b=76.3 c=81.1 beta=90.1) P1 a=46.2 b=60.2 c=60.2 alpha=78.5 beta=67.4 gamma=67.4 I have found a molecular replacement solution in I212121 using an NMR structure of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128 TFZ=12.3), although I can not refine this below R ~45% and Rfree ~50%. The maps look OK in parts but in other regions the connectivity is much reduced. In case of model bias I have used density modification and also used simulated annealing etc in case it is stuck in a local minima - these did not help. This protein is an Ig-like fold (potential for pseudo-internal symmetry) and so I have also played around with rotations of the structure but this has not helped. Although twinning analysis in all spacegroups suggest there is no twinning I have tried refinement in PHENIX and REFMAC using twin laws but this does not help. I do not detect any off origin peaks in a native Patterson map but I do see peaks suggesting NCS in self rotations in I222 (see below for peaks above 50% origin) - there can only be 1 mol/au though. Does this suggest rotational lattice defects? Eulerian anglesPolar angles Alpha Beta Gamma Peak OmegaPhi Kappa Direction cosines Symmetry: 1 2 Peak1 Origin peak 100.0 0.00.00.0 Peak2 1 10.00.0 180.0 100.0 0.00.03.1 0. 0. 1. Origin peak 100.0 0.00.0 180.0 Peak3 1 10.00.0 180.0 100.0 0.00.03.1 0. 0. 1. Origin peak 100.0 180.00.0 180.0 Peak4 1 10.0 180.0 180.0 100.090.00.03.1 1. 0. 0. 1 20.0 180.00.0 100.090.0 90.03.1 0. 1. 0. Origin peak 100.090.00.0 180.0 Peak5 1 10.0 180.0 180.0 100.090.00.03.1 1. 0. 0. 1 20.0 180.00.0 100.090.0 90.03.1 0. 1. 0. Origin peak 100.090.0 180.0 180.0 Peak6 1 10.0 180.00.0 100.090.0 90.03.1 0. 1. 0. 1 20.0 180.0 180.0 100.090.00.03.1 1. 0. 0. 1 30.00.0 180.0 100.0 0.00.03.1 0. 0. 1. Origin peak 100.090.0 90.0 180.0 Peak7 1 1 270.0 89.9 90.0 51.990.00.0 89.9 1. 0. 0. 1 2 270.0 89.9 270.0 51.945.0 270.0 180.0 0. -0.7067 0.7075 1 3 90.0 90.1 270.0 51.990.0 180.0 90.1 -1.0
Re: [ccp4bb] Rfactors stuck very high
Dear James It seems that at this stage you may not be able to distinguish between these space groups. As I see they are subgroup of each other (more precisely P1 < C2 < I222 with the cell parameters you have) and it would not be easy to find out the exact space group at this stage. Highest space group may be more likely than others in the absence of other evidences. It seems that the problem is that the model is sufficiently far and refinement programs struggle to converge. We had some good results for this type of cases when we used jelly body refinement in refmac with 40-100 cycles and sigma set to 0.01. Phenix may have similar tricks. After that you can try either shelxe or arpwarp or one after another. Although at 2.3A they may not produce results as spectacular as in presentations, they may give you improved maps to work with. regards Garib On 8 Jul 2012, at 22:11, James Garnett wrote: > Dear all, > > I have some troublesome data to ~2.3A and I hope someone can help. My data > indexes and scales equally well in I222, C2 and P1 > > I222 a=46.3 b=76.3 c=81.1 > C2 a=111.3 b=46.3 c=76.3 beta=133.2 (reset in I2 a=76.3 b=46.3 c=81.1 > beta=90.1) > C2 a=94.5 b=76.3 c=46.3 beta=119.6 (reset in I2 a=46.3 b=76.3 c=81.1 > beta=90.1) > P1 a=46.2 b=60.2 c=60.2 alpha=78.5 beta=67.4 gamma=67.4 > > I have found a molecular replacement solution in I212121 using an NMR > structure of the same protein and MR-ROSETTA/PHENIX (PHASER LLG=128 > TFZ=12.3), although I can not refine this below R ~45% and Rfree ~50%. The > maps look OK in parts but in other regions the connectivity is much reduced. > In case of model bias I have used density modification and also used > simulated annealing etc in case it is stuck in a local minima - these did not > help. This protein is an Ig-like fold (potential for pseudo-internal > symmetry) and so I have also played around with rotations of the structure > but this has not helped. Although twinning analysis in all spacegroups > suggest there is no twinning I have tried refinement in PHENIX and REFMAC > using twin laws but this does not help. > > I do not detect any off origin peaks in a native Patterson map but I do see > peaks suggesting NCS in self rotations in I222 (see below for peaks above 50% > origin) - there can only be 1 mol/au though. Does this suggest rotational > lattice defects? > > Eulerian anglesPolar angles > > Alpha Beta Gamma Peak OmegaPhi Kappa > Direction cosines > Symmetry: 1 2 > > > > Peak1 > Origin peak 100.0 0.00.00.0 > > Peak2 > 1 10.00.0 180.0 100.0 0.00.03.1 >0. 0. 1. > Origin peak 100.0 0.00.0 180.0 > > Peak3 > 1 10.00.0 180.0 100.0 0.00.03.1 >0. 0. 1. > Origin peak 100.0 180.00.0 180.0 > > Peak4 > 1 10.0 180.0 180.0 100.090.00.03.1 >1. 0. 0. > 1 20.0 180.00.0 100.090.0 90.03.1 >0. 1. 0. > Origin peak 100.090.00.0 180.0 > > Peak5 > 1 10.0 180.0 180.0 100.090.00.03.1 >1. 0. 0. > 1 20.0 180.00.0 100.090.0 90.03.1 >0. 1. 0. > Origin peak 100.090.0 180.0 180.0 > > Peak6 > 1 10.0 180.00.0 100.090.0 90.03.1 >0. 1. 0. > 1 20.0 180.0 180.0 100.090.00.03.1 >1. 0. 0. > 1 30.00.0 180.0 100.0 0.00.03.1 >0. 0. 1. > Origin peak 100.090.0 90.0 180.0 > > Peak7 > 1 1 270.0 89.9 90.0 51.990.00.0 89.9 >1. 0. 0. > 1 2 270.0 89.9 270.0 51.945.0 270.0 180.0 >0. -0.7067 0.7075 > 1 3 90.0 90.1 270.0 51.990.0 180.0 90.1 > -1. 0. 0. > 1 4 90.0 90.1 90.0 51.9 135.0 270.0 180.0 >0. -0.7075 -0.7067 > 2 1 90.0 89.9 90.0 51.9 135.0 270.0 180.0 >0. -0.7067 -0.7075 > 2 2 90.0 89.9 270.0 51.990.0 180.0 89.9 > -1. 0. 0. > 2 3 270.0 90.1 270.0 51.9 135.0 90.0 180.0 >0.
[ccp4bb] 11 PhD positions at the Bijvoet Center in Utrecht
The Bijvoet Center of Utrecht University offers 11 PhD Student Positions in Structural Biology The Bijvoet Center at Utrecht University offers 11 interdisciplinary PhD student projects in structural biology in the Marie Curie Innovative Doctoral Programme (IDP) ManiFold: Manipulating folding, assembly and disassembly of protein complexes – from molecule to disease. ManiFold offers innovative interdisciplinary research and training in structural biology, including biophysics, NMR spectroscopy, protein crystallography, proteomics and cell biology, for a selected group of 11 PhD students. The PhD students have the chance to work with one of the 7 ManiFold group leaders; Rolf Boelens, Ineke Braakman, Piet Gros, Albert Heck, Bert Janssen, Antoinette Killian and Stefan Rüdiger (coordinator)). All 11 research projects focus on one of the central topics in life sciences: Interactions between molecules lead to structures of increasing complexity and ultimately to living organisms and their dynamic relations. Deep understanding of these interactions is one of the most fundamental challenges in the Life Sciences. The Bijvoet Center is a dynamic hub of structural biology providing an integrated infrastructure of cutting edge technology, scientific expertise and pioneering training. In 2012 the Dutch government committed €32 Mio to further strengthen the NMR and proteomics facilities of the Bijvoet Center. Highly motivated and talented students are invited to apply now. The projects start in autumn 2012 in Utrecht. For more information, application procedure and eligibility for Marie Curie ITN training networks please go to: www.ManiFold-itn.nl -- Dr. Bert Janssen Crystal & Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University
