[ccp4bb] 21-23 May workshop on Integrated Software for Integrative Structural Biology
The programme is now available for this CECAM Collaborative Scientific Software Development meeting, sponsored by CCP4 and WeNMR. Please register at: https://eventbooking.stfc.ac.uk/news-events/integratedsoftware-for-integrative-structural-biology Monday 21st May Chair: Dave Stuart 1300 Alexandre Bonvin Incorporating low resolution data into the modelling of macromolecular assemblies using HADDOCK 1400 Johannes Soeding Using the HH-suite software for sequence searching and homology modelling 1500 Coffee 15:15 Michael Habeck Integration of structural data using Bayesian inference 16:15 Marco Biasini Getting more Biology into Homology Models Tuesday 22nd May Chair: Keith Wilson 0900 Mark Sansom Multiscale Simulations for Membrane Proteins 1000 Geerten Vuister Large-scale analysis, validation and computation of NMR-derived biomolecular structures: lessons for integrative approaches 1100 Coffee 11:15 Steve Brewer, EGI Integrated e-infrastructure for integrated software for integrated structural biology: defining the roadmap for collaboration 12:15 Lunch Chair: Martyn Winn 1300 Victor Lamzin TBC 1400 Arwen Pearson TBC 1500 Coffee 15:15 Jose Maria Carazo TBC 16:15 Antonio Rosato Integrated Use of Paramagnetic NMR and X-ray for Structural Biology Wednesday 23rd May Chair: J-M Carazo 0900 Torsten Herrmann The UNIO suite for automated liquid and solid-state NMR structure determination 1000 Gerard Kleywegt the wwPDB/PDBe plans for deposition, annotation and validation of X-ray/NMR/EM structures 1100 coffee 11:15 Ernest Laue Epigenetic inheritance: Structural studies of Chromatin assembly/disassembly 12:15 Lunch Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] finding NCS in water
Simplest is to submit your current structure to PDBe - they have software which moves all waters to lie close to protein. However the waters IDs don't help you know if A OH 123 matches B OH 123 for example. The very old utility water tidy tries to give meaningful names to your waters, but those names are inconsistent with deposition.Maybe you could run water tidy for information about which waters obey NCS although the output is not standard nomenclature.. Alternately just use the coot facility to fit chain A over chain B and see which waters overlap each other in the Copy and original.. (Remember to turn symmetry ON) Eleanor On 22 April 2012 16:33, Rajesh Kumar ccp4...@hotmail.com wrote: Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found Applying NCS to a high resolution structure http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample4chawaterNCS, including water molecules in NCS restraints on autobuster examples. Some how I got error Interpreting card: NOTE BUSTER_SIM_DEFINE ncsUV Chain_U V Number of atoms in template set= 109 Number of related chains (other than template) in SIM set=1 List of chains to be restrained (excluding template)= V *** ERROR a chain specified has less than 3 matching atoms to the template *** ERROR the chain in question is 'V' *** ERROR number of matching atoms is=0 *** ERROR found in finding matching atoms for NCS set up (END) Could you please point me to place where I could find one or two good examples or extended information to learn how this works? Also would like to know if this helps the refinement in general. Thanks Rajesh
Re: [ccp4bb] finding NCS in water
Thank you Professor. Its very helpful. Regards,Rajesh Date: Mon, 23 Apr 2012 12:19:09 +0100 Subject: Re: [ccp4bb] finding NCS in water From: eleanor.dod...@york.ac.uk To: ccp4...@hotmail.com CC: CCP4BB@jiscmail.ac.uk Simplest is to submit your current structure to PDBe - they have software which moves all waters to lie close to protein. However the waters IDs don't help you know if A OH 123 matches B OH 123 for example. The very old utility water tidy tries to give meaningful names to your waters, but those names are inconsistent with deposition.Maybe you could run water tidy for information about which waters obey NCS although the output is not standard nomenclature.. Alternately just use the coot facility to fit chain A over chain B and see which waters overlap each other in the Copy and original..(Remember to turn symmetry ON) Eleanor On 22 April 2012 16:33, Rajesh Kumar ccp4...@hotmail.com wrote: Dear All, I would like to learn how to relate water molecules by NCS and refine them. When I googled, CCP4 utilities sortwater and watncs showed up. I also found Applying NCS to a high resolution structure , including water molecules in NCS restraints on autobuster examples. Some how I got error Interpreting card: NOTE BUSTER_SIM_DEFINE ncsUV Chain_U V Number of atoms in template set= 109 Number of related chains (other than template) in SIM set=1 List of chains to be restrained (excluding template)= V*** ERROR a chain specified has less than 3 matching atoms to the template *** ERROR the chain in question is 'V' *** ERROR number of matching atoms is=0 *** ERROR found in finding matching atoms for NCS set up(END) Could you please point me to place where I could find one or two good examples or extended information to learn how this works? Also would like to know if this helps the refinement in general. ThanksRajesh
Re: [ccp4bb] high temp factor in coot!
On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: baverage program in ccp4 gave average bfactor of 25.0 for the residue but coot is showing 150! Variance is the square of standard deviation, thus var=150 means sigmaB~12 in that particular residue. High, but not impossible. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
Re: [ccp4bb] SeMet protein behaves much different with native protein..
Dear Benini,Tina, Tim, Patrick, Tom, James, Mark and other CCP4ers, Thank you very much for your suggestions! First, as you suggested, I already applied microseeding (strategies: seeds vs precipitants; seeds vs drop ratio) . SeMet protein indeed crystallized in that case, but crystals are extremely small and there were thousands of small crystals around the region of seeds. Second, re-screening using SeMet proteins had some hits, --but strangely, crystals can't be reproduced and optimised. (Does this reflect somehow unstability of SeMet protein?) Well, about how to get better SeMet crystals, do you still have some suggestions? Of course, I'm now still waiting for test my rice shaped/shuttle shaped crystals, and will try S-SAD and heavy atom soaking too. Thank you very much! best, Sarah
[ccp4bb] high R factor calculated by sfcheck
Dear all, I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result). But when I used sfcheck to validate the coordinates and structure factors, I got a high R factor 0.38 ! Could anybody tell me the reason? Is that possible to deposit the coordinate to PDB? Thank you very much!
[ccp4bb] CALL FOR BEAM TIME PROPOSALS: The Protein Crystallography Station @ LANL
Dear User of the Lujan Center, You are invited to submit research proposals for time on the *neutron Protein Crystallography Station* for the 2012 run cycle that begins on August 4, 2012. This run cycle will continue through December, 2012. Thus there will be only *one proposal call for 2012*. *The deadline for receipt of proposals is 5:00 p.m. on May 14, 2012.* *Proposal Submission -- *Proposals will be submitted through a new database and web interface that we hope will result in a more efficient proposal process. Proposals may be submitted by clicking on the “Submit Proposal” link in the left column of the Lujan home page http://lansce.lanl.gov/lujan/index.shtml . The text of your proposal should be *no longer than two pages* and include reference to publications that have resulted from previous time awarded at the Lujan Center. This information is important and will be used by the proposal evaluation committee in ranking the submitted proposals for scientific impact. To submit a classified proposal, please contact the Lujan user program administrator whose contact is given below. *Note: When accessing the proposal submission site for the first time, use your e-mail address as the “Username” and click **on the “forgot password” button. You will be sent a link by email to set your new password. After logging in, fill out or update your personal information. When you hit “save and continue”, you will be directed to the first proposal submission page. Some information has been transferred for proposals submitted in previous years.*** If you are a new user or have a question about the feasibility of a proposed experiment, please contact the instrument scientists *Zoë Fisher *( zfis...@lanl.gov) or *Andrey Kovalevsky* (a...@lanl.gov) before submitting your proposal. We look forward to welcoming you as a user here at the Lujan Center for the 2012 run cycle. If you have any questions or would like assistance with the proposal process, please contact the Lujan user office administrator, Lisa Padilla, l...@lanl.gov or by phone at 505-667-5649.
Re: [ccp4bb] high R factor calculated by sfcheck
On Mon, 2012-04-23 at 23:39 +0800, Qixu Cai wrote: Dear all, I have solved a 3.5ang structure with R/Rfree = 0.23/0.32 (refmac5.6 result). But when I used sfcheck to validate the coordinates and structure factors, I got a high R factor 0.38 ! Could anybody tell me the reason? Is that possible to deposit the coordinate to PDB? Thank you very much! There are differences between the two programs. For instance, sfcheck uses Babinet solvent correction, while Refmac's default is to use mask correction. Perhaps you used TLS, which sfcheck is not likely to use. You do have a relatively large jump, but it's not entirely unexpected given the resolution. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] FW: error
BBers, In my new 6.2.0 installation I'm getting child killed: segmentation violation while running Truncate. The /tmp/Vaheh directory does exist and is writable. Below is the message: [Vaheh] === The program run with command: /usr/bin/ccp4-6.2.0/bin/ctruncate -mtzin /home/Vaheh/[Vaheh] /scala_tern_pointless1.mtz -mtzout /tmp/Vaheh/11-42.tmp -colin /*/*/\[I,SIGI\] -colout 11_42 has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 child killed: segmentation violation #CCP4I TERMINATION TIME 23 Apr 2012 11:49:16 #CCP4I MESSAGE Task failed [Vaheh] === Will appreciate a solution to problem. Thank you. Vaheh To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] high temp factor in coot!
Dear Ed, Why the variance is the square of standard deviation? thank you very much! 在 2012年4月23日，20:53，Ed Pozharski epozh...@umaryland.edu 写道： On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: baverage program in ccp4 gave average bfactor of 25.0 for the residue but coot is showing 150! Variance is the square of standard deviation, thus var=150 means sigmaB~12 in that particular residue. High, but not impossible. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
[ccp4bb] minimum protein concentration for NI-NTA column
Dear All; This is a sort of naive question about the NI-NTA affinity purification. Is the Ni-NTA column from GE health able to capture proteins at 0.2ug/ml to 0.5ug/ml? IF not, then it is necessary to concentrate the mammalian expression supernatant. Thanks a lot and best regards, Jerry McCully
Re: [ccp4bb] minimum protein concentration for NI-NTA column
Hi, At such concentrations, it might be necessary to concentrate the medium. Otherwise you are likely to be working well below the KD of the affinity beads. At 0.5mg/L, 50KDalton gives you 10nM. The KD of Ni-NTA should be around 1uM, according to published SPR data http://www.sciencedirect.com/science/article/pii/S0003269797923265. This means the majority of your protein will stay in solution even at equilibrium. One of my colleagues does use Ni-NTA beads for their secreted mammalian protein, which produces at 10mg/L. And he still concentrates it at least 10x. Zhijie From: Jerry McCully Sent: Monday, April 23, 2012 9:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] minimum protein concentration for NI-NTA column Dear All; This is a sort of naive question about the NI-NTA affinity purification. Is the Ni-NTA column from GE health able to capture proteins at 0.2ug/ml to 0.5ug/ml? IF not, then it is necessary to concentrate the mammalian expression supernatant. Thanks a lot and best regards, Jerry McCully
Re: [ccp4bb] high temp factor in coot!
Dear Johan, the standard deviation is defined as the square root of the variance. while The standard deviation has the same unit as the values you're measuring. So we can say what's the unit of deviation? Is it the square of the unit of standard deviation? I always think that the unit of deviation is the same to the values we're measuring. Maybe I make a mistake... Thank you very much! On 04/24/2012 10:30 AM, Johan Hattne wrote: Hi Qixu; This is by definition--the standard deviation is defined as the square root of the variance. http://mathworld.wolfram.com/StandardDeviation.html The standard deviation has the same unit as the values you're measuring, which makes its interpretation a tad easier. // Best wishes; Johan On 23 Apr 2012, at 18:13, Qixu Cai wrote: Dear Ed, Why the variance is the square of standard deviation? thank you very much! 在 2012年4月23日，20:53，Ed Pozharskiepozh...@umaryland.edu 写道： On Sun, 2012-04-22 at 12:47 +0530, Arka Chakraborty wrote: baverage program in ccp4 gave average bfactor of 25.0 for the residue but coot is showing 150! Variance is the square of standard deviation, thus var=150 means sigmaB~12 in that particular residue. High, but not impossible. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs Postdoctoral Fellow @ Physical Biosciences Division __ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
[ccp4bb] Criteria for Ligand fitting
Dear Crystallographers, We have obtained a 1.7 A dataset for a crystal harvested from crystallization drop after 2 weeks of soaking with inhibitor. The inhibitor has an aromatic ring and also an acidic tail derived from other known inhibitors. The active site hydrophobic crown had been reported to re-orient and a charged residue is known to position for forming a salt-bridge with similar ligands. When compared to apo strucutres, we can clearly see the re-orientation of these protein residues. However, there are no clear density visible for the ligand in the Fo-Fc map. Some density is visible in the 2Fo-Fc map with default settings in COOT. We were expecting co-valent modifcations between the inhbitor, co-factor and protein residues. In fact, the Fo-Fc map suggested the protein residue is no longer bonded to the co-factor (red negative density) and a green positive density is observed nearby for the protein residue. These observations, along with the extended soaking and the pre-determined potency convince us that the inhibitor is present in the complex. When I lower the threshold of the blue 2Fo-Fc map (0.0779 e/A^3; 0.2 rmsd) we can see the densities for the aromatic ring and the overall structural features. These densities were observed without the cofactor and the inhibtor in the initial MR search model. The R/Rfree for this dataset without inhibitor was 0.20/0.24 (overall Bfactor 17.4 A^2). At 50% occupancy, modeling the inhibtor showed no negative desities upon subsequent refinement. With the inhibtor, the R/Rfree was 0.18/0.22 (overall Bfactor 18.8 A^2). The temp factors of the inhibitor atoms (50% occ) were 15-26 A^2. My understanding is phase from the MR search model may influence Fo-Fc maps, and the 2Fo-Fc map minimizes phase bias. Since the inhibitor was absent from the MR search model, can these observations be used to justify the fitting of the ligand in the map? Given the low map-level used to 'see' the ligand, would this be considered noise? Can I justfiy the subsequent fall in R/Rfree and the absence of negative density upon ligand fitting as proof of correct inhibtor modeling? I would appreciate if you could comment on this issue. Or tell me that I'm dying to see the inhibitor and hence imagining things! Kind Regards, Naveed Nadvi.
[ccp4bb] HI
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