Re: [ccp4bb] What could these crystals be?

Dear Careina, Don't forget that the DNA you use is also a variable — you may need to make minor or indeed major tweaks to this is order to improve your crystals; e.g. subtract or add a base / base-pair. Add a 1 base overhang etc.. Good luck! Antony - - - - - - - - - - Dr Antony W. Oliver

Re: [ccp4bb] What could these crystals be?

Looks like classic, poorly-diffracting “potato” crystals to me. Will need additional optimisation to convince them into a nicer morphology. No diffraction indicates that they are likely not to be salt at least. Tony. Antony W Oliver FHEA, PhD Principal Research Fellow Genome Damage and

Re: [ccp4bb] Baculovirus expression system

Dear Dhiraj, It may be perceived as “slow”, but we (still) use the Bac-to-Bac system from ThermoFisher (previously Invitrogen). This coupled with the pFastBac, MultiBac or biGBac vector systems generally works well; some proteins/complexes may express better in High 5 cells over Sf9/Sf21.

[ccp4bb] Post Doctoral Position

A fixed-term (1 year in the first instance) Post-doctoral Research Fellow position is available in the laboratory of Dr. Antony Oliver and Prof. Laurence Pearl, working as part of an ongoing drug discovery programme that seeks to discover small-molecule inhibitors of selected therapeutic

[ccp4bb] Apple Silicon / XQuartz / X11 / CCP4

Perhaps this is a little too soon, but does anyone know if the new M1 system-on-a-chip will continue to run XQuartz/X11 + the CCP4 program suite + other crystallography / EM software? Will CCP4 continue to support the platform? (a quick check of the GitHub page indicates that there is already

[ccp4bb] XCE - Refinement Fails

I am trying to convince XChemExplorer to refine my PANDDA models – i.e. those which have had ligands saved / placed into promising density. However, the large majority of refinement jobs (started by exporting all PANDDA models) simply fail. Is there a log file or something I can look at to see

Re: [ccp4bb] unusual monoclinic relation?

Dear Andrew, If you're sub 2 Angstrom - give Archimboldo a shot. We recently solved the crystal structure of a unknown protein this way. You perhaps have the advantage of knowing what be in there. Antony. --- Antony W Oliver --- --- sent from my mobile account --- On 20 Dec 2016, at 08:18,

Re: [ccp4bb] Modeling protein tertiary structure

Phyre2 absolutely deserves a mention. My 'threader' of choice. --- Antony W Oliver --- --- sent from my mobile account --- On 10 December 2016 at 00:05, Myeongseon Lee (이명선) <0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote: Hi, all.

Re: [ccp4bb] What to interpret??

Oxidation of cysteine. - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ United Kingdom http://www.sussex.ac.uk/lifesci/oliverlab

Re: [ccp4bb] ssDNA

1) Commercially made oligonucleotides 2) M13 rolling circle replication (how people used to make ssDNA for sanger sequencing). ——— Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex

Re: [ccp4bb] Skin on drops

Have you tried crystallising in microbatch format, i.e. under oil? I've had success with this method for exactly the problem you describe. Regards. Antony --- sent from my mobile account --- On 25 Feb 2015, at 08:39, Ulrike Demmer ulrike.dem...@biophys.mpg.de wrote: Dear

Re: [ccp4bb] merging anisotropic datasets

Would the CCP4 program BLEND be a suitable initial option? And then the anisotropic server? Tony. --- sent from my mobile account --- On 12 Nov 2014, at 21:29, Robert Keenan bkee...@uchicago.edumailto:bkee...@uchicago.edu wrote: I have three datasets of varying quality collected from

Re: [ccp4bb] Problem in molecular replacement

Try using DNA as a search model - this has worked very successfully in our hands before. Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton,

Re: [ccp4bb] Unidentified density in coot

Dear Shanti Looks like you’re looking down the symmetry axis - so this could simply be ‘noise’, or a superposition of two bound ligands on top of each other… what’s your cryo-protectant? With regards, Tony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK

[ccp4bb] Rotamer Selection in Low Resolution Data

Dear Crystallographic Community, Apologies for the cross-posting, but I *do* routinely use programs from all three software packages. I find myself refining a relatively low resolution structure (3.5 Angstrom) - with 8 molecules in the asymmetric unit. Is there a *simple* automated way to

Re: [ccp4bb] Rotamer Selection in Low Resolution Data

Hi Pavel, Sorry… the current ‘triumvirate’ is, in no particular order: CCP4, Phenix and Buster (Global Phasing). Any suggestions would indeed be useful. Many thanks, Antony. - - - - - - - - - - - - - - - - - - Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome

Re: [ccp4bb] Xia2 / XDS issues

Dear all, Firstly - many thanks to Kay Diederichs and Graeme Winter. The “memory” error was in fact due to certain diffraction images having very few (weak), if any spots - essentially they were ‘blank’. By excluding these images, and with a combination of Xia2, plus XDS + Aimless, I was

[ccp4bb] Xia2 / XDS issues

Dear CCP4-ers. I am (trying) to use Xia2 (svn/Build 4599) to process some diffraction data. However, I am coming across the following issue, which I don’t seem to be able to solve... Integrating SWEEP1 Status: error [XDS] cannot

Re: [ccp4bb] Xia2 / XDS issues

Dear CCP4-ers. Many apologies for the previous post (with attachments). However, it is true - somewhat crappy data, that I can’t seem to reprocess with XDS / xia2. Tony. HI Graeme, Please find below, what I think it is that you need? Files attached, plus relevant text clips,. NB:

[ccp4bb] Error using Coot supplied with CCP4

Dear CCP4 / Coot community, I am trying to use LIDIA from Coot 0.7.2 - as supplied with CCP4-6.4.0 - to look at a protein / ligand complex. However, when trying to launch LIDIA from the Extensions menu of Coot - I get the following error. I guess this suggests some form of fortran compile

Re: [ccp4bb] changes in small sections of secondary structure

Dear Mahesh, Are all the structures at similar resolution? Definition of secondary structure is, and can be, affected by the level of geometric restraints/constraints used in the refinement process. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome

Re: [ccp4bb] Identity of a Bacterial lipid

Lipid or PEG from your crystallisation condition? --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349

Re: [ccp4bb] REFMAC5: linking a modified amino acid to adjacent residues

For REFMAC, I think you need to alter the cif file for the modified residue - such that the residue type is L-peptide rather than anything else. Tony. Sent from my iPhone On 2 Aug 2013, at 17:08, Arnon Lavie la...@uic.edumailto:la...@uic.edu wrote: Hi: Despite Google and several attempts, I

Re: [ccp4bb] Heterogeneity during purification

Theresa, Are there any cysteines in your protein? Tony. On 9 Jul 2013, at 05:01, Theresa Hsu theresah...@live.com wrote: Dear all I am working on a 30 kDa membrane protein which forms a functional dimer. The protein is His-tagged at N-terminal. In small scale expression screening from

Re: [ccp4bb] Heterogeneity during purification

inappropriate di-suphide formation. Tony. On 9 Jul 2013, at 08:18, Theresa Hsu theresah...@live.com wrote: Dear Tony Yes, there are four cysteines. Theresa On Tue, 9 Jul 2013 06:26:19 +, Antony Oliver antony.oli...@sussex.ac.uk wrote: Theresa, Are there any cysteines in your

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

Er considering this forum, why not try CCP4MG ? Tony. On 30 May 2013, at 22:24, Petr Leiman petr.lei...@epfl.chmailto:petr.lei...@epfl.ch wrote: On May 30, 2013, at 5:31 PM, Phoebe A. Rice pr...@uchicago.edumailto:pr...@uchicago.edu wrote: In the olden days, when dinosaurs did roam,

Re: [ccp4bb] Negative FoFc around ligand

Dear Kavyashree, It is possible that your bound ligand (for which you have strong electron density) is actually a break-down of the parent compound? We have seen this a couple of times now. Also - are the poorly refining areas (those with negative density) part of a pendant ring connected

Re: [ccp4bb] Negative FoFc around ligand

Kavya, Presumably your enzyme is turning over the ATP? Driving it towards ADP? In that case I suspect that you may have a mixture of ATP and ADP (and possibly contaminating AMP). You could either model both ATP and ADP, and set relative occupancies of both (add up to 1). Or, you could assign

Re: [ccp4bb] Diffraction image viewer with display of resolution circles

iMosflm can certainly do this for you. You might have to screen grab to capture the resolution rings though. Tony. On 23 May 2013, at 09:27, Rafal Dolot rdo...@cbmm.lodz.pl wrote: Dear CCP4 users, I'm looking for the diffraction image viewer, which will be able to display of resolution

Re: [ccp4bb] Why the name aimless

I thought it was just a logical pun progression from pointless to aimless. Perhaps the next program will be useless? DISCLAIMER: This is intended as a JOKE... I FULLY appreciate and use the wonderful programs generated by Phil. Just in case I unintentionally start yet another CCP4bb

[ccp4bb] Curious electron density associated with Asp sidechain

Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is

Re: [ccp4bb] gelification of a pure protein

To ask a potentially daft question - but why do you need to reduce the salt? You say you are able to purify it, and that it behaves on gel filtration - but only starts misbehaving when you dialyse, and the NaCl is below 100 mM. We've crystallised many proteins, particularly DNA-binding

Re: [ccp4bb] CCP4 Update victim of own success

Eugene - that's great. I too run a small suite of Macs (12) and was trying to find a practical way of updating all those machines remotely. The command line version of CCP4um will be very useful. Many thanks. Tony. Sent from my iPhone On 11 Apr 2013, at 18:19, eugene.krissi...@stfc.ac.uk

[ccp4bb] Post-Doctoral Research Fellow - University of Sussex

A Cancer Research UK-funded Postdoctoral Research Fellow position is immediately available in the laboratory of Professor Laurence Pearl FRS and Dr Antony Oliver, to study the structural basis for the assembly and specificity of multi-protein complexes involved in the recognition and repair

Re: [ccp4bb] refinement protein structure

Dear Tom, Q1: Are you really supposed to posting this information here? Q2: Is there really NOT anyone you can ask in your own department to help you with this? Some initial hints/ideas/suggestions though - although I actually assume this is meant to be a learning exercise for you …? 1) Have

Re: [ccp4bb] refinement protein structure

At the risk of being somewhat cheeky - perhaps I could claim second author? I too have successfully solved the structure - and I totally concur with Phil. Placing a second molecule in the asymmetric unit, essentially resolves the perceived R-factor problem. A good thorough manual inspection and

Re: [ccp4bb] refinement protein structure

Dear Tom, I think that we've all actually been rather gently teasing you - admittedly a difficult concept to put across via the medium of e-mail. In fact, I think we've all offered sensible constructive suggestions, and indeed pointed out what you should try next. Apologies for any

Re: [ccp4bb] delete subject

Dear Tom, I'm sure the files can be easily removed from the server, if that is what you wish / want to happen. A quick email to the administrators at c...@ccp4.ac.ukmailto:c...@ccp4.ac.uk should do the trick. Reading around all the all leg-pulling / other comments aside - from your post

Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

Or, seeing that this is the CCP4BB smile, you could use the Xia2 pipeline from CCP4i - which will also use XDS if installed on your system. My recommendation would be to process with XDS. By using the autoProc procedure from Global Phasing this is very easy, even for people who are normally

Re: [ccp4bb] laboratory phage infection [SEC=UNCLASSIFIED]

Dear Aidong, Some thoughts... Are you sure the problem is actually phage-related? I ask because you are still having problems using phage-resistant stains... Acid-washing your glassware, and a long-dry autoclave sterilisation (as previously suggested) should really do the trick. A good

Re: [ccp4bb] Unknown density

Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of noise around these regions - and it may not, in fact, be possible to model this satisfactorily. Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and

Re: [ccp4bb] off topic: DSSP

Sorry to cross-pollute… If you don't mind using the ksDSSP implementation, it is already installed with the phenix suite if you have it. phenix.ksdssp from the command line. With regards, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and

Re: [ccp4bb] Mac mini advice

Dmitry... everyone is of course entitled to their opinion - but as one of the brain-washed masses I feel I need to at least reply (!). Sorry Cara... I am not happy with the direction OS X is going. Too much emphasis on eye candy and not enough on underlying technology. Fair enough, but it

Re: [ccp4bb] Mac mini advice

Hi Cara, Any reason for the Mac Mini over the iMac? - presumably as you've got a suitable monitor / keyboard already? We're pretty much exclusively iMac of late (ditched the towers) and finding them absolutely fine for both fairly intensive jobs (refinement) and visualisation/building (Coot

Re: [ccp4bb] drawing topology digram

PDBSUM works equally well for undeposited structures. Hit the generate button on the left hand side. Tony. Sent from my iPhone On 15 Dec 2012, at 21:04, Wenhua ZHANG xtal.zh...@gmail.com wrote: Dear all, Could anyone recommend me an easy program to draw the secondary topology digram

Re: [ccp4bb] [COOT] CCP4 - Coot in Applications

Thanks Scott. Using your stand-alone Coot package - 0.7 (revision 4459) [with guile 1.8.8 embedded] [with python 2.7.3 embedded], everything works perfectly. The previous issue of invalid window errors no longer occurs, and all scripts that use coot now work correctly (as the path

Re: [ccp4bb] [COOT] CCP4 - Coot in Applications

(lab): +44 (0)1273 677512 On Nov 26, 2012, at 10:19 AM, Charles Ballard wrote: You could give /Applications/coot.app/Contents/Resources/script a go. Charles On 23 Nov 2012, at 12:20, Antony Oliver wrote: Forgive what may be a very simple question… I have recently installed coot

Re: [ccp4bb] CCP4 - Coot in Applications

Forgive what may be a very simple question… I have recently installed coot using the very nice CCP4 .dmg (0.7.0-i386) - which now puts coot into /Applications I now need to set a $PATH to coot, such that various home-made scripts now 'know' where it is Here I have hit a hurdle. Which binary

[ccp4bb] Copying R-free flags - possibly daft question.

Am I worrying about something unnecessarily? I have several protein-drug datasets, all in the same spacegroup, but wildly varying resolutions. I wish to use the same reflections for calculating R-free in all cases. Using xia2 with a reference dataset for both indexing and R-free seems to work

Re: [ccp4bb] Copying R-free flags - possibly daft question.

(1/dmax)**2 = 4 sin**2theta/lambda**2 =(1/dmin)**2 NOTE: Defaults are 0.1 and 1000.0 Angstrom. On 5 Nov 2012, at 09:53, Antony Oliver wrote: Am I worrying about something unnecessarily? I have several protein-drug datasets, all in the same spacegroup, but wildly varying resolutions. I

Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window

Unfortunately, that very much depends on which OSX you are running (Leopard, Snow Leopard, Lion, Mountain Lion) and which keyboard you have…! On my keyboard it's F3 and not F10. T. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre

Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window

Eike - This unfortunately, is a well-known feature of coot on OS X - something to do with Apple's implementation of X11. Perhaps Paul knows if this happens on Mountain Lion, now that you need to use Quartz X11? Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes

[ccp4bb] REMINDER: 3 x Postdoctoral Research Fellow positions at the University of Sussex ( DNA Damage Repair and Signalling)

- - REMINDER - - IMMINENT CLOSING DATE: 28th September 2012 3 (Three) Cancer Research UK-funded Postdoctoral Research Fellow positions are available immediately in the laboratory of Professor Laurence Pearl FRS and Dr Antony Oliver, to study the structural basis for the assembly and specificity

Re: [ccp4bb] off topic: reduced glutathione interfering with protein activity?

GSH will reduce your protein quite nicely - is your enzyme activity redox sensitive? --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email:

Re: [ccp4bb] Various OSes and Crystallography

Mountain Lion does not come with X11 preinstalled. However, as Nat states, you can very easily install Xquartz Thus far, all of the crystallography programs that were working under Snow Leopard and Lion are still working on my laptop with Mountain Lion. -Tony --- Dr Antony W Oliver Senior

[ccp4bb] 3 x Postdoctoral Research Fellow positions at the University of Sussex ( DNA Damage Repair and Signalling)

3 (Three) Cancer Research UK-funded Postdoctoral Research Fellow positions are available immediately in the laboratory of Professor Laurence Pearl FRS and Dr Antony Oliver, to study the structural basis for the assembly and specificity of multi-protein complexes involved in the recognition

Re: [ccp4bb] Enhancing Crystal Quality

Have you tried different cryoprotectants? Can make a huge difference. Also, have you shot an xtal at room temp - to see what the intrinsic diffraction limit is? Additive screens? If all else fails you may well need to explore a different expression construct. Tony. Sent from my iPhone On 1

Re: [ccp4bb] NCS rotamers

forgive the cross-posting coot-bb/ccp4-bb Can I second that please? I am possibly in a similar situation - 2.8 Angstrom structure, 6 molecules in the asymmetric unit, refining with ncs torsion restraint. It would be very useful to identify which side-chains are in different rotamers (without

Re: [ccp4bb] SUMO(ULP-1) protease

Gene synthesis and make your own! Tony. Sent from my iPhone On 24 May 2012, at 20:42, Gloria Borgstahl gborgst...@gmail.com wrote: My fellow crystallographers, We are thinking the SUMO/His vectors would be nice to have in the lab aresenal... but. The stumbling block is that the protease

Re: [ccp4bb] pdb and cif file generation from smiles string

Considering all the recent posts on this very forum regarding the excellent Grade; I would suggest a quick visit here… http://grade.globalphasing.org/cgi-bin/grade/server.cgi Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre

[ccp4bb] Off Topic: Sucrose / Glycerol Gradient Maker Fractionator

Dear all, I find myself working on a number of large multi-protein complexes, and am likely to need to use Sucrose / Glycerol gradients in preparing them. IWhilst I can do this manually in the short term, I was wondering if someone could recommend any manufacturer's (preferably Europe/UK

Re: [ccp4bb] negative density at some places in the side chain of residues

Alaksa, 1) What rmsd / sigma are you contouring your density at ? i.e. are you down in the noise or are you at a reasonable value for your Fo-Fc map? 2) It looks like some of your side-chains appear to have more than one conformation - it's fairly easy in Coot to position and model both.

Re: [ccp4bb] Arp/WARP for multi-chain complex

In the absence of a likely, more sensible, answer - I think the trick is/was to simply put everything in one pir file, but link each sequence with a run of 20 or so alanines i.e. sequence A followed by ... sequence B sequence C. There may well be a more

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Apr 2012, at 15:09, Antony Oliver wrote: This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Thanks Ian, Of course it'd have to be something else :-) but the capability of displaying models and maps via a web-browser is at least within current capabilities. Perhaps the whole model or electron density doesn't need to be presented - perhaps just a representative chunk or chunks with

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Tom, that's indeed true. But, the file can be encrypted, and it doesn't necessarily have to be in strict PDB format. Getting out of my comfort and knowledge zone here... But with the advent of HTML5 is a plugin strictly necessary? Tony. Plus if you're only looking at a chunk of structure -

Re: [ccp4bb] Coot chain ID

Dipankar, A little bit of cut-and-paste in a good text editor will sort that out fairly easily. Tony. Sent from my iPhone On 14 Apr 2012, at 07:54, Dipankar Manna dipanka...@aurigene.commailto:dipanka...@aurigene.com wrote: Dear All, I fitted a ligand into a structure along with SO4 and

Re: [ccp4bb] Error in Scala

One quick thought is - are you trying to scale reflections that don't really exist? I.e are you trying to push your resolution a bit too much? Tony. Sent from my iPhone On 6 Apr 2012, at 20:29, Yuri Pompeu yuri.pom...@ufl.edu wrote: Hi everyone, Sorry for the newbie type problems, but I

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

To my mind it just points to the fact that many scientists are generally unable to focus on one task or 'thing' at a time. i.e. very short attention spans... [before the flamer's start ‹ this is meant as a joke] Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

Think the jury might be out on this one... A quick snip from WikiDictionary... The plural word phages refers to different types of phage, whereas in common usage the word phage can be both singular and plural, referring in the plural sense to particles of the same type of phage. Maloy et al:

Re: [ccp4bb] contaminant when overexpressing a GST tagged protein

I would hazard a guess of Gro-EL. With regards, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email:

Re: [ccp4bb] modelling C-terminal COOH in coot

There is a button for doing this - add OXT, which if I recall is hidden in the other modelling tools menu. Tony. Sent from my iPhone On 17 Feb 2012, at 10:26, Hubing Lou louhub...@gmail.com wrote: Dear all, I have a structure solved by molecular replacement. The C-terminus at the end

Re: [ccp4bb] DNA length for crystallization

Lisa, there isn't unfortunately a hard and fast rule for the length of DNA used in co-crystallisation. It usually is just a case of screening different lengths, permuting the sequence, and investigating overhangs or gaps in the DNA duplex. We generally work with oligos between 8 and 21 nts in

Re: [ccp4bb] surface residue mutation

Have you solved the structure? It's just that you don't say why you need different crystal forms. We had to do a bit of crystal engineering in order to get a complex between our protein and a peptide. It turned out to be relatively simple case; visually inspecting the crystal packing (in Coot)

Re: [ccp4bb] extra density ??

Stacy, It looks like it's just some noise on your two-fold symmetry axis. You could probably model some/most of it with a couple of water molecules. Tony. On 19 Jan 2012, at 06:44, stacy William wrote: Dear All, I am working on plant proteins and solved a structure, there is an extra

Re: [ccp4bb] Molprobity Clashscore

Ok, I'm completed baffled... and have obviously started something unintentionally... NB: it was a joke! I was amused that Molprobity, after 'adding' hydrogens to my model, had 'improved' the clashscore of my model by an obviously unnecessary number of decimal places...! [0.0098

Re: [ccp4bb] Molprobity Clashscore

of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 From: Pavel Afonine pafon...@gmail.commailto:pafon...@gmail.com Date: Thu, 12 Jan 2012 08:11:34 -0800 To: Antony Oliver antony.oli

Re: [ccp4bb] Superpose problem

Ph.D candidate College of Life Sciences Nankai University Tianjin, China At 2011-12-29 16:56:03,Antony Oliver antony.oli...@sussex.ac.ukmailto:antony.oli...@sussex.ac.uk wrote: You could use the Superpose program to generate superpositioned/superposed/superimposed models - i.e. to put your

Re: [ccp4bb] a PDB tool

You can simply use the renumber residues function in Coot. Alternatively a good text editor, with a replace function can achieve the same result. Sent from my iPhone On 3 Jan 2012, at 12:33, Dialing Pretty hdc123hdc...@yahoo.commailto:hdc123hdc...@yahoo.com wrote: Dear All, I have a PDB

Re: [ccp4bb] Superpose problem

You could use the Superpose program to generate superpositioned/superposed/superimposed models - i.e. to put your structures on top of each other. There are also a host of other programs available to do the same thing (!) In Phaser, you would then load each of these superimposed models, to

Re: [ccp4bb] Expression of a Selenomethionine Variant in E. coli

Generally no, only in the subsequent protein purification steps. Tony. Sent from my iPhone On 12 Dec 2011, at 21:57, Yibin Lin yyb...@gmail.com wrote: Hi List, I want to preprare sel-met labeling protein. Could someone can tell me if it is necessary to add DTT or BME to medium, which

[ccp4bb] Bug in XIA2 0.3.3.3 Build 3479

Dear CCP4 developers, Forgive the posting here, but I can't find the correct contact details for Graeme Winter… I have just downloaded the latest version of XIA2 (0.3.3.3 build 3479) and tried to integrate a dataset. The program fails with the following error… Build: 3479 XIA2 0.3.3.3

Re: [ccp4bb] Windows 7 and Xtal Software

Erm, somewhat confused — if you are going to buy a Mac — why would you need (or want!) a triple boot system? It all seems to work just fine on OS X. Tony. On 30 Aug 2011, at 07:38, Nian Huang wrote: A dual boot laptop is all you need. I always reinstall the windows to get rid of bloatware

Re: [ccp4bb] Coot File Save Coordinates

If you're running Coot on a Mac - it's also unfortunately a well-documented feature, something to do with Apple's implementation of X11. Sent from my iPhone On 15 Aug 2011, at 21:25, Raji Edayathumangalam r...@brandeis.edumailto:r...@brandeis.edu wrote: Thanks Mischa and Juergen. That was

Re: [ccp4bb] Another paper structure retracted

PIR is fairly similar to Fasta, from addled memory the format is... protein name; empty line MPREIL...rest of amino acid sequence with an optional asterisk to mark the sequence end. Tony Sent from my iPhone On 12 Aug 2011, at 09:14, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Can

Re: [ccp4bb] Another paper structure retracted

had protein GSP etc ... SEN* On 12 Aug 2011, at 09:19, Antony Oliver wrote: PIR is fairly similar to Fasta, from addled memory the format is... protein name; empty line MPREIL...rest of amino acid sequence with an optional asterisk to mark the sequence end. Tony Sent from my

Re: [ccp4bb] Another paper structure retracted

Surely in this ''modern age data could be uploaded to review server whereby a reviewer could be given privileged access - to be able to see the model and maps, via something like AstexViewer, to gauge the quality and reliability of modelling - without actually getting the PDB coordinates or

Re: [ccp4bb] Good performing low resolution iterative model building programs?

Dear Frances, I think the answer is going to somewhat depend on whether you need / want de-novo building, i.e straight from independent phases or if you have a good quality homology model, that you can use as a reference structure, or a good starting point. New good things that are available

Re: [ccp4bb] Another paper structure retracted

the model fits the electron density, by a knowledgable crystallographic reviewer Sent from my iPhone On 11 Aug 2011, at 15:03, Nat Echols mailto:nathaniel.ech...@gmail.comnathaniel.ech...@gmail.commailto:nathaniel.ech...@gmail.com wrote: 2011/8/11 Antony Oliver mailto:antony.oli

Re: [ccp4bb] prescission protease cutting site

Dear Jerry, Our in-house series of vectors encode the Rhinovirus 3C-protease site, followed directly by a NdeI site, which after cleavage leaves just GPHM on the front of your protein. We routinely get 100% cleavage with incubation overnight at 4˚C — and have several xtal structures to boot.

Re: [ccp4bb] Phaser and Molrep gave different solutions

Have you tried using the DNA as your search model? - I have had success this way round - certainly more phasing power than your protein model, I guess. Also, refine with your DNA in place, and your phases/ map should improve - hopefully allowing you to place your protein molecules with ease.

Re: [ccp4bb] Concentrating a protein solution - subbu

You could try loading a small 1ml HiTrap (or similar) Q or S column with your protein - and knocking it off it in one go with high salt, alternatively micro-dialysis against a solution containing PEGs can also work well. Tony Sent from my iPhone On 21 Jul 2011, at 17:54, Narayanan Ramasubbu

[ccp4bb] Postdoctoral Research Fellow - University of Sussex - REVISED CLOSING DATE

*PLEASE NOTE REVISED CLOSING DATE* [ Postdoctoral Research Fellow - Genome Damage and Stability Centre, University of Sussex - Ref 292 ] An MRC-funded post is available in the laboratory of Professor Laurence Pearl and Dr Antony Oliver to study the structure and function of the Smc5/6 complex

[ccp4bb] Postdoctoral Research Fellow - Genome Damage and Stability Centre, University of Sussex - Ref 292

[ Postdoctoral Research Fellow - Genome Damage and Stability Centre, University of Sussex - Ref 292 ] An MRC-funded post is available in the laboratory of Professor Laurence Pearl and Dr Antony Oliver to study the structure and function of the Smc5/6 complex. This project forms part

[ccp4bb] Joint PhD position at the University of Sussex

UNIVERSITY OF SUSSEX An MRC-funded PhD position is available immediately in the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex. The student will be supervised jointly by the laboratories of Professor Keith Caldecott and Dr Antony Oliver

[ccp4bb] PhD position at the Genome Damage and Stability Centre, University of Sussex

UNIVERSITY OF SUSSEX An MRC-funded PhD position is available immediately in the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex. The student will be supervised jointly by the laboratories of Professor Keith Caldecott and Dr Antony Oliver

Re: [ccp4bb] Preparation of seed-stocks without seed-beads

You can melt the end of a thin glass capillary, forming a glass 'bead' at one end. You can then attack your drop, containing the crystals to made into seeds, with the beaded end of the capillary. You can then pipette up the crushed crystals, and dilute and/or spin to make your seed stock. With

[ccp4bb] Off-topic: Carba-NAD

Dear bulletin-boarders... Does anyone know of a good (UK?) source, where I can buy some carba-NAD? I would like to use it in some co-crystallisation experiments. I've looked in the 'usual' places - i.e. Sigma-Aldrich, but can't seem to find it anywhere. Many thanks in advance, Antony

Re: [ccp4bb] Protein-DNA complex prepartion for crystallization

Dilute both the Protein and DNA before mixing them at the molar ratio you require - I would aim to have the protein component at around 1 mg/ml. Mix, then concentrate together, till you reach the concentration you want. Antony. On Wed, Oct 1, 2008 at 6:52 PM, E rajakumar [EMAIL PROTECTED]

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