[ccp4bb] Postdoctoral position - University of Hawaii

Applications are invited for a postdoctoral position in my lab at the University of Hawaii at Manoa, Honolulu, Hawaii, USA. Multiple projects are available involving receptor tyrosine kinases, GPCRs, structure based drug design, protein engineering, and developing methods for membrane protein cryst

Re: [ccp4bb] MTZ file

Hi, Just one correction to this. Phaser doesn't substitute values with the same name in an output MTZ file. To get the anisotropy corrected F and SIGF values, you have to run phaser in the separate anisotropy correction mode, and even then it appends the string "_ISO" to the column names and

[ccp4bb] BCA/CCP4 Summer School 2012

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new

[ccp4bb] precipitation.

Hi all, 1) I have a protein which gives two peaks on the 1ml Histrap column, Has anyone seen this kind of behaviour and does this mean that there are two populations of protein. They are partially seperated. 2) I tried to load the two peaks seperately on the superdex-75pg column. They came out as r

Re: [ccp4bb] precipitation.

Hi, Sounds like your proten gradually aggrgates. Seems tat aggregation is exacerbated by disulphide crosslinking. There might also be a conformational change involved or perhaps one of your dimers is a 'true' dimer (for a given value of true) whilst the other one might be a disulphide- or metal- m

Re: [ccp4bb] MTZ file

Many thnaks for your input. regards Ros On Wed, Feb 29, 2012 at 4:51 PM, Eleanor Dodson wrote: > mtz(1) will contain h k l F SIGF I SIGI and optionally F+ SIGF+ and F- > SIGF- This is your master file, providing the space group is correct > > It may NOT have the correct space group however - MR

[ccp4bb] Temp Fact Variance Analysis

Hello, I run my model in Coot to do "Temp Fact Variance Analysis". There are red bars from the B-factor Variance graphy. I click each red bar to exam the residues in Coot. Many of these residues do not have the electronic density on their side chains, especially Lys residues. Here is my questions

Re: [ccp4bb] Temp Fact Variance Analysis

Ros, I haven't used the "Temp Fact Variance Analysis" in Coot, but can guess that the red bars indicate increased b-factor compared to the average of your protein model? If so, then: *1. The lack of electronic density is the cause of these red-bars?* Likely yes. If there is no density to suppor

Re: [ccp4bb] Temp Fact Variance Analysis

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ros, yes, the lack of electron density is most likely the cause the these red bars (unless you set the map level rather high, but at the default chosen by coot that should be fine). yes - if you don't see electron density you don't have experime

Re: [ccp4bb] Temp Fact Variance Analysis

> 2. How do I fix them? delete the side chains? Here we go again. Take a look at these threads http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html http://phenix-online.org/pipermail/phenixbb/2011-March/016875.html -- Oh, suddenly throwing a giraffe into a volcano to make water is cra

Re: [ccp4bb] Temp Fact Variance Analysis

Here we go again! We neither have evidence that some mysterious side-chainnase has chopped off all flexible surface side chains and in fact, at least I am pretty sure these side chains are still there and moving around in the solvent as indicated by their very/extremely high B-factors, which, aga

Re: [ccp4bb] Temp Fact Variance Analysis

Hi, You could try to lower the threshold used to contour the maps for these side-chains (middle mouse "button" if you have a 3 button mouse with a wheel in the middle). Quite often such side chains have lowish electron density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc ma

Re: [ccp4bb] Temp Fact Variance Analysis

Typo (my fingers type faster than my brain...) Original Message Subject:RE: [ccp4bb] Temp Fact Variance Analysis Date: Thu, 1 Mar 2012 14:56:06 + From: Oganesyan, Vaheh To: Vellieux Frederic References: <4f4f8cb1.1070...@ibs.fr> Fred, After deleting

Re: [ccp4bb] Temp Fact Variance Analysis

Dear All: Thank you very much for your comments. I did not notice that this issue has been dicussed lately. Thank you for your inputs regards Ros On Thu, Mar 1, 2012 at 9:38 AM, Kelly Daughtry wrote: > Ros, > > I haven't used the "Temp Fact Variance Analysis" in Coot, but can guess > that

Re: [ccp4bb] Temp Fact Variance Analysis

On 01/03/12 14:26, Uma Ratu wrote: Hello, I run my model in Coot to do "Temp Fact Variance Analysis". There are red bars from the B-factor Variance graphy. I click each red bar to exam the residues in Coot. Many of these residues do not have the electronic density on their side chains, especial

Re: [ccp4bb] precipitation.

Rashmi, >Has anyone > seen this kind of behaviour? Yes, have seen differentially Glycosylated protein samples elute off affinity resins as separate peaks. but not that they behave different on gelfiltration like you described in your case. possible the samples interact with resin > Will there be

[ccp4bb] Let's GO, with Dora the PDBeXplorer!

Hi all, As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched a number of PDB archive browsers in the past two years. These allow users to explore and analyse what is in the PDB based on concepts and classifications they are familiar with, such as the EC syste

[ccp4bb] NCONT chain selection issue

Hello all - Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize comma-separated chain IDs with the source or target keyword. I'm trying to use NCONT to determine contacts between antibody chains and their bound epitope as part of a programmatic workflow. I'm using a Biopython Bio

Re: [ccp4bb] NCONT chain selection issue

Thats why I love distang! Eleanor On Mar 1 2012, Sampson, Jared wrote: Hello all - Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize comma-separated chain IDs with the source or target keyword. I'm trying to use NCONT to determine contacts between antibody chains and their

Re: [ccp4bb] Temp Fact Variance Analysis

Hard to know for sure - I often set occ to 0.0, then redo refinement and maps, only to find they have reappeared in the density at a low level.. In the end all our models are defective - LYS and ARg and GLU etc often have alternate conformations which we cant model at low resolution, and the te

Re: [ccp4bb] NCONT chain selection issue

Thanks to Pius for the tip that I can use more than one "source" keyword. ncont xyzin my.pdb

[ccp4bb] twin refinement in refmac

Dear CCp4ers, A good morning to everyone. Today, I have a structure that I initially refined in space group P6522, 1mol/asu. Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; / > 3 2.61-2.55A: Rsym=39.6%, / > 10 50.00-6.13: Rsym=6.4% Some mild anisotropy in the resolution limits is apparent on the

Re: [ccp4bb] twin refinement in refmac

Hi Wolfram, a few points: - R-factors in twin refinement vs non-twin refinement are not directly comparable: G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261 http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf - did you make sure free-R flags assigned "having twinnin

[ccp4bb] Na acetate as purification buffer

Hi all, Has anyone used sodium acetate buffer pH (4-5) for purifying histag protein on Histrap column (AKTA) followed by SEC? My protein has a pI of 9. I tried pH7.4 but it has precipitation problems. While doing buffer screening using 24 well hanging drop I found that lower pI onces are clear, so

Re: [ccp4bb] Na acetate as purification buffer

This pH is generally incompatible with Ni IMAC, sorry :) If you have a high pI your best bet is to employ ion exchange as primary capture, specifically SP resin or if you're really lucky - CM resin. There are only relatively few proteins in E. coli that bind to CM resin at pH 5 and virtually none (

Re: [ccp4bb] precipitation.

hi rashmi ,,, I have one suggestion dont use KCL in your buffer for crystallization b'coz u ll get lots of salt crystals mostly of K2SO4 . i faced this problem for one of my halophilic protein . most of the condition where NH4So4 is there u ll get salt crystals. On Thu, Mar 1,

Re: [ccp4bb] twin refinement in refmac

I'm worried when you say that you use the initial job's output MTZ. Refmac replaces F with a detwinned F in the output file so you wouldn't be refining against your measured data in the subsequent round. Best wishes Randy Read Randy J. Read On 2 Mar 2012, at 02:00, wtempel wrote: > De