[ccp4bb] OT: MagiXstick

Dear All, I have come up with a handy electromagnetic pin mounting stick. I manufactured a first batch, which I am selling pretty much for parts and labor. I thought some practitioners in the ccp4 crowd might be interested. Feedback and suggestions by users would be welcome. Description and v

Re: [ccp4bb] Unexplained density

While it would not be unreasonable for zinc ions to be coordinated to the asp residues (perhaps with bridging waters or hydroxides), I am a little troubled by the lack of electron density around the coordinating residues. If there are zinc ions tightly coordinated at full occupancy, I would nor

Re: [ccp4bb] a simple query: atom selection for CNS

Hello, Just for your information, there is a mailing list for CNS: http://groups.yahoo.com/group/cnsbb/ And there is some activity on it. Regards, F. AMIT wrote: Just type in CNS refine.inp in the atom select option: {===>} atom_select=(not((chainid A and resid 10:15 ) or (chainid B and resi

Re: [ccp4bb] Unexplained density

I think it could be zinc ion. On Fri, Apr 30, 2010 at 5:38 AM, Daniel Bonsor wrote: > Hello again > > I currently have some unexplained density in my structure. As you can > hopefully see from the images (see file), the density is dumbbell shaped. > Whatever it is, it is coordinated by Asp and G

Re: [ccp4bb] Understanding Conformational Differences

Date:Thu, 29 Apr 2010 12:18:38 -0500 From:Jacob Keller Subject: Understanding Conformational Differences Dear Crystallographers, I am looking at ~20 unique crystal structures of the same protein in somewhat different conformations, although not radically different, and would like to or

Re: [ccp4bb] Unexplained density

The close approach of the two Zinc atoms may not be too implausible if the charges are being quenched by coordination of the negatively charged residues. William Ho On Thu, Apr 29, 2010 at 5:38 PM, Daniel Bonsor wrote: > Hello again > > I currently have some unexplained density in my structure

Re: [ccp4bb] Unexplained density

It's hard to see clearly the density, but judging from the abundance of carboxy groups, it may be a metal. Maia Daniel Bonsor wrote: Hello again I currently have some unexplained density in my structure. As you can hopefully see from the images (see file), the density is dumbbell shaped. Wha

Re: [ccp4bb] NADP behaviour in crystal

Sorry for the mistake. It is co-crystallised with protein. And there is difference in the cell parameter between, apo protein and the co-crystallised structure. The difference is 10A in one axis and 5A at another axis, third axis are same in both crystal. Thank you Sajid __

Re: [ccp4bb] Understanding Conformational Differences

Hi Jacob, please have a look at the program ESCET from Thomas Schneider, which I have used to look at changes in over hundred structures of kinases upon ligand binding. cheers Stefan On Thu, 29 Apr 2010 12:18:38 -0500 Jacob Keller wrote: > Dear Crystallographers, > > I am looking at ~20 uni

[ccp4bb] NADP behaviour in crystal

Hi All I had a soaked crystal with NADP; and the crystal diffracted to 2.5A. I was looking for NADP at its binding site, I came up with wierd density which I could not fit with any end of NADP. The density is upto 3.5 A in Fo-Fc map; and is spherical long enough to put nicotine. But the density

Re: [ccp4bb] Precipitation of protein-protein complex under most of the crystallization condition

a most approapriate paper for the method that i described earlier is in the following paper. Follow the link Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins http://journals.iucr.org/d/issues/2004/09/00/dz5020/dz5

[ccp4bb] Understanding Conformational Differences

Dear Crystallographers, I am looking at ~20 unique crystal structures of the same protein in somewhat different conformations, although not radically different, and would like to order them somehow to gain an understanding of how the protein can move. Is there software that does this somewhat

Re: [ccp4bb] automise ncont

On Thu, Apr 29, 2010 at 4:25 PM, Edward A. Berry wrote: > Command-line param like XYZIN don't seem to be shell variables, > but can be set by variables: > > bin/ncont XYZIN $XYZIN

Re: [ccp4bb] automise ncont

Seems I confuse atom-selection syntax with filespec syntax here. Anyway the idea is that shell variables will be substituted in the input lines before they are passed to the program Command-line param like XYZIN don't seem to be shell variables, but can be set by variables: bin/ncont XYZIN $XYZIN

[ccp4bb] Protein X-Ray Crystallographers, Oxford

Senior Scientist X-Ray Crystallographers within our Structural Biology Department Salary: £26,000 - £39,000 + benefits Location: Oxfordshire, UK Full time; Permanent and Temporary (12 month contract) Evotec (UK) Ltd is currently seeking X-Ray Crystallographers for our Structural B

Re: [ccp4bb] automise ncont

And passing parameters (I haven't tested this): #!/bin/csh -f foreach ncB ( `ls /*/B` ) foreach ncJ ( `ls /*/J` ) set ncMAXD=6.0 bin/ncont XYZIN 1FNT_BJ.pdb

Re: [ccp4bb] automise ncont

c-shell syntax would be: bin/ncont XYZIN 1FNT_BJ.pdb

Re: [ccp4bb] automise ncont

See $CCP4/examples/unix/runnable/ncont.exam Run as e.g. ncont.exam > ncont.log Cheers Martyn On Thu, 2010-04-29 at 06:42 -0700, Thomas Juettemann wrote: > Dear all, > > I am pretty new to the CCP4 suite. I am trying to automise the > execution and parsing of ncont. > Could someone advise me how

[ccp4bb] automise ncont

Dear all, I am pretty new to the CCP4 suite. I am trying to automise the execution and parsing of ncont. Could someone advise me how (if possible) to pass parameters to the program? I am trying to do something like bin/ncont XYZIN 1FNT_BJ.pdb source /*/B target /*/J maxdist 6.0 and have the out

Re: [ccp4bb] Precipitation of protein-protein complex under most of the crystallization condition

On Thu, 2010-04-29 at 16:23 +0530, Jhon Thomas wrote: > This is a strange behaviour of the protein complex. Why is this strange? 20 mg/ml is fairly high, just dilute the protein to 10 mg/ml and repeat the screen. Or better yet, repeat the screen with 1:2 protein:reservoir ratio for precipitated

[ccp4bb] Precipitation of protein-protein complex under most of the crystallization condition

Hello BB I am working with small protein-protein complex of Molecular weight 40kDa. This protein expresses well and soluble in 20mM Tris-Cl pH-8.0 and 50mM of KCl, could be concentrated upto 20mg per ml in this buffer. I have purifed this protein with Ni-NTA resin and they are free from any contam