Re: [ccp4bb] Wavelength of Copper Kalpha

I don't know what it is to 6 decimal places, and I'm pretty sure it isn't known. The sixth decimal place for ~8 keV is 0.008 eV, which is about the energy of a thermally-induced vibration. Changes in chemical environment of the copper atom (and hence the "starting energy" of the electron that f

Re: [ccp4bb] SFALL grid

SFALL is calculating structure factors from the map you supplied, so there is only one grid, the one you used when you created the map in NCSMASK. The choice of sampling rates for maps to be Fourier transformed is a deep topic. The mathematical law is that you have to sample the map at, at

Re: [ccp4bb] SFALL grid

Hi, Use keyword "GRID" in the script to set values: GRID The following general restrictions must be observed: >= 2 * HMAX + 1 >= 2 * KMAX + 1 >= 2 * LMAX + 1 In addition there are further space group dependent conditions as follows

[ccp4bb] SFALL grid

Hi: I am trying to generate structure factors from a mask/map that I made with NCSMASK. I get the following error message in SFALL: The program run with command: sfall HKLOUT "/tmp/whittle/109_5_7_1_mtz.tmp" MAPIN "/home/whittle/projects/109_5/CCP4/center_50.msk" has failed with error message S

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Re: [ccp4bb] His tag does not bind.

i suppose this is not from a thermophile or anything but one could try changing the temperature, we need to do this in one case (up in temp to 37-40C or no binding), but its a very thermostable thing. is the protein functional after e.coli expression? -tommi Quoting Chun Luo <[EMAIL PROTECTED]

Re: [ccp4bb] atomic FF used in SFALL

> what is the limit of N in a practical case for the Gaussian approximation. The resolution. Less resolution, less terms needed. see Acta papers TenEyck 1977 particularly Agarwal 1978, and the cctbx section in newsletter: http://

Re: [ccp4bb] His tag does not bind.

Let me make three short notes: 1. If the protein does not bind in a 'normal' buffer try first under denaturing conditions to see if everything is expressed correctly (a repeat of Artem's suggestion basically!). Protocols for that are in all materials manuals. 150 kD in E.coli is very very tou

Re: [ccp4bb] His tag does not bind.

Many brands of pH paper give 0.5-1 pH reading lower for Hepes buffer. pH meter is more reliable to measure the pH of Hepes buffers. Tris pH increases in cold. If TCEP is used as reducing agent, make sure the stock solution has been pH-adjusted. --Chun -Original Message- From: CCP4 bulletin

Re: [ccp4bb] His tag does not bind.

Try batch binding. Sometimes batch binding for 30 min is more efficient than column binding. If your protein binds DNA, treat with DNase or Benzonase. Adding detergent may help as has been suggested. --Chun _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of changrui lu

Re: [ccp4bb] His tag does not bind.

Recently, a make-or-break difference for me was making sure the pH was what I thought it was: In the presence of 50mM HEPES pH 7.0 (at room temp), the pH of my protein sample was actually nearer to 6 at 4degC, as judged by pH paper. I am not sure whether the pH difference was mainly because of

Re: [ccp4bb] atomic FF used in SFALL

It seems that 5-Gaussian is indeed the accepted technical term for the 9-parameter expansion: Given that a5=c and b5=0, the 5th Gaussian can be a constant. Continuing this reasoning, even a binary mumber can be represented as series of Gaussians.a=0,b=0; a=1, b=0 This is called 'Gomputing'.

Re: [ccp4bb] His tag does not bind.

150Kd is a fairly large protein for a MBP (55Kd) fusion. Six His-tag may not strong enough for it to bind to the Ni-column. If protein overexpression and solubility is not an issue, I would avoid using MBP fusion. Depend on how your protein fold, sometimes N-terminal His-tag works, sometimes C-term

Re: [ccp4bb] His tag does not bind.

We have found that our His-MBP fusion doesn¹t bind well after we cut off the protein of interest, and are trying to remove it. We have to use very low salt, cold temp, and slow loading rates. You might also try batch instead of column loading. We have also had good luck adding 1-2M urea to uncut Hi

[ccp4bb] b-factor sharpening and FFT/CAD

Hi all, I know this was most addressed by Eleanor back on June 14, 2007... and I've had no problems making such "sharpened" maps. But I'm confused as to why FFT decides to put "SCALE 2.0 -100.0" in the command file by default, and not "SCALE 1.0 -100.0"; I've been correcting this manually. Any th

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Re: [ccp4bb] Refmac and planar amide restraint

Dear Jason, you will have to include the planarity either by introducing torsion restraints for the specified bonds, or by using the plane definition. Pls. be aware that in the current refmac versions the plane definitions will be used with a fixed sigma, i.e. the value of the dictionary is not

Re: [ccp4bb] atomic FF used in SFALL

In any case it will become a Gaussian because presumably the atomic B's are added to the b terms for the density calculation? -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson > Sent: 11 October 2007 09:26 > To: [EMAIL PROTECTE

[ccp4bb] Refmac and planar amide restraint

Dear all, How does one tell Refmac that the bond between two non-amino-acid monomers should be planar (in the case that this bond is an amide)? My ligand has amino-acid and non-animo-acid constituents that are connected via amides. I have made library definitions for all of the non-standard

Re: [ccp4bb] atomic FF used in SFALL

I wrote that - is a constant a Gaussian? Anyway that is how I got 5 - and it is the 9-parameter Cromer-Mann approximation.. And Yes - each component is added to the B value to build up the real space atomic density. as you show. Eleanor Bernhard Rupp wrote: Dear All, I read in SFALL docu