Re: [ccp4bb] Zn fingers and Ni columns

Phoebe, It just so happens that we've been working on a C4 Zn-finger (or something very much like a Zn-finger) very recently without knowing that we had one (it's in the PheRS from S. haemolyticus, link to paper below) and we've purified the protein w/o any issues on an IMAC column (His-SELECT). W

[ccp4bb] Zn fingers and Ni columns

This has probably been discussed before, so apologies in advance. We're eyeing a protein that has a probable C4 Zn finger in the middle. The collaborators who are nicely going to PCR it up want to know if we'd like it with or without a His tag. Is it a bad idea to co-mingle Zn-binders and Ni co

[ccp4bb] Refmac_5.2.0019 failed in macbook

Hi, I did install ccp4 in my macbook( intel and 10.5 OS X). It is working for most of the programs(ccp4). But, when I submit a refmac job it failed with the following message. I am using GUI. The same version of the program is running successfully in pc-linux. Does anyone have solution to this

Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

I guess it was since summer and was only in cases if you gave anom formfactor SE If you did not then nothing was done. Garib On 3 Jan 2008, at 18:01, Ethan Merritt wrote: On Thursday 03 January 2008 01:25, Boaz Shaanan wrote: Is the wrong value pointed out by Ethan the reason why we tend

Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

On Thursday 03 January 2008 01:25, Boaz Shaanan wrote: > > Is the wrong value pointed out by Ethan the reason why we tend > to nearly always see +ve difference peaks over Se-met after refinement ? Could be. I have attached a plot of the net scattering factor for the two sets of values. I a

Re: [ccp4bb] Protein DNA complex refinement

It should. At the moment it is dealt with using synonyms. I have only done few tests. If it does not solve it then I have done something wrong need to correct it. If coot uses synonyms then it should be able to deal with these. Complete solution of this problem with backward compatablity require

Re: [ccp4bb] Protein DNA complex refinement

Also, the PDB now uses prime (') instead of asterisk (*) for the ribose numberings, and uses OP1 instead of O1P, and so forth. Do the new refmac dictionaries have that (I haven't been able to get it to work in the context of coot). Garib Murshudov wrote: > If you take new dictionary with new refm

Re: [ccp4bb] Protein DNA complex refinement

If you take new dictionary with new refmac it may solve this and some other naming problems. Try from the website: www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Garib On 3 Jan 2008, at 16:53, Daouda TRAORE wrote: Hi all, I'm trying to refine a protein DNA complex using Refmac. Unfortunately t

[ccp4bb] Protein DNA complex refinement

Hi all, I'm trying to refine a protein DNA complex using Refmac. Unfortunately the job fails because of the definition of nucleosides : In the pdb file I use for molecular replacement (and it's the same for all protein-DNA complex I found in the PDB) nucleosides are labelled DG, DT, DA , DC. In

Re: [ccp4bb] resolution & R-free -- addenda

> And is there any good software for refinement? > Of course, I forgot to mention TNT (with its great manual!) -:) Pavel.

Re: [ccp4bb] resolution & R-free

Hi Liuquing, > For example,first,the resolution is 2.25,R-free is 30,completeness is 90%. > Then I changed resolution to 2.35,R-free became 28.0,completeness is 91%. > When I changed resolution to 2.45,R-free became 27.5,completeness is 92%. > So,when resolution from 2.25 to 2.35,R-free goes down

[ccp4bb] Neutron Diffraction Instrument Scientist

Neutron Diffraction Instrument Scientist Summary: The Neutron Sciences Directorate at Oak Ridge National Laboratory (ORNL) invites applications for Neutron Diffraction Instrument Scientist. With the world’s highest flux reactor-based neutron source (the High Flux Isotope Reactor) and the world

Re: [ccp4bb] Webcast of the CCP4 study weekend ?

Here is the web address for the streaming http://extrplay.dl.ac.uk/ Cheers Martyn On Wed, 2008-01-02 at 09:29 -0800, Juergen Bosch wrote: > Hi CCP4 study weekend organisers, > > will there be a live webcast of the event, or alternatively can one view > on demand certain lectures ? > > Tha