[ccp4bb] merge data from multiple isomorphous crystals.

Dear all, I have a crystal that can diffract to 3.0A for the first few frames at synchrotron, after procession only up to 3.6A data are useful. The structure has been solved by MAD. In order to get a 3.0A dataset, I am going to collect the first few images from dozens of isomorphous crystals and me

[ccp4bb] cell constants in MTZ file after transfer of Rfree flag

Dear colleagues, trying to be a responsible citizen, I occasionally activate the "Copy Rfree from another MTZ" button in the {Data Reduction|Import Integrated Data|Import Merged Data} CCP4I task. This appears to have the unintended effect of setting the "relevant/dataset" (as opposed to the "obsole

[ccp4bb] Glitch/problem with using refmac for pure TLS refinement

Hi all, I've been exploring the use of pure TLS models at various resolutions. By "pure" I mean that there is no individual atomic Biso component for the protein atoms. The net B factors for each atom are described only by the TLS group it belongs to. I have had really good success with this for

Re: [ccp4bb] phenix refinement peptide bond poor geometry

Hi Mohd, - if it is a regular peptide bond then they are linked automatically and this problem should never happen, otherwise there must be something not right with your input PDB file. - check in .geo file if this particular bond is restrained; If you send me (and not to the whole bb) the P

[ccp4bb] phenix refinement peptide bond poor geometry

Dear all, I'm about to deposit a structure into the protein data bank and I'm encountering a disturbing problem, I have a protein site where the peptide bond is not properly linked, the distance of C-N bond is 2.23 Angstrom, I tried to restrain that site by modifying my def file but the problem p

Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo

On Thu, 2009-12-17 at 18:25 -0500, Ajit Datta wrote: > I just talked to the NVIDIA pre-sales people and they told me that this > driver (195.22 beta) should work with 120Hz lcd monitors together with Nvidia > 3D vision kit on a quadro graphics card. > > Ajit B. http://www.phoronix.com/scan.php

Re: [ccp4bb] 3D search for peptide conformers?

And if you liked SPASM, you'll love the SPASM web-server that Mark Harris has made: http://eds.bmc.uu.se/eds/spana.php?spasm The decapeptide search is similar to the quest for left-handed helices described in the original publication. Recipe: - from the start page, upload a small

Re: [ccp4bb] How to reduce R-factor and Free-R

What is the space group? Is there unmodeled density? Are all residues in your construct built? What is the refinement protocol? FR On Dec 18, 2009, at 6:47 AM, james09 pruza wrote: Dear All, I am trying to solve a 2.55 A resolution data set. The R-factor is around 24% while Free-R is

[ccp4bb] How to reduce R-factor and Free-R

Dear All, I am trying to solve a 2.55 A resolution data set. The R-factor is around 24% while Free-R is 30%. The Residues in most favourable region is 95% while additionally allowed region is 5%. What are the ways to reduce the R-factor and Free-R? Around 100 water molecules are placed. Thanks in

Re: [ccp4bb] Unresolved density

I would try placing waters in the positive difference Fourier peaks (waters could make hydrogen bonds, if you follow the standard colour coding for the atoms), refine and see how the density looks like then. Kadhirvel Saraboji wrote: Hi all, In one of my 1.6Ang resolution structure, I came ac

[ccp4bb] Unresolved density

Hi all, In one of my 1.6Ang resolution structure, I came across a strange density. I tried to model this with PEG but after refinement still peaks appear around PEG at ~1.45-1.7 Ang. The images before and after PEG insertion is at:  http://mole.mbfys.lu.se/~saraboji/peg_density.jpg (Fo-Fc and

Re: [ccp4bb] mystery-blob-itis

Thank you very much for your suggestions. The truth is that I am following more or less the usual pathways for ligand identification as you Boaz suggested but I was just wondering if there was something to identify ligands in a bit less intuitive/classical manner (some sort of pattern recog

Re: [ccp4bb] Enzyme-Ligand complexes

This paper might provide some inspiration! Crystallization of protein–ligand complexes A Hassell et al Acta Crystallogr D Biol Crystallogr 2006 vol. 63 (1) pp. 72-79 HTH, Dave David C. Briggs PhD University of Manchester E-mail: david.c.b

[ccp4bb] mystery-blob-itis

Dear all, Curiously, I think I am just suffering an acute attack of mystery- blob-itis as well. I try to finish up the refinement of two structures and I am puzzled about a few blobs I found (from waters than could be ions to density that could be PEG). I have been digging out ligands from

[ccp4bb] Enzyme-Ligand complexes

Dear all, I am trying to get enzyme-ligand complexes crystals. I have already tried co-crystallization and soaking, but it was just failed. Are there some new methods developed for geting enzyme-ligand complexes crystals, or new strategies for co-crystallization and soaking recently? Thanks