Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

Dear Graeme, some points for further clarification- The CORRECT corrections you mention all depend on the geometric description of the experiment. This geometric description of the experiment is refined by CORRECT, to come up with accurate values for a) application of polarization correction

[ccp4bb] Empty CORRECT.LP file

Hello, I have a question regarding the XDS output file CORRECT.LP. I have a dataset collected on a Pilatus which has 4960 frames. XDS ran over night to process the data with the ALL job activated and terminated successfully but the output CORRECT.LP file contains ZERO bytes, no data. I ran XDS

Re: [ccp4bb] Empty CORRECT.LP file

Dear Chris, you can replace the JOB=ALL with JOB=CORRECT and rerun xds. It won't take long and this way you can check of CORRECT.LP is written correctly or if you receive an error message (your partition might be full or your disk quota exceeded). Regards, Tim On 11/18/2014 10:42 AM,

[ccp4bb] Post-doc position - membrane protein complex

A candidate is thought for a two-year position (an extension is possible) to work on structural characterisation of respiratory complex I from T. thermophilus. Complex I is central to bioenergetics – it is the first and largest enzyme of the respiratory chain in mitochondria and bacteria. It

Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

Hi Tim, While we did not make this information available yet, there is a way to get non-bonded clash score that does take into account symmetry related clashes using the Phenix command: phenix.pdb_interpretation .pdb nonbonded_clashscore=True Testing for clashes is done in a slightly

[ccp4bb] Plasmid for cloning scFV into Fab format and Bacterial expression for crystallography

Hi everyone, I have a few single chain antibodies (scFV) that I would like to express in a Fab format in bacteria for crystallization purposes. Could you suggest some plasmids that have success in such kind of projects? Are there commercial plasmids consisting of antibody constant regions ready

[ccp4bb] how to combine two derivative datasets that are not isomorphous?

Hi All, I have two derivative datasets (heavy atom A and B) and two native datasets (a and b), A and a are isomorphous, B and b are isomorphous, however, a and b (or A and B) are not isomorphous. I was able to make two difference patterson maps (FA-Fa and FB-Fb) and search for heavy atoms

Re: [ccp4bb] Plasmid for cloning scFV into Fab format and Bacterial expression for crystallography

Hi Ivan, Just have a look at this paper: Skerra, A. (1994) A general vector, pASK84, for cloning, bacterial production, and single-step purification of antibody Fab fragments. Gene 141, 79-84. We (and other labs) have used this plasmid as well as its successors for the cloning and preparation

Re: [ccp4bb] how to combine two derivative datasets that are not isomorphous?

You don't mention any quality indicators on your derivatives, nor resolution. Presuming they actually have some decent phasing power, you may be able to generate phases maps using SIR phasing + solvent flattening. If you can do that for each isomorphous set, then you could combine them using

[ccp4bb] superpose bug?

Hi: I have a bunch of pdb files and would like to superpose them to one of them based on secondary structure matching. I would like to get a script to do so (not a one-by-one job by hand). I tried superpose but it seemed to have some problems with output option. Assuming C.pdb is the output

[ccp4bb] Fwd: [ccp4bb] B-factor blurring

My sincere thanks to all who are responding to my request below. To be explicit, my question relates to B-factor blurring (+B correction), not to B-factor sharpening (-B correction). thanks Mike Begin forwarded message: From: Mike Lawrence lawre...@wehi.edu.au Subject: [ccp4bb] B-factor

[ccp4bb] Postdoctoral position at Houston, TX, USA

Dear colleagues, There is an open postdoctoral position in an infectious disease lab at Houston Methodist Hospital Research Institute. Please see the announcement below. Postdoctoral Fellow position - Houston Methodist Research Institute (HMRI) We are seeking a structural biologist/biochemist to

[ccp4bb]

Gesendet:Dienstag, 18. November 2014 um 18:34 Uhr Von:Mike Lawrence lawre...@wehi.edu.au An:CCP4BB@JISCMAIL.AC.UK Betreff:[ccp4bb] Fwd: [ccp4bb] B-factor blurring My sincere thanks to all who are responding to my request below. To be explicit, my question relates to B-factor blurring (+B

[ccp4bb] Water molecules after refinement

Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using find waters in coot. After adding water refinement was done using Refmac 05. Now when I look on the

Re: [ccp4bb] Water molecules after refinement

Dear Jeorge are the water molecules without electron density properly coordinated? These could be ghosts... Additionally, did you solve the structure by molecular replacement? If so, in your search model, do you see these water molecules at the same / nearby location? Again, those could be