[ccp4bb] Reading LCF files.

For those who suffer from 80's nostalgia, I have worked-out a simple-man's way of recovering the reflection data from this, now obsolete, format. Its here: https://readingccp4lcffiles.blogspot.com and it works for most of my VAX lcf files. Just thought this might be of interest as the question h

Re: [ccp4bb] HKL2000 - Error model

You should not adjust the error model manually, instead please select the button "use auto corrections" and rely on the automatically adjusted error model. This way you do not have to analyze the changes in the resolution shells. D. On 2019-07-01 01:44 PM, Weston Lane wrote: When you fix th

Re: [ccp4bb] HKL2000 - Error model

When you fix the error model in HKL2000 you only have a set of numbered boxes (1-20) and knowing which box corresponds to which resolution bin and corresponding chi^2 value isn't apparent without looking at the log file. Besides using a script the easiest method IMO is graphically: hover your mo

Re: [ccp4bb] HKL2000 - Error model

What are we meant to make of that picture? Eleanor On Mon, 1 Jul 2019 at 18:39, De La Torre Marquez, Pedro L. < delatorremarque...@osu.edu> wrote: > Hi all, > > Highly recommended for people working with HKL2000. Please check the > attached picture. > > By: Jesse Sandhu from Sotomayor Laboratory,

Re: [ccp4bb] inter- and atomic interactions comparison

For dynamics, you have probably already found VMD which is fairly easy to get started with. Sent from Yahoo Mail on Android On Mon, 1 Jul 2019 at 16:17, Mirella Vivoli Vega wrote: Dear CCP Fo(r)lks, I wonder if someone could help me about prediction servers or programs or molecular dynam

[ccp4bb] inter- and atomic interactions comparison

Dear CCP Fo(r)lks, I wonder if someone could help me about prediction servers or programs or molecular dynamics I could use/run to compare the wild type protein structure and a mutant (I do not have the structure for the mutant), with/without substrate. The mutation (Asparagine to Aspartate) e

[ccp4bb] Mandatory PDBx/mmCIF format for crystallographic PDB depositions

>From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provi

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

But then you would loose the info on the solvent mask parameters. These are only implicitly stored in FC_ALL. These values too are things to get from data.json. Cheers, Robbie On 1 Jul 2019 15:31, Eleanor Dodson wrote: Old program RSTATS would give r factor.. But easist to run 0 cycles of REF

Re: [ccp4bb] post-doctoral position structural biology of ion channels

A post-doctoral position is available at the Laboratory of Structural Neurobiology, KU Leuven Belgium (http://www.xtal.be ). The research in our laboratory is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our method relies on X-ray crystallogra

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

Many thanks to all for the prompt and great inputs. Best regards, Andre. Em seg, 1 de jul de 2019 às 10:32, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> escreveu: > Old program RSTATS would give r factor.. > > But easist to run 0 cycles of REFMAC - at least then you know what t

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

Old program RSTATS would give r factor.. But easist to run 0 cycles of REFMAC - at least then you know what the scaling algorithm might be Eleanor On Mon, 1 Jul 2019 at 14:22, Robbie Joosten wrote: > If you are using SFTOOLS you might as well use the CORREL function to > calculate things. >

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

If you are using SFTOOLS you might as well use the CORREL function to calculate things. Datamining is easier though. Every PDB-REDO entry has a data.json file that has all the numbers you need. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.

Re: [ccp4bb] R values from an .mtz file containing Fobs and Fcalc

Dear Andre, easiest would be to select the FP and FC_ALL with sftools, write out the values to a text file and calculate the R-value with a scripting language like awk. Best, Tim Am 01.07.2019 15:02, schrieb Andre LB Ambrosio: Dear colleagues, Can a CCP4 program calculate r_work and r_free

[ccp4bb] Error information during opening ccp4 in mac

Dear all, I got such kind of error information during opening ccp4 in mac. Can anyone tell me how to fix it ? Thanks a lot! Application initialization failed: couldn't connect to display "/private/tmp/com.apple.launchd.hH7rs61iI7/org.macosforge.xquartz:0" Error in startup script: can't read "tk_

[ccp4bb] R values from an .mtz file containing Fobs and Fcalc

Dear colleagues, Can a CCP4 program calculate r_work and r_free directly from a .mtz file containing FP and FC_ALL (from PDB_REDO)? this without inputing the matching .pdb file and ideally using a commando line. Many thanks in advance, -- Andre LB Ambrosio #

[ccp4bb] PhD student position at Umeå University

Dear all, A PhD position in biochemistry/structural biology is available at Umeå University, Sweden. The overall aim of the project is to obtain structural and functional data of bacterial fimbrial proteins and associated proteins involved in maturation of fimbria. Please forward to any suitabl

[ccp4bb] Structural Biologist/biochemist position at Broad institute of MIT and Harvard

The Zhang Lab (zhanglab.bio) focuses on discovering and harnessing novel biological systems for development as molecular tools. In addition to our work with CRISPR-Cas systems, we have recently identified a number of additional exciting biological systems and we are working to understand their