[ccp4bb] how to calculate error for DNA parameters

Dear all, I have a protein-DNA complex structure at 2 A resolution and I used 3DNA to calculate the step and base-pair parameters. I am wondering how to estimate the error for e.g. buckle angle, slide, etc. given the estimated coordinate error for this data set? Thank you very much! Best, Melody

[ccp4bb] problem restraining angles formed between cysteine and a ligand

Dear all, I am refining a structure that has a ligand which contains a thiol group and forms a disulfide with the cysteine. I created the cif file with the Dundee server for the ligand and modified the BME-cysteine link cif file to fit my ligand. I combined these two cif files and feed it to Refmac

[ccp4bb] refining nucleic acid structures: Refmac or CNS?

Dear all, I was refining complex structures with a DNA oligo that have some noncanonical bent regions in the middle, the resolutions are fairly good, around 1.8-2.2A. I used both CNS and Refmac. I found (not surprisingly) that with Refmac, I got a lot of unusual sugar puckers like C1'-exo that is

[ccp4bb] refining nucleic acids structure with Refmac

Dear all, I was refining complex structures with a DNA oligo that have some noncanonical bent regions in the middle, the resolutions are fairly good, around 1.8-2.2A. I used both CNS and Refmac. I found (not surprisingly) that with Refmac, I got a lot of unusual sugar puckers like C1'-exo that is

[ccp4bb] How to restrain angles in cif

Dear all, I was refining a structure with a modified DNA base, and I generated a cif file for that base using Dundee server with previously solved coordinates of this base. However, when I refine with Refmac, the base has distorted angles and bonds. I wonder how I can edit the cif file and restrai

[ccp4bb] a question about CNS composite omit map

Dear all, Sorry this might be another naive, non-ccp4 question~ I was trying to make a composite omit map with CNS, but during torsion angle dynamics, it always reports an "argument out of range" error like the following: -- step= 5 at 0.02000 ps

Re: [ccp4bb] question about processing data

Dear all, Thank you very much for the useful suggestions! I definitely learned a lot from these discussions. Now looking back at my datasets, I think the incompleteness likely results from high mosaicity (1.009) and anisotropy of the crystal. Detector is square, but the distance is short enough fo

Re: [ccp4bb] question about processing data

l, judge it from: > > 1. Completeness > 2. Redundancy > 3. I / Sigma > 4. R merge statistics > > Not just one of them. If you are pushing it too far, you will see the > effect in later refinement step.. > With 74% completeness, how does the other parameters look like? &g

[ccp4bb] question about processing data

Hi all, I have always been wondering... for a data set diffracting to say 2.15Angstrom but in the highest resolution shell ( 2.25-2.15) the completeness is 74%, should I use merge all the data and call it a 2.15 A dataset or I should cut the data set to say 2.25 A where the highest resolution shel

[ccp4bb] normal protein in detergent?

Dear all, sorry for the off-topic and possibly very naive question- but does anyone know what happens if normal protein is put in detergent-containing aqueous solution? how much detergent can a regular protein tolerate? I was trying to search literature but couldn't find any... Thank you greatly

[ccp4bb] problem loading coot 0.4.1

Dear all, I just installed coot 0.4.1 by fink on my Mac OS X tiger ppc, and strangely when I am loading it, I receive a series of warning "Error loading pixmap file:/sw/share/coot/pixmaps/*.svg" (which also come up when I click on calculate->model/fit/refine, and the loading pauses at that ponit

[ccp4bb] elusive DNA density

ycles of coordinate/B factor refinement enough to get rid of model bias? (3) Does weak DNA density have to do with data processing? Thanks very much for any suggestion, Melody Lin