:: took a working dataset and increased (only) the error on unit cell
dimensions in the instruction file for the final round of full matrix :: least
squares refinement in shelxl. Sure enough, the errors on the bonds and angles
shot up. I was more careful
Question: did you change the unit cell
I'm fairly sure that the 300-ish micron focus on my old (and retired) Rigaku
RuH3R home system - a perfectly good workhorse - was consider micro-focus by
precisely nobody.
Phil Jeffrey
Princeton
From: CCP4 bulletin board on behalf of Gianluca Santoni
Sent:
"Very decent" means different things to different people. Is your Rmerge < 20%
in the 0.84 Å shell ? If so that's a small molecule quality data set and
something like that should solve relatively straightforwardly with e.g. SHELXT.
However the classical program would be SHELXD and perhaps a
Jacob,
If you fine slice and everything is then a partial, isn't that *more* sensitive
to lack of synchronization between the shutter and rotation axis than the
wide-frame method where there's a larger proportion of fulls that don't
approach the frame edges (in rotation space) ? Especially if
Mohamed,
You always list the sequence of what's actually in the crystal, e.g. 1-105.
(Not: what's in the model or what the sequence of the full length protein is).
Make sure that if there's any lingering residues from any affinity/purification
tags they get included in the sequence too.
Phil
Hello Yafang,
The answer lies in the fact that you used HKL2000. Scalepack has a long
standing feature where it reports Rmerge 100% as zero. Quite why they do
that is a mystery, but your Rmerge in the outermost shell is NOT zero - the
Rmerge for the lower resolution shells will show up as
Are all the APIs open source ? I was under the impression that CCP4 had moved
away from that, which might justifiably reduce interest in any
limited-availability API.
Phil Jeffrey
Princeton
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
I.e. programs would look like this
---
GRAB protein FROM FILE best_model_ever.cif;
SELECT CHAIN A FROM protein AS chA;
SET chA BFACTORS TO 30.0;
GRAB data FROM FILE best_data_ever.cif;
BIND protein TO data;
REFINE protein USING BUSTER WITH TLS+ANISO;
DROP protein INTO FILE
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset or many
other tools. Writing code for
this should only be necessary if you're processing large numbers of models,
or have a spectacularly
misformatted PDB file.
Problem. Coot is bad at the chain label
Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5 Angstrom
resolution (arbitrary cut):
Number of entries in histogram: 14864
Total number of instances : 195481
0 14502 0.0742 GOL(glycerol)
1 10952 0.0560 SO4
2 8064 0.0413 ZN
3 7628 0.0390 MG
4 6930
That sounds like the bug in Phenix.refine v1.8 that a few of us encountered -
updating to the latest release will help.
Actually wasn't so much a bug but a feature, albeit not the best one
imaginable. Anyone using older v1.8 versions should update.
---
Phil Jeffrey
Princeton
On Nov 2, 2012,
Hi Tim,
While I use Scalepack2mtz (not from the gui) all the time, Scalepack has the
unfortunate feature that once Rsym 1.0 it gets reported as 0.0. Now that I'm
exploring higher resolution limits along the lines of the recent Karplus and
Diederichs paper (Science Vol. 336, pp. 1030-33
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