Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes

2013-05-21 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] mmCIF as working format?

2013-08-07 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?

2012-07-04 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Jeffrey, Philip D.
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,

Re: [ccp4bb] PDB deposition - sequence file

2014-12-30 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Jeffrey, Philip D.
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

Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Jeffrey, Philip D.
"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

Re: [ccp4bb] Quote source inquiry

2020-07-15 Thread Jeffrey, Philip D.
:: 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

Re: [ccp4bb] How many microfocus beamlines are in the world?

2020-06-24 Thread Jeffrey, Philip D.
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: