Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-09-02 Thread MARTYN SYMMONS
Hi Martyn     can you give me a reference where the rationale for this preference for mmcif is set out? I tried a pubmed search but cannot find anything.    thanks    regards    Martyn  From: Martyn Winn To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 2 September 2013

Re: [ccp4bb] Resolution, R factors and data quality

2013-09-02 Thread Robbie Joosten
Hi Frank and Ian, We struggled with the small changes in free R-factors when we implementing the paired refinement for resolution cut-offs in PDB_REDO. It's not just the lack of a proper test of significance for (weighted) R-factor changes, it's also a more philosophical problem. When should you r

Re: [ccp4bb] x-ray diffraction data analysis (XDS)

2013-09-02 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yu, I hope you have somebody in your lab to share their expertise with you, because you will benefit to a much greater extend in learning data integration from somebody sitting next to you than from the limited possibilities of online resources.

Re: [ccp4bb] Average B-factor

2013-09-02 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Dhana, if you used refmac5 or phenix.refine, these data ought to be in the header of the PDB-file you are submitting to the PDB. Best, Tim On 08/30/2013 11:45 PM, Dhanasekaran Varudharasu wrote: > Dear crystallographers, > > I need to complete

Re: [ccp4bb] Dependency of theta on n/d in Bragg's law

2013-09-02 Thread Peter Keller
On Sun, 2013-09-01 at 22:28 +0200, James Holton wrote: > ... but Bragg's genius was in simplifying all this to a little > rule which tells you how much to turn the crystal to see a given spot. > We sort of take this for granted now that we have automated > diffractometers that do all the math

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-09-02 Thread Martyn Winn
Hi, There have been many discussions along these lines over the years. The problem is understood well. The favoured solution is the use of mmCIF (as posted several times on the BB). But I would rather leave it to those officially involved to comment on the pros and cons. On the practical side,

Re: [ccp4bb] Resolution, R factors and data quality

2013-09-02 Thread Ian Tickle
On 1 September 2013 11:31, Frank von Delft wrote: > >> 2. >> I'm struck by how small the improvements in R/Rfree are in Diederichs & >> Karplus (ActaD 2013, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689524/); >> the authors don't discuss it, but what's current thinking on how to >> estimate the

Re: [ccp4bb] Fractional coordinate shift with two-character chain names?

2013-09-02 Thread Dirk Kostrewa
Dear Martyn, Pavel and other interested, I think, an official extension by the PDB to two characters for the chain names and 5 digits for residues would really help. I'm currently working on a structure with 6x15 chains (through NCS) - it is huge and only a few programs can handle this by exte

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2013-09-02 Thread Rob Van Montfort
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Re: [ccp4bb] x-ray diffraction data analysis (XDS)

2013-09-02 Thread Yu Longjiang
Dear all, thank you very much for your kind suggestions. my crystals are very anisotropic, and usually about 1A between the two different orientations. here, I post a brief statistic table treated by HKL2000. In fact, I am mainly working on the crystallization and characterization of proteins,