[ccp4bb] AW: [ccp4bb] Stop Refmac from refining B factors?

Dear Eva and Harry and others, I am not sure that an overall B-factor is the best solution for a 3.2 Å structure. In general, the true B-factors will vary a lot for different parts of the protein and poor diffracting proteins often have parts which are partially or completely disordered. An

Re: [ccp4bb] Stop Refmac from refining B factors?

On 18 Apr 2007, at 14:39, Eva Kirchner wrote: (But I'm still curious about the B-factor refinement when there is no REFI BREF ISOT in the com-file...) Eva, Refmac internal default is REFI BREF ISOT that's why even if you remove the above line from the com file (or deselect that

Re: [ccp4bb] Stop Refmac from refining B factors?

Harry M. Greenblatt wrote: You should be refining an overall temperature factor at that resolution. It's one of the choices in the list, instead of isotropic. I disagree with this. At that (3.2 Angstrom) resolution I've often found than a tightly restrained individual B-factor refinement

Re: [ccp4bb] Stop Refmac from refining B factors?

Thank you Roberto, I saw that line in the log file, too. So it is as I feared: Refmac cannot be stopped from refining B-factors ;-) Maybe I'll use CNS... Eva 2007/4/18, Roberto Steiner [EMAIL PROTECTED]: On 18 Apr 2007, at 14:39, Eva Kirchner wrote: (But I'm still curious about the

Re: [ccp4bb] Stop Refmac from refining B factors?

On Wednesday 18 April 2007 07:40, Phil Jeffrey wrote: Harry M. Greenblatt wrote: You should be refining an overall temperature factor at that resolution. It's one of the choices in the list, instead of isotropic. I disagree with this. At that (3.2 Angstrom) resolution I've often

Re: [ccp4bb] twin fraction varies between crystals?

Here's an interesting paper on The Genesis of Twinned Crystals (from 1945! - it's even printed on simulated aged paper and if you look closely the aging has an unrealistic plane-group pattern!): http://www.minsocam.org/msa/collectors_corner/arc/twinorig.htm It's by the eminent crystallographer

Re: [ccp4bb] disorder, solvent content, and diffraction limit

Mike, This is a complicated question :) The floppy bits can contribute to packing in several non-obvious ways. I may be able to help you get a better crystal form, if you're willing to share the specifics of the protein (which will be kept confidential of course). I've developed new procedures

[ccp4bb] tcltkblt and python distributions

Hello, I have been running into issues with the tcl/tk and python bundles currently distributed with ccp4-6.0.2 (x86 system running Centos5). 1. The tcl/tk/blt package for Linux now extracts into a ./tcltkblt subdirectory. Apart from making upgrades slightly easier, this does not seem to make

Re: [ccp4bb] tcltkblt and python distributions

You would probably be better off using the CentOS5-supplied python, tck, tk, blt, and so forth (and if they aren't supplied, then consider a linux distro that provides these things). Also, if you compile your own ccp4, you can include the latest patches and direct it to use whatever versions of

[ccp4bb] How to run SIGMAA twice in a row?

My previous posting did not get answer, it might be a bit confusing. My questions is if I want to conbine phases from three different sources, 2 MAD data sets and a partial model, can I run SIGMAA twice? Combining MAD phases first, and then add in the model phases to the pre-combined MAD

[ccp4bb] protein or salt?

Hi, i collected a diffraction pattern today of a protein crystal, hoping to answer the question, is it a protein or salt? The crystals appear as typical proteins crystals (from my experience), forming both plates and rods, easily crushed into millions of tiny crystals, and are bouyant.

Re: [ccp4bb] protein or salt?

Hi, In my opinion this is clearly a twinned crystal of some sort of a small molecule. If you have a small ice crystal on top of a completely non-diffractive protein crystal, sometimes the pattern may also look like this - but I would bet this is just 'salt'. Artem _ From: CCP4