[ccp4bb] twin refinement

Hi i am refining a protein strucutre with space group P61. Intesity statistics doesnot suggest any twining but refmac and phenix xtriage suggest a twin operator with fraction 0.48. when refined with this twin operator R factors come dowm by 3-5% and also map looks much better. but upon closer ins

Re: [ccp4bb] reforigin on 2FKA

James, it's just the C centring: (1/2,y,1/2) + (1/2,1/2,0) = (0,1/2+y,1/2) which is the alternate origin so you will indeed get the same F's and different phases (don't forget that shifts along y are arbitrary!). Cheers -- Ian On Tue, Mar 2, 2010 at 11:13 PM, James Holton wrote: > Apologies for

Re: [ccp4bb] reforigin on 2FKA

Apologies for bringing back an old thread, but I recently returned home to my dear copy of the ITC vol. B, and decided to double-check that my "personal" list of origin shifts matches the one found in there. To my surprise, there seems to be at least one real difference: C2 The "allowed orig

Re: [ccp4bb] increse atom radius in chimera

Command: vdwdefine 2.0 #...@c -> changes radius of all atoms of model #19 beginning with C to 2.0 Angstroem. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html Oliv On Tue, Mar 2, 2010 at 10:53 AM, james09 pr

[ccp4bb] increse atom radius in chimera

Dear All, Sorry for the non-ccp4 query. I am looking for an option to increase the atom radius in chimera. Can anyone help me out? Thanking you. James

Re: [ccp4bb] Deposition of a BUSTER refined structure

On Tuesday 02 March 2010 07:09:47 Melanie Vollmar wrote: > Hi all > > I did my first deposition of a BUSTER refined structure and I was very > surprised when I was asked for an "estimated error of free R value" and > "estimated error of bin free R value" as well an "ESD based on Luzzati Plot"

Re: [ccp4bb] Deposition of a BUSTER refined structure

Dear Melanie On 2 Mar 2010, at 15:09, Melanie Vollmar wrote: Hi all I did my first deposition of a BUSTER refined structure and I was very surprised when I was asked for an "estimated error of free R value" and "estimated error of bin free R value" as well an "ESD based on Luzzati Plot"

Re: [ccp4bb] cryoprotection for fragile crystals

I believe this is the article that you are looking for: http://www.xtals.org/crystal_cryo.pdf Cheers, Sean

Re: [ccp4bb] Deposition of a BUSTER refined structure

Dear Melanie, Thank you for your message. You can find the number for the ESD based on the Luzzati Plot in the REMARK3 section of the header. Several other coordinate ESD values are listed as well, based on the DPI definitions of Cruickshank and of Blow. There is a line for the Estimated erro

[ccp4bb] cryoprotection for fragile crystals

I found within the last few years a nice flowchart that someone (I think it was Artem Evdokimov) had posted somewhere for a protocol for dealing with crystals that you couldn't just quick dip, and now I can't find it - maybe he can send it to me offbb??? Thanks Laurie Betts UNC CHapel Hill

[ccp4bb] Deposition of a BUSTER refined structure

Hi all I did my first deposition of a BUSTER refined structure and I was very surprised when I was asked for an "estimated error of free R value" and "estimated error of bin free R value" as well an "ESD based on Luzzati Plot" during the deposition process. I had a detailed look into the refi

Re: [ccp4bb] low resolution phasing protocols

This was done in total despair: http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ActaCrystD.pdf Francis E Reyes wrote: > Hi all > > I'm in search of literature *detailing* low resolution [4-5A] phasing > protocols. Heck I'll take detailed thesis chapters (since they tend to be > more detailed

Re: [ccp4bb] low resolution phasing protocols

The heavy hammer - metal clusters eg Ta6Br12(2-). You need all the phasing you can get! Phil On 2 Mar 2010, at 14:11, Francis E Reyes wrote: > Hi all > > I'm in search of literature *detailing* low resolution [4-5A] phasing > protocols. Heck I'll take detailed thesis chapters (since they te

[ccp4bb] low resolution phasing protocols

Hi all I'm in search of literature *detailing* low resolution [4-5A] phasing protocols. Heck I'll take detailed thesis chapters (since they tend to be more detailed than pubs anyway). If you ribosome people are on this board I'd love to hear from you. [sarcasm]Searching for 'grasping at stra

[ccp4bb] EMBO Conference Series: "Catalytic mechanisms by biological systems: at the interface between chemistry and biology"

Please observe the upcoming registration deadline for: EMBO Conference Series "Catalytic mechanisms by biological systems: at the interface between chemistry and biology" EMBL Hamburg, Germany Wednesday 5 May - Friday 7 May 2010 Application deadline is 8th March 2010. For more information and to

Re: [ccp4bb] coot.App from ccp4-6.1.3 release suddenly started segmentation-faulting and dumping core on OSX- how to troubleshoot

Thanks a tonne Paul . Once I deleted the ~/.fontconfig directory the ccp4-6.1.3 provided coot.App [0.6 (revision 2540) [with guile 1.8.3 embedded]] launched right up. So I guess this is a gtk2 or Xquartz peculiarity because the fink compiled coot (0.6.1 (revision 2740) , guile 1.8.2) launched

Re: [ccp4bb] coot.App from ccp4-6.1.3 release suddenly started segmentation-faulting and dumping core on OSX- how to troubleshoot

hari jayaram wrote: Hi I just started having segmentation faults with the coot downloaded from the ccp4 releases page for ccp4-6.1.3. This release was working quite well, and I even convinced a few people to stop "fink-ing" and just download the coot dmg from ccp4. The problem started after