Re: [ccp4bb] DNA RNA annealing problem

Hi Weifei, We use SSC buffer for annealing oligos (we use DNA). That works pretty fine with us. Give a try. Composition is in below URL http://www.bioprotocols.info/reagent_and_buffer_recipes/20x-SSC.php Good Luck, Venkatareddy. On Fri, Jul 3, 2015 at 8:44 PM, ChenWeiFei wrote: > Dear all, >

Re: [ccp4bb] Cis-peptide bond checking

Hi all, Just revisiting this old thread, since it would seem I owe Paul Emsley something of an apology... after discussion with various people prior to submission of my manuscript, I concluded that overly-aggressive manual model building in Coot was probably the most common source of erroneous

Re: [ccp4bb] Optimal settings for finding NCS from density

Dear William, since it is a question to CCP4bb, I might suggest a CCP4-based solution ... On Fri, Jul 03, 2015 at 04:24:04PM +, William Chao wrote: > What would be the best settings to look for NCS using > phenix.find_ncs_from_density on an elongated (~150A) molecule? No > coordinate is avail

[ccp4bb] Optimal settings for finding NCS from density

Dear all, What would be the best settings to look for NCS using phenix.find_ncs_from_density on an elongated (~150A) molecule? No coordinate is available unfortunately and there should be 2 copies in a P21 space group. Many thanks in advance! William --- The Francis Crick Institute Limited is

Re: [ccp4bb] paired refinement

Dear Kay, You are right. I had forgotten the normalization part of the CC calculation. Dale On 7/3/2015 12:01 AM, Kay Diederichs wrote: > Hi Dale, > > On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud wrote: > >> While I was puzzling over an entry in the PDB some years ago (since >> obsol

[ccp4bb] DNA RNA annealing problem

Dear all, I want to get a complex of DNA-RNA-protein. But I have a big problem of annealing DNA-RNA. The length of DNA is 19nt and RNA is 17nt. Annealing protocol: 2uM DNA 2uM RNA 10mM Tris-Hcl 100mMNaCl 1mMEDTA Heated to 95 for 5min, cooling down slowly for nearly 2h to room temperature. I can

Re: [ccp4bb] CCP4 setup (LIBCHECK)

Thanks Lu, May be I should reinstall the software. It was the right one for Ubuntu 14.04. Pankaj On Friday, July 3, 2015, luzuok wrote: > > Dear Pankaj, > You haven't pointed out which version you use. > like: > coot-0.8.1-binary-Linux-x86_64-ubuntu-12.04.3-python-gtk2.tar.gz >

[ccp4bb] CCP4-6.5 Update 013

Dear CCP4 Users An update for the CCP4-6.5 series has just been released, consisting of the following changes programs: * seqwt - sequence length limit increase * zanuda - update * pointless - update to 1.9.33 * amiless - update to 0.5.12 libraries: * clipper - correction to setting of NaN

Re: [ccp4bb] paired refinement

Hi Dale, On Thu, 2 Jul 2015 10:45:45 -0700, Dale Tronrud wrote: > While I was puzzling over an entry in the PDB some years ago (since >obsoleted) I noticed that all the high resolution amplitudes were equal >to 11.0! This was before CC1/2 but for this structure it would have >been equal to on

Re: [ccp4bb] paired refinement

On Thu, 2 Jul 2015 13:25:07 -0400, Edward A. Berry wrote: >My take on this- >No one has been willing to specify a cutoff (and probably there is no rigorous >way to >mathematically define the cutoff) and say "If CC* (or CCfree or whatever) is >below X >then it will not improve your structure, if