eement with the target.
Best regards,
Tristan
--------
*From:* Leonid Sazanov
*Sent:* 11 December 2020 12:32
*To:* Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more
thinking and
ign 109 of 134 CAs with an RMSD of
0.46 A.
*From:* CCP4 bulletin board on behalf of
Leonid Sazanov
*Sent:* 11 December 2020 10:36
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: m
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS > 90
(supposedly as good as experimental model) the RMS_CA (backbone) is > 3.0
Angstrom? Such a deviation can hardly be described as good as experimental.
Could it be that GDT_TS is kind of designed to evaluate how
Hi, after updating to ccp4/7.0, I get this error when trying to run Refmac:
Dictionary path has not been defined
Check the environment variable CLIBD_MON
Current value of CLIBD_MON is
/mnt/nfs/clustersw/shared/ccp4/7.0/ccp4-7.0/lib/data/monomers
It should be set to wherever_dict/dic/
===> Error:
-school/phd-program/. The
deadline for applications is 15th of January 2015. Informal queries should be
forwarded to Dr. Leonid Sazanov (saza...@mrc-mbu.cam.ac.uk).
. Leonid Sazanov (saza...@mrc-mbu.cam.ac.uk).
Hi, you could try dehydration in microdialysis buttons - this allows for slow
gradual increase in PEG over few days and full control of other parameters,
including lowering salt concentration.
It was the only dehydration method that worked well for our large membrane
protein:
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
ccp4/refmac - as 0.
That would explain your Rfree going down - because your Rfree reflections were
refined by refmac.
It would be nice if default setting was the same in different suites.
Best wishes.
In case if dehydration needs to be done slowly and under tight control of all
parameters, one possibility is to use micro-dialysis buttons.
We used it for a large membrane protein complex and diffraction improved from
~7 to 2.7 A. The crystal is fished out and put into mother liquor solution
Hi, as we reported in our paper in Table 1 (actually Supplementary Table 1), at
the end of Scaling 2, completeness in the outer shell after aniso truncation
was 54%. Whilst 96% completeness and I/sigma 0.8 is of course before aniso
truncation. I/sigma after truncation would be higher, but it is
Hi, we had the same case in apparent C2221, with many similarly shifted Phaser
solutions with high scores. The reason was that crystals were actually nearly
perfectly twinned in P21, so indexing and processing indicated C2221. Once data
was re-processed in P21, Phaser could easily find two
Hi,
If I have two somewhat different overlayed models, is it possible in
COOT to replace part of one model by another?
Similarly to O command: merge_atoms from_molecule residue_start
residue_end to_molecule residue_start ?
That's a useful feature in O, but could not find it so far in COOT.
the
desired job.
Thanks!
Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge
On 19/10/2011 14:41, Ed Pozharski wrote:
On Wed, 2011-10-19 at 12:20 +0100, Leonid Sazanov wrote:
Hi,
If I have two
Is there information somewhere on what is new or modified in Buccaneer 1.4 (any
new keywords?) - could not find it?
Thanks!
Dear all, I will highly appreciate if the ad below is brought to the attention
of
students who may be interested. Thanks!
Applications are invited from recent graduates or final year undergraduates for
the following PhD project in the MRC Mitochondrial Biology Unit, Cambridge, UK:
Structure
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