If the correct atoms are in place, resetting the b factors of those atoms/residues to a constant e.g. 5.00 and refining in phenix with individual B-factors ON should take care of these.Best,RezaSent from my iPhoneOn Aug 2, 2023, at 7:42 AM, Thomas, Leonard M. wrote:
Hello All,
A general qu
1. Completeness is primarily an issue with using the right point group
and crystal system, not the actual space group (e.g. in primitive point
group mmm the space groups P222, P2221, P21212, P212121 should all have
essentially the same completeness).
2. If "refinalize" in CrysAlisPro doesn't l
Hello,
So I'm trying to get the data processed that I gathered from XRD for the
protein BsAlaDH. Unfortunately from the method that I know of on
CrysAlisPro I cannot select the recommended space group for the protein.
This results in the data not being complete. Still I can get good unit
cells and
Hi everyone,
Can the hive mind recommend particular video tutorials that introduce PyMol?
I’m looking for a beginner-level introduction, suitable for undergrads or
early-career grad students.
My hope is that some kind soul(s) can save me from slogging through hours on
YouTube in order to find
Postdoctoral position in drug discovery An opening is available in the drug
discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of
protein x-ray crystallography. Responsibilities will include protein
production, fragment screening by NMR, and all aspects of x-ray crystallograp
Hello, is it definitely due to the TLS refinement? I guess you have tried
without TLS and don't see the same effect i.e. the B-factors are more
consistent. It would be good to know.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
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Original Message
Although the effect should be quite small, is the wavelength in your reflection
file consistent with the actual wavelength?
Another option is that specific filters on atom types were used in the TLS
refinement. I would refine the models with another program
(REFMAC/Buster/PDB-REDO) to see if t
So the Phosphates are actually the end of the ADP which the Sulfer atoms are
Cystiene suffers. The Fo-Fc maps show large positive peaks for each position
also. The TLS groups is the whole protein chain, there are 4 in the asymmetric
unit as the biological unit I think is a dimer of 2 differen
On 02/08/2023 13:53, Andrea Smith wrote:
Dear all,
I used refmac in CCP4Cloud and then I opened the generated .pdb and
.mtz from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot
0.9.6. I can see different anomalous maps in Coot and Wincoot - see
attached printscreen where on the left t
One possible explanation for high B-factors, assuming the coordinates are
refined correctly, is partial occupancy and high mobility (dynamics) at
those heavy atom sites.
Also, one should check Fo-Fc maps of those positions. Are other atom types
substituting for some of those heavy atoms (such as
You need to tell us more details - is this a deposited structure?
Eleanor
On Wed, 2 Aug 2023 at 15:42, Thomas, Leonard M. wrote:
> Hello All,
>
> A general questions though phenix.refine is being used for refinement. A
> student I am working with has a structure that was solved and initially
>
Hello All,
A general questions though phenix.refine is being used for refinement. A
student I am working with has a structure that was solved and initially refined
using TLS and NCS parameters. They were given the structure to gain some
experience in refinement and they have been asking me so
I’ve just been playing with a difference map to check something. If you fail to
set the map as a difference map (either when opening the map initially, or
using Calculate->Map Tools->Set map is a difference map), there’s nothing in
the Display Manager->Properties window that tells you. I was won
It looks like it is not applying the 90 degree phase shift for anomalous data.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
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Original Message
On 2 Aug 2023, 14:32, Andrea Smith wrote:
> Dear Eleanor,
>
> yes, I made the printscreen with the
Hmmm -are the two ano maps contoured at the same level?
You can check this by setting the SCROLL option to the ano map.
The 2mFo-DFc maps look pretty identical..which suggests the two input mtz
files are similar.
You can get more information by viewing the inputs to make sure the values
are the sa
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