Dear Shubhashish,
in most cases the "just doing rigid body refinement" is working. But,
depending on the space group, there are multiple possibilities for
indexing the same set of reflections and then your simple refinement
strategy will fail. Check the section "Alternative indexing" in
if the spacegroup is the same as wt and the cell params are similar, just do
rigid body refinement and forget about MR (I’ll never understand people running
MR needlessly in these cases…apart from wasting computer time it risks placing
the new solution in a different place than the wt)
if the
Hello,
I have a maybe naive question, did you check the results for the Matthew
Probabilities calculation ?
Are you 100% certain that's your protein of interest in the crystal?
Sometimes we can have surprise.
Nicolas
On 03/03/2022 05:43, Shubhashish Chakraborty wrote:
Hello,
I am trying
bulletin board Im Auftrag von Shubhashish
Chakraborty
Gesendet: Donnerstag, 3. März 2022 05:44
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] MR solution not working
Hello,
I am trying to solve a dataset using molecular replacement. However, neither
Phaser MR nor Molrep can give any solution
collection)?
Ice rings or other problems leading to rejections in a systematic region?
Best,
Bruno
From: CCP4 bulletin board On Behalf Of Shubhashish
Chakraborty
Sent: 03 March 2022 05:44
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MR solution not working
Hello,
I am trying to solve a dataset using
Well - there are various traps towards a MR solution.
Maybe the data is not very good? What is the resolution and merging r
factor?
Assuming data is ok...
Most common is that the spacegroup is wrong. Have you tested all possible
spacegroups for the Laura group? Both phaser and molrep have options
ndt: 3. marts 2022 05:43:42
Til: CCP4BB@JISCMAIL.AC.UK
Emne: [ccp4bb] MR solution not working
Hello,
I am trying to solve a dataset using molecular replacement. However, neither
Phaser MR nor Molrep can give any solution.
In Phaser, I have received an advisory that Top FTF has not packed.
I have
On Wednesday, 2 March 2022 20:43:42 PST Shubhashish Chakraborty wrote:
> Hello,
> I am trying to solve a dataset using molecular replacement. However, neither
> Phaser MR nor Molrep can give any solution.
> In Phaser, I have received an advisory that Top FTF has not packed.
> I have tried
Hello,
I am trying to solve a dataset using molecular replacement. However, neither Phaser MR nor Molrep can give any solution.
In Phaser, I have received an advisory that Top FTF has not packed.
I have tried molecular replacement using the wild-type protein at different resolutions (I am
Hi,
In addition to all the great suggestions, you can also look into using
Rosetta_MR/Phenix and CNS DEN refinement. Can be useful if all fine with your
data and space group analysis and primary issue is remote model
homology/significant model dissimilarity.
Rosetta MR:
Dear Madhu,
At the resolution that you mention, which is at the edge of the resolution
limit for ARCIMBOLDO_LITE, and considering that you have already some
information about the possible fold, I would suggest you to use our tool
ARCIMBOLDO_SHREDDER, as it will derive fragments starting from your
Dear all,
We are trying to solve a protein structure of 37KDa using molecular
replacement method. Protein secondary structure indicates that it has
4-Heat repeat (α-helical hair pin) i.e. 16 α-helices. It has about 40%
sequence identity with templates in PDB, using which we tried MR, but we
Hi, Dear group,
I recently collected a dataset about 2.5 A and integrated with P4. When I
tried phaser I got a sol file looks like this, is this real solution? Is
LLG high enough?
SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265
Dear Rui,
If your search model is itself a homodimer, you expect to find 2
equivalent solution
And indeed in your case:
50.3 + 128.6 = 178.3 (= aboput 180)
0.2 + 179.8 = 180
219.8 - 38.7 = 181.1 (= about 180)
indicating that both solutions are crystallographically equivalent.
What does
Actually, the symmetry relating these solutions is a 2-fold around the y-axis,
which is not a crystallographic operator in P41. So either this is a twinned
crystal, and the two solutions relate to the two twin components, or the true
symmetry is higher.
What is special about the solutions
Hi all,
I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1
and c=93.5 however I do not get a right MR solution with this. So I went
back and scaled it in p222 space group and asked phaser to find the right
spacegroup solution for it, this time phaser gave me the right
Scaling should be the same in P222 vs. P212121. The only difference is
the exclusion of systematic absences. You may have run into some quirk
of Phaser in the way it handles multiple space groups vs. a single one.
On 07/09/12 14:06, Shya Biswas wrote:
Hi all,
I have a dataset that I scaled
If there is such a quirk then it's not one we know about. We would definitely
appreciate being sent whatever is needed to reproduce the behaviour.
Dimers in orthorhombic space groups can lead to translational NCS, which is
handled much better in the latest versions of Phaser. Is it possible
Phaser no longer fixes the space group after the first translation
function. Phaser carries the space group with each potential solution. If
the solution is clear at the end, so will the space group be clear.
In practice, we found that the space group was not correct after the first
19 matches
Mail list logo
