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 the
file
https://www.ccp4.ac.uk/schools/DLS-2015/course_material/Datareduction2015.pdf
for an example.
So, if the space group is indeed the same make sure that you use a
dataset of one of the crystals of the native protein as a reference in
the indexing step. It is also possible to provide it as reference in
the scaling step with AIMLESS. POINTLESS is normally run before the
actual scaling process and it will compare your data with the
reference and will use the correct indexing scheme.
Cheers,
Renato
Zitat von "Mark J. van Raaij" <mjvanra...@cnb.csic.es>:
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 spacegroup is different, check cell parameters in the pdb
and/or run Contaminer to see if you’ve crystallised a contaminant
try MR with packing restraints relaxed or switched off, just in case
the mutant has loop in a new orientation that might clash with
crystal neighbours in the old orientation.
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
On 3 Mar 2022, at 05:43, Shubhashish Chakraborty
<0000750c9a1ca48b-dmarc-requ...@jiscmail.ac.uk> 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 molecular replacement using the wild-type protein at
different resolutions (I am working on a mutant).
Also, I have truncated the loops from the input structure. However,
none have worked.
So, what can be the possible way to solve this data set?
Thank you
Shubhashish Chakraborty
PhD JRF 2018
Structural and Molecular Biology Lab (Varma Lab)
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai
E-mail: schakrabo...@actrec.gov.in <mailto:schakrabo...@actrec.gov.in>
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--
Dr. Renato Weiße
Biotechnologisch-Biomedizinisches Zentrum
Institut für Bioanalytische Chemie
Strukturanalytik von Biopolymeren
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Mail renato.wei...@bbz.uni-leipzig.de
Tel. +49 341 97 31316
Fax +49 341 97 31131310
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