Being of an untrusting disposition, I would ask your collaborator for
the reflection data as well as the PDBs - it is always a good idea to
look at the maps when there is some unexpected structural feature! -
The DB provides an electron density server, if the structures have
been deposited, otherwi
Dear Mahesh,
Are all the structures at similar resolution? Definition of secondary
structure is, and can be, affected by the level of geometric
restraints/constraints used in the refinement process.
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Dama
Hello experts
Thanks for your insights.
For one of the structures, it turned out to be a rendering issue by pymol
like matt pointed out. For the other, the residues are clearly in a less
than ideal position. Even if I see deviation from the RMSD plots, i cannot
be sure that the structure were refi
o:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Swastik
Phulera
Sent: 21 October 2013 07:52
To: ccp4bb
Subject: Re: [ccp4bb] changes in small sections of secondary structure
Dear Mahesh,
Instead of bothering with the secondary structure assignments why may try to
superpose your structures and then view y
Dear Mahesh,
In addition to RMSD plots, you could try to quantitatively analyse the
protein residue flexibility in order to detect backbone conformational
transitions by means of the method proposed in:
Local Fluctuations and Conformational Transitions in Proteins
Rocco Caliandro, Giulia Ross
Dear Mahesh,
Instead of bothering with the secondary structure assignments why may
try to superpose your structures and then view your RMSD
plots(Superpose program in CCP4 can do the trick). You might then be
better off focusing on the regions with high RMSD.
Regards
On Sat, Oct 19, 2013 at 3:20
Hi Mahesh,
If you have made these screen shots using pymol, then you really need to be
careful before you jump to conclude anything from these secondary
structural changes (Matt already mentioned it). Assign secondary structures
using DSSP or see the secondary structure restraints in the structure
Dear Mahesh -
I can't comment on the energy changes for the protein, but I can say
that the changes you've highlighted are not really due to alterations of
the protein, but rather inconsistency in assignment of secondary
structure. If you look closely at the areas you've highlighted, you
wil
