Choose another graph from the loggraph - it also gives the main chain
alone and the side chains alone (not so useful!)
Eleanor
Salameh, Mohd A., Ph.D. wrote:
Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon and/or the backbone atoms and I wonder if
@jiscmail.ac.uk
Subject: Re: [ccp4bb] backbone b-factor
Choose another graph from the loggraph - it also gives the main chain
alone and the side chains alone (not so useful!)
Eleanor
Salameh, Mohd A., Ph.D. wrote:
Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon
Hi Mohd:
The script below should also be able to edit the PDB file according to
both of your needs. Think it is also easily modified to use for other
similar PDB file editing needs.
Best wishes,
Navdeep
#
#! /usr/bin/gawk -f
#
#
Dear All,
I would like to prepare a plot showing the b-factor of only the alpha
carbon and/or the backbone atoms and I wonder if somebody knows a module
or software that I can use, I tried the structure analysis/Temperature
factor analysis module in CCP4 but it plots the average b-factor of all
Dear Mohd,
to plot the B-factors, I would read the pdb file in Excel (or similar).
Take care that 5.45 is read as a number and not as a string, which
happens at least in German versions because of the . instead of the
German,.
Specify the decimal separator.
The sort by Atmon name to get all
Hi Mohd,
here is how using PHENIX tools:
Step 1:
phenix.pdbtools model.pdb keep=backbone
Step 2:
phenix.pdbtools model_backbone_only.pdb --show-adp-statistics
Please let me know if you have questions about the above tools.
Pavel.
On 9/15/09 9:37 AM, Salameh, Mohd A., Ph.D. wrote:
Dear
Hi Salameh,
Not sure if you mean a graph of B-factor vs sequence, or a 3D structure
plot.
Either way you can get such a plot using aline
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ which can
produce a sequence alignment (or single sequence) coloured by B-factor
(CA, Main, Side
