Great! I'm glad the CSA should be easy. However, I realized another problem with multiple nuclei. How do we choose different PDB nuclei to form the bond? Again, i was thinking something along the lines of:
Also, will this work in full analysis?
# Load the PDB file.
if not local_tm:
if
residue.name == 'G'
pdb(name, self.alex_pdb, heteronuc='N1', proton='H1')
if
residue.name == 'U'
pdb(name, self.alex_pdb, heteronuc='N3', proton='H3')
self.alex_pdb is my pdb which I decided to define where I define local_tm/sphere/etc.
Is this anywhere close to something that would work?
Alex H.
On 9/28/06, Edward d'Auvergne <
edward.dauvergne@xxxxxxxxx> wrote:
Unfortunately this approach won't work. You would need to create an
additional loop where you loop through the residues (in the future
maybe data sets) and set the value on a per residue basis. You would
need something like:
value.set(name, 1.01 * 1e-10, 'bond_length')
# Loop over the sequence.
for residue in self.relax.data.res:
# Guanium.
if
residue.name == 'G':
value.set(name,- 130 * 1e-6, 'csa',
res_num=residue.num, res_name=residue.name
)
# Uracil.
if
residue.name == 'U':
value.set(name, -100 * 1e-6, 'csa',
res_num=residue.num, res_name=
residue.name)
That should do the job. However a much more powerful approach would
be to take this out of the hands of the user. This could be done by
modifying the 'value.set()' user function to set values based on the
residue name. Actually, I just checked the code - I implemented this
feature years ago!!! That simplifies things, all you need to do is
supply the residue name to the 'value.set()' function and it will set
the values based on the name. The solution is therefore extremely
basic:
# Set the bond length.
value.set(name, 1.01 * 1e-10, 'bond_length')
# Set the NH CSA values of the four bases.
value.set(name, - 130 * 1e-6, 'csa', res_name='G')
value.set(name, - 100 * 1e-6, 'csa', res_name='U')
That's it!
Edward
On 9/29/06, Alexandar Hansen <
viochemist@xxxxxxxxx> wrote:
> As I was running the full_analysis.py for an RNA data set of U and G data, I
> realized that it's trying to use the same CSA for each residue. Looking
> into the script, it would seem to be relatively easy to code the "set the
> bond length and CSA values" section in such a way that it chooses a
> different CSA value for the given residue types. Currently it's simply:
>
> value.set(name, 1.02 * 1e-10, 'bond_length')
> value.set(name, -170 * 1e-6, 'csa')
>
> to modify this for RNA, could one edit it to say:
>
> value.set(name, 1.01 * 1e-10, 'bond_length')
> if residuename = G
> value.set(name, -130 * 1e-6, 'csa')
> else if residuename = U
> value.set(name, -100 * 1e-6, 'csa')
>
> Am I overtrivializing this, or should it be pretty straight forward?
>
>
> Alex Hansen
>
>
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Re: Accounting for N1 and N3 CSA differences in RNA