Hi,
I need to calculate the RMSD for the same residue, e.g. 131Thr, from 2 pdb
files for the same target. As I need a local alignment, I use a sliding window
of 5 residues (the residue of interest is in the middle.)
I have adapted the script from https://pymolwiki.org/index.php/RmsdByResidue
(also see below my code below) by adding a sliding window, but I need advice on
the following:
- I would need to check whether I am actually comparing the intended residues,
e.g. 131Thr, 131Thr, or whether the same residues (e.g. His, Asp, His), with
specific residue names and numbers are in the selection I have chosen from
both pdb files for my sliding window.
The reason:
I have coded up the script below, but often it skips and doesn't compare two
residues, because the atom count is different between the residue from protein
A and protein B.
(It is exactly double the number, I have already checked and excluded problems
like occupancy and different conformations as potential causes.)
- I constructed a sliding window by selecting two residues before the residue
of interest and two residues which follow said residue. (I know that residues
can be missing, I am working on this.)
Is there a better way for constructing a sliding window? I have not found such
a method in pymol.
For anyone interested, I have attached a code snipplet below.
I am sorry, if these seem like obvious questions, but I tried various
approaches and I feel that I need a push in the right direction. I have the
feeling that I am missing something fundamental.
Many thanks for any suggestion!
Anne (Newbie in Pymol)
######################################
Code snipplet (Python/Pymol interface):
referenceProteinChain = cmd.fetch(pbdstructure1)
targetProteinChain = cmd.fetch(pdbstructure2)
sel = referenceProteinChain
list_atoms = [[133, 133]] # example list, I want to calculate the rmsd
between residue 133 and residue 133 of two pdb structures
for j in list_atoms:
# I formulate my sliding window of 5 residues, my residue of interest is in
the middle
ref_begin = int(j[0])-2
ref_end = int(j[0])+2
target_begin = int(j[1])-2
target_end = int(j[1])+2
# I create a selection for the reference protein and the target protein
cmd.create("ref_gzt", referenceProteinChain+" and polymer and not alt B and
not Alt C and not alt D and resi %s-%s"
cmd.alter("ref_gzt", "chain='A'")
cmd.alter("ref_gzt", "segi=''")
cmd.create("target_gzt", targetProteinChain+" and polymer and not alt B
and not Alt C and not alt D and resi %s-%s" %(target_begin,target_end) )
cmd.alter("target_gzt", "chain='A'")
cmd.alter("target_gzt", "segi=''")
# I align my selected 5 residues for a local alignment window
cmd.align("target_gzt","ref_gzt",object="align", cycles =5)
# select alpha carbon of in reference structure to loop over
calpha=cmd.get_model(sel+" and name CA and not alt B and not Alt C and not
alt D and resi %s-%s" %(ref_begin,ref_end) )
## here I loop over all residues in the sliding window and calculte the rmsd
for my residues of interest.
for g in calpha.atom : I loop over the slinding window
if g.resi == str(j[0]): ## we select only our residue of interest
within the sliding window
if cmd.count_atoms("ref_gzt and polymer and resi
"+g.resi)==cmd.count_atoms("target_gzt and polymer and resi "+g.resi):
## calculte the pairwise RMSD between the residues I specified
in list_atoms
rmsdRes=cmd.rms_cur("ref_gzt and polymer and resi
"+g.resi,"target_gzt and polymer and resi "+g.resi)
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