Re: [PyMOL] Polar interactions within selection
By the way how I have the slightly another task- I want to see all VDV
contacts surrounded selected residues. What should I make changes in the
Thomas's script for that ?
e.g firstly I've defined another residues in that case I have only one type
of residues- all hydrophobic residues. But what exaclty cutt-offs and
addition python modules should I use?
James
2012/4/17 James Starlight jmsstarli...@gmail.com
Thanks, Thomas!
Your script works fine. I've tested in one pdb structure and it finds all
polar and salt-bridges perfectly.
As I've understood this script also is usefull for examination of the
ensemble of pdb structures in NMR-like format ( each pdb structure as the
individual state in pymol) isn't it?
So now I must find a way to save my trajectories in this NMR-like pattern
by means of vmd software. I have found only possibility to save individual
snapshots as the individual pdb files or as the set pdb in one pdb in one
state ( i think this is not very usefull). Do you know how any python
modules for working with and extracting snapshots from big trr files from
gromacs runs ?
Thanks again
James
16 апреля 2012 г. 19:18 пользователь Thomas Holder
spel...@users.sourceforge.net написал:
Hi James,
maybe something like this could help. It finds contacts between charged
sidechains and prints the number of contacts in each state (requires
get_raw_distances from [1] or [2]).
--**--
# region of interest
select roi, chain A
# charged residues
select positive, resn ARG+LYS and not name N+O
select negative, resn GLU+ASP and not name N+O
# increase cutoff
set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge , 5.0
# find polar contacts
delete saltbridges
distance saltbridges, roi and negative, roi and positive, mode=2
hide label
# count contacts in each state
python
try:
get_raw_distances
except NameError:
from psico.querying import get_raw_distances
for state in range(1, cmd.count_states()+1):
sb = get_raw_distances('**saltbridges', state)
print ' %2d charged contacts in state %d' % (len(sb), state)
python end
--**
[1]
http://pymolwiki.org/index.**php/Get_raw_distanceshttp://pymolwiki.org/index.php/Get_raw_distances
[2]
http://pymolwiki.org/index.**php/Psicohttp://pymolwiki.org/index.php/Psico
Cheers,
Thomas
On 04/16/2012 03:22 PM, James Starlight wrote:
Hi Thomas!
Yes I'd like find possible way for quick examining of the polar
interactions ( nor only h-bonds but mainly salt-bridges) within
selection. As the consequence I'd like to examine the ensemble of the
pdb fies obtained as the different snapshots from MD trajectory for the
evolution of the new salt-bridges occuring during simulation.
James
16 апреля 2012 г. 15:58 пользователь Thomas Holder
spel...@users.sourceforge.net
mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net
написал:
Hi James,
I just noticed that this question is without any answer on the
mailing list. Do you still need help on this topic?
Cheers,
Thomas
On 04/04/2012 09:26 AM, James Starlight wrote:
Dear PyMol users!
I'm analysing polar interactions occured during MD simulation of
my
protein. In particular I have PDB file obtained from such
trajectory
where I'd like to check new polar contacts ( salt bridges first
of all)
within selection region. I've tried to select specified region
and use
Find polar contact- within selection as well as other options
from
this context meny but results was blank and I have not seen any
polar
contacts despite some charged residues were presented in the
adjacent
interface positions in the selected region.
IS there any else way to study dynamics of the salt-bridges
formation
based on the selected regions in the snapshots ?
Thanks for help,
James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Re: [PyMOL] Polar interactions within selection
Thanks, Thomas!
Your script works fine. I've tested in one pdb structure and it finds all
polar and salt-bridges perfectly.
As I've understood this script also is usefull for examination of the
ensemble of pdb structures in NMR-like format ( each pdb structure as the
individual state in pymol) isn't it?
So now I must find a way to save my trajectories in this NMR-like pattern
by means of vmd software. I have found only possibility to save individual
snapshots as the individual pdb files or as the set pdb in one pdb in one
state ( i think this is not very usefull). Do you know how any python
modules for working with and extracting snapshots from big trr files from
gromacs runs ?
Thanks again
James
16 апреля 2012 г. 19:18 пользователь Thomas Holder
spel...@users.sourceforge.net написал:
Hi James,
maybe something like this could help. It finds contacts between charged
sidechains and prints the number of contacts in each state (requires
get_raw_distances from [1] or [2]).
--**--
# region of interest
select roi, chain A
# charged residues
select positive, resn ARG+LYS and not name N+O
select negative, resn GLU+ASP and not name N+O
# increase cutoff
set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge , 5.0
# find polar contacts
delete saltbridges
distance saltbridges, roi and negative, roi and positive, mode=2
hide label
# count contacts in each state
python
try:
get_raw_distances
except NameError:
from psico.querying import get_raw_distances
for state in range(1, cmd.count_states()+1):
sb = get_raw_distances('**saltbridges', state)
print ' %2d charged contacts in state %d' % (len(sb), state)
python end
--**
[1]
http://pymolwiki.org/index.**php/Get_raw_distanceshttp://pymolwiki.org/index.php/Get_raw_distances
[2]
http://pymolwiki.org/index.**php/Psicohttp://pymolwiki.org/index.php/Psico
Cheers,
Thomas
On 04/16/2012 03:22 PM, James Starlight wrote:
Hi Thomas!
Yes I'd like find possible way for quick examining of the polar
interactions ( nor only h-bonds but mainly salt-bridges) within
selection. As the consequence I'd like to examine the ensemble of the
pdb fies obtained as the different snapshots from MD trajectory for the
evolution of the new salt-bridges occuring during simulation.
James
16 апреля 2012 г. 15:58 пользователь Thomas Holder
spel...@users.sourceforge.net
mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net
написал:
Hi James,
I just noticed that this question is without any answer on the
mailing list. Do you still need help on this topic?
Cheers,
Thomas
On 04/04/2012 09:26 AM, James Starlight wrote:
Dear PyMol users!
I'm analysing polar interactions occured during MD simulation of my
protein. In particular I have PDB file obtained from such
trajectory
where I'd like to check new polar contacts ( salt bridges first
of all)
within selection region. I've tried to select specified region
and use
Find polar contact- within selection as well as other options
from
this context meny but results was blank and I have not seen any
polar
contacts despite some charged residues were presented in the
adjacent
interface positions in the selected region.
IS there any else way to study dynamics of the salt-bridges
formation
based on the selected regions in the snapshots ?
Thanks for help,
James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second
resolution app monitoring today. Free.
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Re: [PyMOL] Polar interactions within selection
Hi James,
maybe something like this could help. It finds contacts between charged
sidechains and prints the number of contacts in each state (requires
get_raw_distances from [1] or [2]).
# region of interest
select roi, chain A
# charged residues
select positive, resn ARG+LYS and not name N+O
select negative, resn GLU+ASP and not name N+O
# increase cutoff
set h_bond_cutoff_center, 5.0
set h_bond_cutoff_edge , 5.0
# find polar contacts
delete saltbridges
distance saltbridges, roi and negative, roi and positive, mode=2
hide label
# count contacts in each state
python
try:
get_raw_distances
except NameError:
from psico.querying import get_raw_distances
for state in range(1, cmd.count_states()+1):
sb = get_raw_distances('saltbridges', state)
print ' %2d charged contacts in state %d' % (len(sb), state)
python end
--
[1] http://pymolwiki.org/index.php/Get_raw_distances
[2] http://pymolwiki.org/index.php/Psico
Cheers,
Thomas
On 04/16/2012 03:22 PM, James Starlight wrote:
Hi Thomas!
Yes I'd like find possible way for quick examining of the polar
interactions ( nor only h-bonds but mainly salt-bridges) within
selection. As the consequence I'd like to examine the ensemble of the
pdb fies obtained as the different snapshots from MD trajectory for the
evolution of the new salt-bridges occuring during simulation.
James
16 апреля 2012 г. 15:58 пользователь Thomas Holder
spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net
написал:
Hi James,
I just noticed that this question is without any answer on the
mailing list. Do you still need help on this topic?
Cheers,
Thomas
On 04/04/2012 09:26 AM, James Starlight wrote:
Dear PyMol users!
I'm analysing polar interactions occured during MD simulation of my
protein. In particular I have PDB file obtained from such trajectory
where I'd like to check new polar contacts ( salt bridges first
of all)
within selection region. I've tried to select specified region
and use
Find polar contact- within selection as well as other options from
this context meny but results was blank and I have not seen any
polar
contacts despite some charged residues were presented in the
adjacent
interface positions in the selected region.
IS there any else way to study dynamics of the salt-bridges
formation
based on the selected regions in the snapshots ?
Thanks for help,
James
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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[PyMOL] Polar interactions within selection
Dear PyMol users! I'm analysing polar interactions occured during MD simulation of my protein. In particular I have PDB file obtained from such trajectory where I'd like to check new polar contacts ( salt bridges first of all) within selection region. I've tried to select specified region and use Find polar contact- within selection as well as other options from this context meny but results was blank and I have not seen any polar contacts despite some charged residues were presented in the adjacent interface positions in the selected region. IS there any else way to study dynamics of the salt-bridges formation based on the selected regions in the snapshots ? Thanks for help, James -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
