Re: [PyMOL] Write in a file the number of water at a distance from a protein surface
Hi Stephane,
you can select those waters using the within or gap selection
operators. within measures from the atom centre, whereas gap takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell, solvent within 3.5 of polymer
# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)
# shows the selected water molecules as a sphere
show spheres, firstshell and elem O
# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print stored.out, '## At 0.5 Ang of the protein surface there are',
print stored.out, cmd.count_atoms('firstshell and elem O'),
print stored.out, 'water molecules'
print stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print stored.out, ID, resi')
stored.out.close()
python end
http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate
Hope that helps,
Cheers,
Thomas
On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
Hi All,
I have simulated a protein in water cubic box and I would like to
know how to show and obtain the number of water in the first shell of
the protein (or at x Ang of the protein surface) using a pymol
script. I can to do this using the pymol GUI but I would prefer that
the script :
- shows the selected water molecules as a sphere
- and writes the results in a file with the water ID (i.e. residue
number), for example like this:
## At x Ang of the protein surface there are XX water molecules
## Water ID are
Thanks in advance for your help.
Stephane
--
Thomas Holder
MPI for Developmental Biology
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[PyMOL] Write in a file the number of water at a distance from a
Hi All,
With the help of Thomas Holder (thanks to him), now I can show and obtain
the number of water in the first shell of my six peptides (an amyloid
fibrils). However, I have a little problem with the command count_atoms in
my script
Below my script (*.pml) for Pymol 1.3 :
mstop
dss
hide all
select CL, resn CL
delete CL
## Select WATER with residue ID SOL
select WATER, resn SOL
## Select Amyloid, resi 1-54
select Amyloid, resi 1-54 and not WATER
## Show in cartoon Amyloid
show cartoon, Amyloid
## Show in different colors peptides because it is nice.
set cartoon_color, black, resi 2-8
set cartoon_color, red, resi 11-17
set cartoon_color, green, resi 20-26
set cartoon_color, blue, resi 29-35
set cartoon_color, yellow, resi 38-44
set cartoon_color, chocolate, resi 47-53
## Not use for the moment
##set cartoon_color, gray50, resi 56-62
##set cartoon_color, wheat, resi 65-71
##set cartoon_color, aquamarine, resi 74-80
##set cartoon_color, pink, resi 83-89
##set cartoon_color, orange, resi 92-98
##et cartoon_color, forest, resi 101-107
## Select water in the first shell (e.g. within 3.5 A of the Amyloid atoms)
select WATER_firstshell, WATER within 3.5 A of Amyloid
## Give the number of water in the first shell of the fibrils
## Works --- Give number of water atoms (including oxygen and Hs)
print cmd.count_atoms(WATER_firstshell)
## Print the residu ID of each water in the first shell
iterate (WATER_firstshell), print resi
set cartoon_fancy_helices=1
set cartoon_discrete_colors, on
set antialias = 1
ray
---
As you can imagine the firstshell_WATER variable contains the water O and
H atoms. It is not what I want! Indeed I want that count_atoms command
counts only the number of Water oxygen. So I use
count_atoms(firstshell_WATER and elem O)
This command works if I use the pymol GUI but If I use the command in my
script. Indeed
print cmd.count_atoms(firstshell_WATER and elem O) show a syntax error
Thanks in advance for your help.
Stephane
--
Message: 7
Date: Thu, 22 Sep 2011 11:14:36 +0200
From: Thomas Holder spel...@users.sourceforge.net
Subject: Re: [PyMOL] Write in a file the number of water at a distance
from a protein surface
To: ABEL Stephane 175950 stephane.a...@cea.fr
Cc: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID: 4e7afc7c.4060...@users.sourceforge.net
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Stephane,
you can select those waters using the within or gap selection
operators. within measures from the atom centre, whereas gap takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell, solvent within 3.5 of polymer
# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)
# shows the selected water molecules as a sphere
show spheres, firstshell and elem O
# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print stored.out, '## At 0.5 Ang of the protein surface there are',
print stored.out, cmd.count_atoms('firstshell and elem O'),
print stored.out, 'water molecules'
print stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print stored.out, ID, resi')
stored.out.close()
python end
http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate
Hope that helps,
Cheers,
Thomas
On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
Hi All,
I have simulated a protein in water cubic box and I would like to
know how to show and obtain the number of water in the first shell of
the protein (or at x Ang of the protein surface) using a pymol
script. I can to do this using the pymol GUI but I would prefer that
the script :
- shows the selected water molecules as a sphere
- and writes the results in a file with the water ID (i.e. residue
number), for example like this:
## At x Ang of the protein surface there are XX water molecules
## Water ID are
Thanks in advance for your help.
Stephane
--
Thomas Holder
MPI for Developmental Biology
--
Message: 8
Date: Thu, 22 Sep 2011 10:05:46 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [PyMOL] RE : Write in a file the number of water at a
distance from a protein surface
To: Thomas Holder spel...@users.sourceforge.net
Cc: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID:
3e39b768bb199548ab18f7289e7534af0ad...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=iso-8859-1
Thank you for your response, i will try your suggestion
A bientot
Stephane
De : Thomas Holder [ad...@thomas-holder.de] de la part de Thomas Holder
[spel...@users.sourceforge.net]
Date d'envoi : jeudi 22 septembre 2011 11:14
? : ABEL Stephane 175950
Cc :
Re: [PyMOL] Write in a file the number of water at a distance from a
Thanks Marius
With the second it works
A bientot
Stephane
-Message d'origine-
De : Marius Retegan [mailto:marius.s.rete...@gmail.com]
Envoyé : jeudi 22 septembre 2011 18:02
À : intra\sa175950
Objet : Re: [PyMOL] Write in a file the number of water at a distance from a
Hello Stephane,
Water molecules are composed of 3 atoms, so this
print cmd.count_atoms(WATER_firstshell)/3
should give you the right answer.
If you really want it your way:
print cmd.count_atoms(firstshell_WATER and elem O)
P.S. I haven't tried any of these commands. I hope they work.
Best regards,
Marius
--
Dr. Marius Retegan
Postdoctoral Fellow
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7Hd0Y
On Thu, Sep 22, 2011 at 5:38 PM, intra\sa175950 stephane.a...@cea.fr
wrote:
Hi All,
With the help of Thomas Holder (thanks to him), now I can show and obtain
the number of water in the first shell of my six peptides (an amyloid
fibrils). However, I have a little problem with the command count_atoms in
my script
Below my script (*.pml) for Pymol 1.3 :
mstop
dss
hide all
select CL, resn CL
delete CL
## Select WATER with residue ID SOL
select WATER, resn SOL
## Select Amyloid, resi 1-54
select Amyloid, resi 1-54 and not WATER
## Show in cartoon Amyloid
show cartoon, Amyloid
## Show in different colors peptides because it is nice.
set cartoon_color, black, resi 2-8
set cartoon_color, red, resi 11-17
set cartoon_color, green, resi 20-26
set cartoon_color, blue, resi 29-35
set cartoon_color, yellow, resi 38-44
set cartoon_color, chocolate, resi 47-53
## Not use for the moment
##set cartoon_color, gray50, resi 56-62
##set cartoon_color, wheat, resi 65-71
##set cartoon_color, aquamarine, resi 74-80
##set cartoon_color, pink, resi 83-89
##set cartoon_color, orange, resi 92-98
##et cartoon_color, forest, resi 101-107
## Select water in the first shell (e.g. within 3.5 A of the Amyloid
atoms)
select WATER_firstshell, WATER within 3.5 A of Amyloid
## Give the number of water in the first shell of the fibrils
## Works --- Give number of water atoms (including oxygen and Hs)
print cmd.count_atoms(WATER_firstshell)
## Print the residu ID of each water in the first shell
iterate (WATER_firstshell), print resi
set cartoon_fancy_helices=1
set cartoon_discrete_colors, on
set antialias = 1
ray
---
As you can imagine the firstshell_WATER variable contains the water O
and
H atoms. It is not what I want! Indeed I want that count_atoms command
counts only the number of Water oxygen. So I use
count_atoms(firstshell_WATER and elem O)
This command works if I use the pymol GUI but If I use the command in my
script. Indeed
print cmd.count_atoms(firstshell_WATER and elem O) show a syntax error
Thanks in advance for your help.
Stephane
--
Message: 7
Date: Thu, 22 Sep 2011 11:14:36 +0200
From: Thomas Holder spel...@users.sourceforge.net
Subject: Re: [PyMOL] Write in a file the number of water at a distance
from a protein surface
To: ABEL Stephane 175950 stephane.a...@cea.fr
Cc: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID: 4e7afc7c.4060...@users.sourceforge.net
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Stephane,
you can select those waters using the within or gap selection
operators. within measures from the atom centre, whereas gap takes
the VDW radius into accout but selects everything beyond instead of
near. Have a look at those examples:
# use '... within ...'
select firstshell, solvent within 3.5 of polymer
# or use 'not (... gap ...)'
select firstshell, solvent and not (polymer gap 0.5)
# shows the selected water molecules as a sphere
show spheres, firstshell and elem O
# writes the results in a file
python
stored.out = open('/tmp/water-IDs.txt', 'w')
print stored.out, '## At 0.5 Ang of the protein surface there are',
print stored.out, cmd.count_atoms('firstshell and elem O'),
print stored.out, 'water molecules'
print stored.out, '## Water ID and resi are'
cmd.iterate('firstshell', 'print stored.out, ID, resi')
stored.out.close()
python end
http://www.pymolwiki.org/index.php/Selection_Algebra
http://www.pymolwiki.org/index.php/Iterate
Hope that helps,
Cheers,
Thomas
On 09/21/2011 11:03 PM, ABEL Stephane 175950 wrote:
Hi All,
I have simulated a protein in water cubic box and I would like to
know how to show and obtain the number of water in the first shell of
the protein (or at x Ang of the protein surface) using a pymol
script. I can to do this using the pymol GUI but I would prefer that
the script :
- shows the selected water molecules as a sphere
- and writes the results in a file with the water ID (i.e. residue
number), for example like this:
## At x Ang of the protein
