Re: [PyMOL] Python script with iterate_state and selection command

[ABEL Stephane]

Thank you very much, 

It was very helpful since i did not find similar examples on the web that 
combine this directives 

Thanks again 

Stéphane
--

Envoyé : mardi 23 juin 2020 09:10
À : ABEL Stephane
Cc : Pedro Lacerda; pymol-users
Objet : Re: [PyMOL] Python script with iterate_state and selection command

Hi Stéphane,

Pedro is correct, you should change the selection like he suggested.

You also need to:
- Make a state specific selection with cmd.select(..., state=i)
- Adjust the loop to start at 1 and not at 0
- Use "stored.resid.append(resv)" as the expression

This should work:

###
from pymol import cmd, stored

objname = "mytraj"

cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb",
 objname)
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc",
 objname)

nb_states = cmd.count_states(objname)

for i in range(1, nb_states + 1):
stored.resid = []
cmd.select("water_channel", "resn SOL within 3.5 of resn CHO", state=i)
cmd.iterate("water_channel", 'stored.resid.append(resv)')
print("frame " + str(i) + ":" + str(stored.residues))
###


Hope that helps.

Cheers,
  Thomas


> On Jun 22, 2020, at 4:52 PM, ABEL Stephane  wrote:
>
> Hi Pedro
>
> It does not work, the pymol crashes if I use this selection
>
> Stéphane
>
> --
> Stéphane Abel, Ph.D.
> CEA Centre de Saclay
> DRF/JOLIOT/I2BC-S/SB2SM/LBMS
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ____
> De : Pedro Lacerda [pslace...@gmail.com]
> Envoyé : lundi 22 juin 2020 16:26
> À : ABEL Stephane
> Cc : pymol-users
> Objet : Re: [PyMOL] Python script with iterate_state and selection command
>
> Hi,
>
> Not sure if I understood your code but maybe you want change Myselection to:
>
> Myselection="resname SOL within 3.5 of resname CHO"
>
> -- Pedro Lacerda
>
> Em seg, 22 de jun de 2020 10:44, ABEL Stephane 
> mailto:stephane.a...@cea.fr>> escreveu:
> Hello all,
>
> I would like to write a basic python script to select residues for each state 
> using the iterate_state and output the results first in pymol console window 
> with the following format
>
> frame 1 : resid ...
> frame 2 : resid ...
> ...
>
> ### my script ##
>
> from pymol import cmd, stored
>
> mytraj=""
> mytraj2=""
>
> ## Load PDB
> cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"),
>  mytraj
>
> ## Load XTC
> cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"),
>  mytraj2
>
> stored.resid = []
>
> Myselection="select water_channel, resname SOL within 3.5 of resname CHO"
>
> nb_states=cmd.count_states(mytraj2)---> Contains 102 states
> print(mytraj2, nb_states)
>
> state=1
> for i in range (nb_states) :
>print(i)
>cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   > 
> Should to ireate for all the states
>print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the 
> results of the Myselection command in the console
>
> ###
>
> But the first problem I have is the syntax of the iterate_state. I obtain the 
>  following error
> "Selector-Error: Invalid selection name "select".
> ( select water_channel, resname SOL within 3.5 of resname CHO )<--"
>
> When I put this selection command directly in Pymol, it works and i can 
> obtain the desired waters that was near 3.5 A of the CHO over all the states 
> . So What is the correct syntax for the selection with "iterate_state" ? And 
> how to output the results again for each state in the screen .
>
> Thanks in advance for your help
>
> Stéphane
>
>
> ___
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Python script with iterate_state and selection command

[ABEL Stephane]

Hi Pedro 

It does not work, the pymol crashes if I use this selection

Stéphane

--
Stéphane Abel, Ph.D.
CEA Centre de Saclay
DRF/JOLIOT/I2BC-S/SB2SM/LBMS
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

De : Pedro Lacerda [pslace...@gmail.com]
Envoyé : lundi 22 juin 2020 16:26
À : ABEL Stephane
Cc : pymol-users
Objet : Re: [PyMOL] Python script with iterate_state and selection command

Hi,

Not sure if I understood your code but maybe you want change Myselection to:

Myselection="resname SOL within 3.5 of resname CHO"

-- Pedro Lacerda

Em seg, 22 de jun de 2020 10:44, ABEL Stephane 
mailto:stephane.a...@cea.fr>> escreveu:
Hello all,

I would like to write a basic python script to select residues for each state 
using the iterate_state and output the results first in pymol console window 
with the following format

frame 1 : resid ...
frame 2 : resid ...
...

### my script ##

from pymol import cmd, stored

mytraj=""
mytraj2=""

## Load PDB
cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"),
 mytraj

## Load XTC
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"),
 mytraj2

stored.resid = []

Myselection="select water_channel, resname SOL within 3.5 of resname CHO"

nb_states=cmd.count_states(mytraj2)---> Contains 102 states
print(mytraj2, nb_states)

state=1
for i in range (nb_states) :
print(i)
cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   > 
Should to ireate for all the states
print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the 
results of the Myselection command in the console

###

But the first problem I have is the syntax of the iterate_state. I obtain the  
following error
"Selector-Error: Invalid selection name "select".
( select water_channel, resname SOL within 3.5 of resname CHO )<--"

When I put this selection command directly in Pymol, it works and i can obtain 
the desired waters that was near 3.5 A of the CHO over all the states . So What 
is the correct syntax for the selection with "iterate_state" ? And how to 
output the results again for each state in the screen .

Thanks in advance for your help

Stéphane


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[PyMOL] Python script with iterate_state and selection command

[ABEL Stephane]

Hello all, 

I would like to write a basic python script to select residues for each state 
using the iterate_state and output the results first in pymol console window 
with the following format 

frame 1 : resid ...
frame 2 : resid ... 
...

### my script ## 

from pymol import cmd, stored

mytraj=""
mytraj2=""

## Load PDB 
cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"),
 mytraj

## Load XTC
cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"),
 mytraj2

stored.resid = []

Myselection="select water_channel, resname SOL within 3.5 of resname CHO"

nb_states=cmd.count_states(mytraj2)---> Contains 102 states
print(mytraj2, nb_states)

state=1
for i in range (nb_states) :
print(i)
cmd.iterate_state (i, (Myselection), 'resid.append(resv)')   > 
Should to ireate for all the states
print("frame " + str(i) + ":" + str(stored.residues))   ---> Print the 
results of the Myselection command in the console

### 

But the first problem I have is the syntax of the iterate_state. I obtain the  
following error 
"Selector-Error: Invalid selection name "select".
( select water_channel, resname SOL within 3.5 of resname CHO )<--"

When I put this selection command directly in Pymol, it works and i can obtain 
the desired waters that was near 3.5 A of the CHO over all the states . So What 
is the correct syntax for the selection with "iterate_state" ? And how to 
output the results again for each state in the screen .  

Thanks in advance for your help

Stéphane 


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[PyMOL] Write the number of molecules for each state in a file

[ABEL Stephane]

Hello PyMOLers

I have PDB file that contains different frames ( or state or models) extracted 
from a MD simulation and I would like to select the number the water near (say 
3.5 Angstroms) a protein for each state and write the results in the file.

For instance like this where resid is a list of the water that satisfy the cut 
off below

Frame 0 : residX, residY, , 
Frame 1:  residZ, residY, , 

In the pml script I have selected the water molecules near the protein within 
the pymol commands below

### 

select GrA_Channel, (id 1-267+277-542) and name CA+C+O+N
select water_channel, resname SOL within 3.5 of GrA_Channel

f=open("toto.txt","w")

iterate_state 0, water_channel, state + ':' + water_channel ")   ## How to use 
this command

f.close()

but I do not know to use the iterate_state for each frame with above selected 
command

Can you help me ?

Thank you in advance

Stéphane



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[PyMOL] Membrane protein view according to X/Y axis and to Z=0 with Pymol

[ABEL Stephane]

Hello Pymol users 

I have a snapshot of a membrane protein embedded in a model of bilayer. And I 
would like to have a picture of the protein according to X/Y axis and at z=0 

It is possible with a script. If yes how ?

Thank you 

Stéphane



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Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]

[ABEL Stephane]

Thank you vevry much Annemarie  it worked 

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

--

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg 
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] colored secondary structure of two chains with
different colors
Message-ID: 
Content-Type: text/plain;   charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the 
c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the 
cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger


Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +
> From: ABEL Stephane 
> To: "h. adam steinberg" 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>   different colors
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what 
> I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do 
> this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this 
> even if I use your suggestion
>
> I would like in two representations at the same time and the necessary 
> commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> --
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : h. adam steinberg [h.adam.steinb...@gmail.com]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different 
> colors
>
> If you change your mouse / selection mode to chains, you can then click on 
> one of the monomers and choose a color for it from the (sale) in the right 
> side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
>> color the  beta sheets of each monomer with different colors (for instance 
>> in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> --
>
>
>
> --
>
> Subject: Digest Footer
>
> ___
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> ***




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Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

[ABEL Stephane]

Dear Annemarie, 

Thank you very much it worked !!! 

Stéphane

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


--

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg 
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] colored secondary structure of two chains with
different colors
Message-ID: 
Content-Type: text/plain;   charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the 
c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the 
cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger


Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +
> From: ABEL Stephane 
> To: "h. adam steinberg" 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>   different colors
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what 
> I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do 
> this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this 
> even if I use your suggestion
>
> I would like in two representations at the same time and the necessary 
> commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> --
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : h. adam steinberg [h.adam.steinb...@gmail.com]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different 
> colors
>
> If you change your mouse / selection mode to chains, you can then click on 
> one of the monomers and choose a color for it from the (sale) in the right 
> side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
>> color the  beta sheets of each monomer with different colors (for instance 
>> in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> --
>
>
>
> --
>
> Subject: Digest Footer
>
> ___
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Re: [PyMOL] colored secondary structure of two chains with different colors

[ABEL Stephane]

Hi Adam 

OK I can colored each chain with different colors. But it is not exactly what I 
want. Indeed in the figure* 

- the AA are  in sticks with the different colors for each atom --> I can do 
this 
- the beta sheet in the monomer are in red and blue ---> I can "not" do this 
even if I use your suggestion

I would like in two representations at the same time and the necessary commands 
for adding them in a script. 
ript. 

*https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg

Thank you again. 

Stéphane


--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

De : h. adam steinberg [h.adam.steinb...@gmail.com]
Envoyé : mercredi 5 juin 2019 21:36
À : ABEL Stephane
Objet : Re: [PyMOL] colored secondary structure of two chains with different 
colors

If you change your mouse / selection mode to chains, you can then click on one 
of the monomers and choose a color for it from the (sale) in the right side 
panel drop down menu. Then click on the other monomer and do the same.

Is that what you are asking for?

> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>
> Hello all
>
> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
> color the  beta sheets of each monomer with different colors (for instance in 
> red and blue colors) in Figure
>
> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> How to do this ?
>
> Thank you
>
> Stéphane
>
>
>
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[PyMOL] colored secondary structure of two chains with different colors

[ABEL Stephane]

Hello all

I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
color the  beta sheets of each monomer with different colors (for instance in 
red and blue colors) in Figure 

https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg

How to do this ?

Thank you 

Stéphane



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[PyMOL] how to keep the atom order when convert mol2 file to pdb in pymol

[ABEL Stephane 175950]

Hello 

Did you try to use the following command* before to save your pdb file?


* set retain_order,[0,1] : http://www.pymolwiki.org/index.php/Retain_order 

Stephane

--

Message: 4
Date: Sat, 13 Aug 2016 00:25:06 +0800 (CST)
From: windy 
Subject: [PyMOL] how to keep the atom order when convert mol2 file to
pdb in  pymol
To: pymol-users 
Message-ID: <2b26344c.24a.1567f924065.coremail.chxp_m...@163.com>
Content-Type: text/plain; charset="gbk"

Hi,

   Everyone.

   I always using pymol to prepare the pdb files for MD simulations. However, 
when I merge the extra small molecular (substrate optimized from the 
Gaussian09, mol2 formats) and the protein file (PDB formats) into the a single 
pdb, I found the atom order of substrate is not the same as the original mol2 
files.

   It seems the pymol would put the the hydrogen atom after the heavy atom. It 
also rearrange the atom when convert the mol2 file to mol2 file when using the 
pymol. (The attachments, from the test1 to test2 by using pymol)

   However the rearrangement of the atom is not very convenient for the 
following actions. I wonder how to keep the original atom order when convert to 
other formats by using pymol. ?I using PYMOL 1.7.0 in Ubuntu 14.04?

   Thanks very much.

Chen





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[PyMOL] Pymol Script to automatize the construction of alkyl chain bonded to a molecule

[ABEL Stephane 175950]

Hello, 

I would like to add a long alkyl  chain to a molecule with Pymol. I know that i 
can use the Build---> Fragment ---> Carbon command. However doing this manually 
is quite painful and error prone, since only one carbone is add, so I am 
wondering if possible to use a script to automatize this task. If yes, how?

Thanks

Stéphane 


   
Stéphane Abel, Ph.D.

CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C 
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
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[PyMOL] Problem with loadBfact.py on windows

[ABEL Stephane 175950]

 Stéphane,

It looks like a slash/backslash issue between windows and linux:

C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py
  

Thanks Jed,

How to change it, since I can not to modify it with text editor (it seems to be 
used by another program, even if pymol is closed 

S 





Hi Pymol users

I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py 
(http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here, 
loadB2Fact.py) to change the B factor value according to other values stored in 
an external txt file. On my linux machine, I use the following script that 
works well

### Script ##
bg black
hide all
select BENZ, resname BEN
hide BEN
select SOL, resname SOL
hide SOL
select DOP, resname DOP
hide DOP
select protein, resi 1-76

run loadB2Fact.py

loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat

cartoon automatic, protein

set_view (\
-0.252517521,0.895963371,0.365354568,\
 0.693045497,0.430974960,   -0.577881873,\
-0.675220251,0.107282706,   -0.729772329,\
-0.30319,   -0.10751, -106.549461365,\
30.012023926,   31.324144363,   31.591945648,\
66.820175171,  146.280471802,  -20.0 )

###End Script

But on windows, i obtained the following errors

PyMOLrun ./loadB2Fact.py
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parsing.py, line 
455, in run_file
execfile(file,global_ns,local_ns)
IOError: [Errno 2] No such file or directory: './loadB2Fact.py'
PyMOLloadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
464, in parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1
 loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
  ^
 SyntaxError: invalid syntax

And I see nothing on the screen

Could you help me ?

Thanks

St?phane



--

Message: 3
Date: Fri, 10 Jul 2015 18:14:41 +0530
From: Gazal gazal...@gmail.com
Subject: [PyMOL] How to find RMSD values using fitting.py using Shell
script
To: pymol-users@lists.sourceforge.net
Message-ID:
CAC-EGRpq9ORP2p7HT9icysLDWQDVnfmem=pfvcn+izijtr+...@mail.gmail.com
Content-Type: text/plain; charset=utf-8

Hi,

I'm trying to find the RMSD values for batch purposes. The command which I
found works for the Pymol-command line.
I was hoping if I could get an idea about using the python script
fitting.py in my shell script without triggering the Pymol GUI.

Thanks in advance.

Gazal
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Message: 4
Date: Fri, 10 Jul 2015 10:04:24 -0400
From: Stephen P. Molnar s.mol...@sbcglobal.net
Subject: [PyMOL] Optimize Geometry {rpblem
To: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID: 559fd0e8.8090...@sbcglobal.net
Content-Type: text/plain; charset=utf-8

I have a bit of a strange problem.  I have evaluated a number of Linux
distributions in a VMware Player environment on my  64 bit laptop.

I compile PyMol using the attached protocol.

The OS is BioLinux v-8.0.5 with Avogadro Version 1.1.1
 Library Version 1.1.1
 Open Babel Version 2.3.2
 Qt Version 4.8.6

The problem involves the Extensions/Optimize Geometry feature with
cyclohexane as the test molecule.  Cyclohexane as built is a planar
molecule, but when I optimize the geometry it remains in a planar
conformation.  However in some of my test systems the geometry is
returned as the chair isomer, which, of course, is correct!

I will make the wild assumption (yes, I know how the word can be broken
down) that there is a missing library.  Which one might it be?  Is any
other information needed in order to address this rather nagging problem?

Thanks in advance.

--
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www.FoundationForChemistry.com  Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1

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sudo apt-get install subversion build-essential python-dev python-pmw 
libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev

cd /tmp
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
cd pymol

prefix=/home/comp/Apps/pymol
modules=$prefix/modules
export CPPFLAGS=-std=c++11
python setup.py build install \
--home=$prefix \
--install-lib=$modules \

[PyMOL] Problem with loadBfact.py on windows (ABEL Stephane 175950

[ABEL Stephane 175950]

I have reinstall the program and removed an old version of Pymol. Now the 
script works

Thanks


--

Message: 2
Date: Fri, 10 Jul 2015 12:44:40 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [PyMOL] Problem with loadBfact.py on windows
To: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID:
3e39b768bb199548ab18f7289e7534af1b471...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=iso-8859-1

Hi Pymol users

I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py 
(http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here, 
loadB2Fact.py) to change the B factor value according to other values stored in 
an external txt file. On my linux machine, I use the following script that 
works well

### Script ##
bg black
hide all
select BENZ, resname BEN
hide BEN
select SOL, resname SOL
hide SOL
select DOP, resname DOP
hide DOP
select protein, resi 1-76

run loadB2Fact.py

loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat

cartoon automatic, protein

set_view (\
-0.252517521,0.895963371,0.365354568,\
 0.693045497,0.430974960,   -0.577881873,\
-0.675220251,0.107282706,   -0.729772329,\
-0.30319,   -0.10751, -106.549461365,\
30.012023926,   31.324144363,   31.591945648,\
66.820175171,  146.280471802,  -20.0 )

###End Script

But on windows, i obtained the following errors

PyMOLrun ./loadB2Fact.py
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parsing.py, line 
455, in run_file
execfile(file,global_ns,local_ns)
IOError: [Errno 2] No such file or directory: './loadB2Fact.py'
PyMOLloadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
464, in parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1
 loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
  ^
 SyntaxError: invalid syntax

And I see nothing on the screen

Could you help me ?

Thanks

St?phane


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[PyMOL] TR : Problem with loadBfact.py on windows - FIXED

[ABEL Stephane 175950]

De : ABEL Stephane 175950
Envoyé : vendredi 10 juillet 2015 18:39
À : pymol-users@lists.sourceforge.net
Objet : Problem with loadBfact.py on windows (ABEL Stephane 175950

I have re installed the program and removed an old version of Pymol and now my 
script works

Thanks


--

Message: 2
Date: Fri, 10 Jul 2015 12:44:40 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [PyMOL] Problem with loadBfact.py on windows
To: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID:
3e39b768bb199548ab18f7289e7534af1b471...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=iso-8859-1

Hi Pymol users

I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py 
(http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here, 
loadB2Fact.py) to change the B factor value according to other values stored in 
an external txt file. On my linux machine, I use the following script that 
works well

### Script ##
bg black
hide all
select BENZ, resname BEN
hide BEN
select SOL, resname SOL
hide SOL
select DOP, resname DOP
hide DOP
select protein, resi 1-76

run loadB2Fact.py

loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat

cartoon automatic, protein

set_view (\
-0.252517521,0.895963371,0.365354568,\
 0.693045497,0.430974960,   -0.577881873,\
-0.675220251,0.107282706,   -0.729772329,\
-0.30319,   -0.10751, -106.549461365,\
30.012023926,   31.324144363,   31.591945648,\
66.820175171,  146.280471802,  -20.0 )

###End Script

But on windows, i obtained the following errors

PyMOLrun ./loadB2Fact.py
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parsing.py, line 
455, in run_file
execfile(file,global_ns,local_ns)
IOError: [Errno 2] No such file or directory: './loadB2Fact.py'
PyMOLloadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
Traceback (most recent call last):
  File C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py, line 
464, in parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1
 loadBfacts protein, 1, 
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
  ^
 SyntaxError: invalid syntax

And I see nothing on the screen

Could you help me ?

Thanks

St?phane

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[PyMOL] time bar in a movie done with pymol

[ABEL Stephane 175950]

Hello Pymol users

I want to add a time bar in movie  done with pymol.  Is it possible with a 
pymol script ? If not do you know an alternative (except VMD)?

Thanks in advance

Stéphane



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[PyMOL] Replicate a cubic unit cell in the x, y, z directions

[ABEL Stephane 175950]

Hi all,

I want to know if is possible to replicate a cubic unit cell in the x, y, z 
directions (as with the graphic representation - periodic command in VMD) 
with pymol(v1.3)? if yes how I can do that ?

Thanks in advance

Stephane

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[PyMOL] How to install Psico module for pymol with window 7

[ABEL Stephane 175950]

Hello 

I have downloaded the Psico module of T. Holder to use the command supercell. I 
have followed the wiki http://www.pymolwiki.org/index.php/Psico and  
https://github.com/speleo3/pymol-psico/.

I did the followings: 

1) Installed the ccbtx and numpy librairies
2) Dowloaded the Psico archive from https://github.com/speleo3/pymol-psico/ 
3) Copied the Psico directory in my C:\Program Files (x86)\DeLano 
Scientific\PyMOL\modules\psico
4) Lauched pymol (0.99rc6) and typed import import psico.fullinit

But i obtain the following error   

File C:\Program Files (x86)\DeLano 
Scientific\PyMOL/modules\psico\fullinit.py, line 10
 from . import init
  ^
 SyntaxError: invalid syntax

What's wrong ?

Thanks for your help

Stephane
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[PyMOL] RE : Replicate a cubic unit cell in the x, y, z directions

[ABEL Stephane 175950]

Hi Jason

It is exactly what I want !!!

Merci beaucoup 

Cheers 

Stephane

De : Jason Vertrees [jason.vertr...@schrodinger.com]
Date d'envoi : vendredi 10 mai 2013 20:25
À : ABEL Stephane 175950
Objet : Re: [PyMOL] Replicate a cubic unit cell in the x, y, z directions

Hi Stephane,

For your object, just click A  Generate  Symmetry Mates  Within X Angstroms.

Cheers,

-- Jason

On Fri, May 10, 2013 at 7:01 AM, ABEL Stephane 175950
stephane.a...@cea.fr wrote:
 Hi all,

 I want to know if is possible to replicate a cubic unit cell in the x, y, z 
 directions (as with the graphic representation - periodic command in VMD) 
 with pymol(v1.3)? if yes how I can do that ?

 Thanks in advance

 Stephane

 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and
 their applications. This 200-page book is written by three acclaimed
 leaders in the field. The early access version is available now.
 Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
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Director of Core Modeling Products
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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[PyMOL] Showing secondary structure of coarse grained protein

[ABEL Stephane 175950]

Hello everybody, 

I have done several MD simulations with the Martini force field of systems that 
contain a small protein and surfactant with GROMACS. It is possible to show 
with pymol the secondary structure of the protein with a cartoon representation 
and the detergent molecules with beads at the same time. I know from you that I 
can use for the detergent molecules, the connects but for protein i don't 
know how to do (with the alter command?). 

Can you help me? 

Thanks you in advance

Stephane
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[PyMOL] RE : Pymol Scripts for Coarse grained for non-protein molecules

[ABEL Stephane 175950]

Hi Tsjerk,

Many thanks for your help, once again ;0 It works and it gives what i want. 
cool !!

Stephane

De : Tsjerk Wassenaar [tsje...@gmail.com]
Date d'envoi : vendredi 1 mars 2013 13:56
À : ABEL Stephane 175950
Cc: pymol-users@lists.sourceforge.net
Objet : Re: [PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

Hi Stephane,

You can convert a Gromacs run input file (.tpr) to a pdb file with
CONECT records using the Gromacs tool 'editconf' with the '-conect'
flag. The CONECT records will be set according to the bonds in the
topology. Pymol will read the CONECT records and set the bonds. If you
have a trajectory or a snapshot you want to visualize, you can load
the convert run input file first, and load the other structure(s) in
that object:

load tpr.pdb, cg
load traj.pdb, cg

Hope it helps,

Tsjerk


On Thu, Feb 28, 2013 at 1:18 PM, ABEL Stephane 175950
stephane.a...@cea.fr wrote:
 Hi all,

 I am looking for pymol scripts for showing coarse grained representation of 
 non-protein molecules. I am currently using the sphere representation for 
 each bead, but the bond between two beads are not shown, so it does not nice 
 figures.

 Can you help me or give some advices

 Thanks you in advance

 Stephane
 --
 Everyone hates slow websites. So do we.
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post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada

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[PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

[ABEL Stephane 175950]

Hi all, 

I am looking for pymol scripts for showing coarse grained representation of 
non-protein molecules. I am currently using the sphere representation for each 
bead, but the bond between two beads are not shown, so it does not nice 
figures.  

Can you help me or give some advices

Thanks you in advance

Stephane
--
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[PyMOL] Obtain the number of molecule in the first hydration shell of a peptide.

[ABEL Stephane 175950]

Dear pymol users,

I would like to obtain with Pymol (v1.3) the number of urea molecules in the 
first shell of a peptide. To do this I have defined the object urea as 
following 

select UREA, resn URE 

and used the following cutoff for the first hydration shell:

select UREA_firstshell, UREA within 3.5 of peptide

And finally used the command: 

print cmd.count_atoms(UREA_firstshell) to obtain the number of atom at the 
distance of 3.5 A from the peptide. 

Of course, these commands work well, but my aim is to obtain the number of 
molecules instead of the number of atoms.  How to do  that ?

For info,  urea has 8 atoms.  

Thank you for you help 

Stephane
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Re: [PyMOL] Obtain the number of molecule in the first hydration shell of a peptide.

[ABEL Stephane 175950]

for the pymol-users mailing list archive and to close my message 

Tsjerk Wassenaar gave the command : 

print cmd.count_atoms(byres resn URE within 3.5 of peptide)/8. it works !!!

Thanks to him !!!

Bye 

Stephane

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Message: 8
Date: Fri, 28 Sep 2012 12:59:27 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [PyMOL] Obtain the number of molecule in the first hydration
shell of a peptide.
To: pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Message-ID:
3e39b768bb199548ab18f7289e7534af02c4d...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=us-ascii

Dear pymol users,

I would like to obtain with Pymol (v1.3) the number of urea molecules in the 
first shell of a peptide. To do this I have defined the object urea as following

select UREA, resn URE

and used the following cutoff for the first hydration shell:

select UREA_firstshell, UREA within 3.5 of peptide

And finally used the command:

print cmd.count_atoms(UREA_firstshell) to obtain the number of atom at the 
distance of 3.5 A from the peptide.

Of course, these commands work well, but my aim is to obtain the number of 
molecules instead of the number of atoms.  How to do  that ?

For info,  urea has 8 atoms.

Thank you for you help

Stephane


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End of PyMOL-users Digest, Vol 76, Issue 10
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[PyMOL] Create a dummy atom

[ABEL Stephane 175950]

Dear all, 

I have a simple question but i have found no response: i have downloaded a 
pymol script COM.py from the pymol wiki to obtain the coordinates x, y and z of 
the center of mass of my protein. Now i would like to create a dummy at these 
coordinates. How to do that with pymol ?

Thank for your help

Stephane
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[PyMOL] Create a dummy atom

[ABEL Stephane 175950]

Thank you Jason and Troels for your quick response. 

I have an additional question. Now if i want to pass the COM coordinates x, y 
and z obtained with the COM script  in the pseudoatom pos. For example to use 
in the script

How i can do that ?

Thank you again for your response.

Stephane
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[PyMOL] RE : Write in a file the number of water at a distance from a protein surface

[ABEL Stephane 175950]

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
À : ABEL Stephane 175950
Cc : pymol-users@lists.sourceforge.net
Objet : 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

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MPI for Developmental Biology

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