Re: [PyMOL] Steps to create a movie with objects and cameras moved independently of each other in PyMOL

[Riccardo]

Found the solution in [this page][1]: *object motions—keeping the camera
still, but moving the objects around the scene*.

There is a working example:

# setup PyMOL for movies
reinitialize set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
config_mouse three_button_motions, 1

# download the complex and setup it up fetch 1te1, async=0
extract AA, c. A
extract BB, c. B
color marine, AA
color grey, BB
as surface, BB
as cartoon, AA

# intialize the movie
mset 1 x410

# orient the scene
set_view (\
0.423117876, 0.061672822, 0.903973043,\
0.789699256, -0.514252067, -0.334546506,\
0.444237947, 0.855418444, -0.266292989,\
0.000107866, -0.27858, -196.784057617,\
28.171787262, 70.919288635, 52.095287323,\
155.143981934, 238.418914795, -20.0 )

# move the inhibitor off the screeen
translate [0,0,100], object=AA

# first movie scene
frame 1
wizard message, "Let's watch the binder float it, while the camera
doesn't move."
mview store, object=AA
mview store, object=BB

# 2 second pause for the user to catch up frame 60
mview store, object=AA
mview store, object=BB

# slide the inhibitor in from over the camera. :-)
frame 300
translate [0,0,-100], object=AA
mview store, object=AA
mview interpolate, object=AA

# store & wait 2 seconds...
frame 360
mview store, object=AA
mview store, object=BB
mview reinterpolate, object=AA
mview reinterpolate, object=BB

# 'explode' apart
frame 380
translate [-70, 70, 70], object=AA
translate [70, -70, -70], object=BB
mview store, object=AA
mview store, object=BB
mview reinterpolate, object=AA
mview reinterpolate, object=BB

mplay

Cheers

  [1]: https://pymolwiki.org/index.php/MovieSchool_5


Il sab 21 lug 2018, 02:06 Riccardo  ha scritto:

> Hello, PyMOL community,
>
> I have compiled open-source PyMOL v2.2.0a0 under Linux OS.
>
> Reading this webpage  and seeing this
> video , I tried the
> "*copy to object / new*" command on selections, moving them indipendently
> with the mouse in "*edit mode*", saving the state of the scene after each
> edit, but I can't interpolate between them.
>
> In other words, I still can not understand how to realize a video like the
> one shown in that webpage. Could someone kindly explain how to proceed for
> such an animation?
>
> Thank you for your help,
>
> best regards,
>
> Riccardo
>
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Re: [PyMOL] Preventing Output of pair_fit

[Jarrett Johnson]

Hello Nathan,

While we prepare to rollout the "quiet" argument for pair_fit, in the
meantime try:

cmd.feedback("disable", "executive", "results")

Jarrett J.

On Sun, Jul 22, 2018 at 6:47 PM, Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Hello Nathan,
>
> We actually just implemented a 'quiet' argument for the pair_fit command
> on Friday. This should be live in an upcoming update.
>
> Jarrett J.
>
> On Sun, Jul 22, 2018 at 6:32 PM,  wrote:
>
>> Hi,
>>
>> Consider the following (simplified) Pymol script, test.py:
>>
>> -
>> import sys
>> cmd.load(sys.argv[1], 'prot1')
>> cmd.load(sys.argv[2], 'prot2')
>> rms = cmd.pair_fit('prot1 & n. ca','prot2 & n. ca')
>> print 'This should print', rms
>>
>> -
>>
>> I would like the only output for this program to be created by the line,
>> 'This should print.' However, here is what I actually get, with a few
>> different options:
>>
>> $ pymol -qc test.py -- protein.pdb protein.pdb
>>  ExecutiveRMS: RMS =0.000 (96 to 96 atoms)
>> This should print 0.0
>> $ pymol -Qc test.py -- protein.pdb protein.pdb
>> $
>>
>> (The first prints output from ExecutiveRMS, and the second prints nothing
>> at all.)
>> Is there any way to prevent the ExecutiveRMS output? Either
>> programmatically or on the command line?
>>
>> Thanks much,
>>
>> Nathan
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Jarrett Johnson,
> Schrödinger
>



-- 
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Schrödinger
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[PyMOL] Amber .nc

[Stejskal, Lenka]

Dear Pymol users,


Can somebody advise how I can open amber trajectory file in .nc format?


Thank you


Lenka
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Re: [PyMOL] Amber .nc

[Mateusz Bieniek]

Hi Lenka,

Let me first state that the command "help load_traj" points to the webpage
which in turns says that the .nc format is supported by pymol.

I come from the gromacs background. Once you load the topology/state of
your system (in my case .gro or .pdb), then use "load_traj", ie
*load_traj trajectory.nc  *

There are other options for this command (start, end, shift, etc).

Hope this helps, Mat

On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka <
lenka.stejskal...@ucl.ac.uk> wrote:

> Dear Pymol users,
>
>
> Can somebody advise how I can open amber trajectory file in .nc format?
>
>
> Thank you
>
>
> Lenka
>
> --
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Re: [PyMOL] Amber .nc

[Stejskal, Lenka]

Hi Mat,


I have of course read that but I am still unable to load the trajectory. I was 
looking for an actual successful example not just a guide.


Thanks


Lenka


From: Mateusz Bieniek 
Sent: 23 July 2018 14:04:22
To: Stejskal, Lenka
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Amber .nc

Hi Lenka,

Let me first state that the command "help load_traj" points to the webpage 
which in turns says that the .nc format is supported by pymol.

I come from the gromacs background. Once you load the topology/state of your 
system (in my case .gro or .pdb), then use "load_traj", ie
load_traj trajectory.nc

There are other options for this command (start, end, shift, etc).

Hope this helps, Mat

On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka 
mailto:lenka.stejskal...@ucl.ac.uk>> wrote:

Dear Pymol users,


Can somebody advise how I can open amber trajectory file in .nc format?


Thank you


Lenka

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Re: [PyMOL] Amber .nc

[Mateusz Bieniek]

Can you share what error/message you get when you try to load the
trajectory with the command?

The snippet of code I shared works for me. According to this page it should
just work: https://pymolwiki.org/index.php/Load_Traj

Do you happen to use a truncated octahedron?

Best, Mat

On Mon, Jul 23, 2018 at 2:27 PM Stejskal, Lenka 
wrote:

> Hi Mat,
>
>
> I have of course read that but I am still unable to load the trajectory. I
> was looking for an actual successful example not just a guide.
>
>
> Thanks
>
>
> Lenka
> --
> *From:* Mateusz Bieniek 
> *Sent:* 23 July 2018 14:04:22
> *To:* Stejskal, Lenka
> *Cc:* pymol-users@lists.sourceforge.net
> *Subject:* Re: [PyMOL] Amber .nc
>
> Hi Lenka,
>
> Let me first state that the command "help load_traj" points to the webpage
> which in turns says that the .nc format is supported by pymol.
>
> I come from the gromacs background. Once you load the topology/state of
> your system (in my case .gro or .pdb), then use "load_traj", ie
> *load_traj trajectory.nc  *
>
> There are other options for this command (start, end, shift, etc).
>
> Hope this helps, Mat
>
> On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka <
> lenka.stejskal...@ucl.ac.uk> wrote:
>
> Dear Pymol users,
>
>
> Can somebody advise how I can open amber trajectory file in .nc format?
>
>
> Thank you
>
>
> Lenka
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
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Re: [PyMOL] Amber .nc

[Thomas Holder]

Hi Lenka and Mat,

Unfortunately, Amber ".nc" (NetCDF) files are currently not supported. Can you 
convert the file to one of the supported formats, like ".crd"?

We can probably add NetCDF support to the next release. It's included in the 
VMD molfile plugins, and only excluded in PyMOL to avoid the dependency on the 
libnetcdf library. I can also give you instruction how to compile PyMOL from 
source and patch in a modified version of the molfile plugins, but it's a bit 
of work and requires some understanding of how to build software.

Cheers,
  Thomas

> On Jul 23, 2018, at 3:27 PM, Stejskal, Lenka  
> wrote:
> 
> Hi Mat, 
> 
> I have of course read that but I am still unable to load the trajectory. I 
> was looking for an actual successful example not just a guide. 
> 
> Thanks
> 
> Lenka
> From: Mateusz Bieniek 
> Sent: 23 July 2018 14:04:22
> To: Stejskal, Lenka
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Amber .nc
>  
> Hi Lenka, 
> 
> Let me first state that the command "help load_traj" points to the webpage 
> which in turns says that the .nc format is supported by pymol. 
> 
> I come from the gromacs background. Once you load the topology/state of your 
> system (in my case .gro or .pdb), then use "load_traj", ie 
> load_traj trajectory.nc 
> 
> There are other options for this command (start, end, shift, etc). 
> 
> Hope this helps, Mat
> 
> On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka 
>  wrote:
> Dear Pymol users,
> 
> Can somebody advise how I can open amber trajectory file in .nc format? 
> 
> Thank you 
> 
> Lenka

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Amber .nc

[Stejskal, Lenka]

I had to change the trajectory into .mdcrd and took the take care of the box I 
believe. I am not sure you can keep .nc format without the truncated octahedron 
tbf.


Thank you!


Lenka


From: Mateusz Bieniek 
Sent: 23 July 2018 14:28:12
To: Stejskal, Lenka
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Amber .nc

Can you share what error/message you get when you try to load the trajectory 
with the command?

The snippet of code I shared works for me. According to this page it should 
just work: https://pymolwiki.org/index.php/Load_Traj
Load Traj - PyMOLWiki
pymolwiki.org
load_traj loads a trajectory as "states" into an already loaded molecular 
object.. Since version 1.0, PyMOL uses the Molfile Plugin backend, which 
supports a variety of trajectory file formats.



Do you happen to use a truncated octahedron?

Best, Mat

On Mon, Jul 23, 2018 at 2:27 PM Stejskal, Lenka 
mailto:lenka.stejskal...@ucl.ac.uk>> wrote:

Hi Mat,


I have of course read that but I am still unable to load the trajectory. I was 
looking for an actual successful example not just a guide.


Thanks


Lenka


From: Mateusz Bieniek mailto:bieniek...@gmail.com>>
Sent: 23 July 2018 14:04:22
To: Stejskal, Lenka
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Amber .nc

Hi Lenka,

Let me first state that the command "help load_traj" points to the webpage 
which in turns says that the .nc format is supported by pymol.

I come from the gromacs background. Once you load the topology/state of your 
system (in my case .gro or .pdb), then use "load_traj", ie
load_traj trajectory.nc

There are other options for this command (start, end, shift, etc).

Hope this helps, Mat

On Mon, Jul 23, 2018 at 11:42 AM Stejskal, Lenka 
mailto:lenka.stejskal...@ucl.ac.uk>> wrote:

Dear Pymol users,


Can somebody advise how I can open amber trajectory file in .nc format?


Thank you


Lenka

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[PyMOL] cartoon range transparency help

[Paul Miller]

Hi




I have Pymol version 2




When I try to make a range of a cartoon transparent




e.g. I type: set cartoon_transparency, 0.5, /4COF//A/1:20




 it comes up with following error:




Setting-Warning: 'cartoon_transparency' is a object-state-level setting




Does this mean one cannot make part of a cartoon transparent?




Cheers, Paul



Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN


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Re: [PyMOL] cartoon range transparency help

[Paul Miller]

Hi Jarrett




Thanks for this, however, the trajectories of the cartoon change when only part 
of it is shown so that the transparent and non-transparent segments to not 
connect seamlessly.




Cheers, Paul



Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN
 

-Original Message-
From: "Jarrett Johnson" 
To: "Paul Miller" 
Cc: "Pymol User list" 
Date: 07/23/18 15:47
Subject: Re: [PyMOL] cartoon range transparency help

Hello,

That seems to be the case for that command. One workaround for this is to use 
the 'create' command to create a new object identical to your source object and 
make that one transparent. I've attached a quick example.

Jarrett J.

On Mon, Jul 23, 2018 at 9:36 AM, Paul Miller  wrote:


Hi




I have Pymol version 2




When I try to make a range of a cartoon transparent




e.g. I type: set cartoon_transparency, 0.5, /4COF//A/1:20




 it comes up with following error:




Setting-Warning: 'cartoon_transparency' is a object-state-level setting




Does this mean one cannot make part of a cartoon transparent?




Cheers, Paul



Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN


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Schrödinger


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Re: [PyMOL] cartoon range transparency help

[Christian Becke]

Hi Paul,

check out
https://pymolwiki.org/index.php/Cartoon#Breaking_Up_a_Visualization_with_Cartoon_Skip

You'll want to skip the residues you want to make transparent in the
original (opaque) object, and include some more residues on both ends in
the copy you want to make transparent. Skip the additional residues and
make the copy transparent.

HTH,

Christian


Am 23.07.2018 um 17:00 schrieb Paul Miller:
>
> Hi Jarrett
>
>
> Thanks for this, however, the trajectories of the cartoon change when
> only part of it is shown so that the transparent and non-transparent
> segments to not connect seamlessly.
>
>
> Cheers, Paul
>
>
> Paul Steven Miller (PhD)
> Postdoctoral Researcher
> University of Oxford
> Wellcome Trust Centre for Human Genetics
> Division of Structural Biology
> Roosevelt Drive
> Oxford
> OX3 7BN
>  
>
> 
> -Original Message-
> From: "Jarrett Johnson"  >
> To: "Paul Miller" mailto:p...@strubi.ox.ac.uk>>
> Cc: "Pymol User list"  >
> Date: 07/23/18 15:47
> Subject: Re: [PyMOL] cartoon range transparency help
>
> Hello,
>
> That seems to be the case for that command. One workaround for
> this is to use the 'create' command to create a new object
> identical to your source object and make that one transparent.
> I've attached a quick example.
>
> Jarrett J.
>
> On Mon, Jul 23, 2018 at 9:36 AM, Paul Miller  > wrote:
>
> Hi
>
>
> I have Pymol version 2
>
>
> When I try to make a range of a cartoon transparent
>
>
> e.g. I type: set cartoon_transparency, 0.5, /4COF//A/1:20
>
>
> it comes up with following error:
>
>
> Setting-Warning: 'cartoon_transparency' is a
> object-state-level setting
>
>
> Does this mean one cannot make part of a cartoon transparent?
>
>
> Cheers, Paul
>
>
> Paul Steven Miller (PhD)
> Postdoctoral Researcher
> University of Oxford
> Wellcome Trust Centre for Human Genetics
> Division of Structural Biology
> Roosevelt Drive
> Oxford
> OX3 7BN
>
> 
> --
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> 
>
>
>
>
> --
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>
>
>
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[PyMOL] Color backbone amide nitrogen

[Santrupti Nerli]

Hi,

I want to color backbone nitrogen atoms together with side-chain nitrogen 
atoms. The side-chain nitrogens get the color, however the backbone nitrogens 
don’t (see below; I have selected backbone nitrogens). I tried some options 
such as

select bb, name n
color by element 



But, the backbone nitrogens aren’t getting colored. Is there a way to color 
them without showing them as spheres?

Thanks a lot.--
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Re: [PyMOL] Color backbone amide nitrogen

[Marko Hyvonen]

  
  
The problem is that you are not visualising
  the backbone nitrogens. You
  only show the side chains as sticks and the
  backbone is shown as cartoons.These schematic
  representations of secondary structure are drawn using
Calpha atom positions and (typically)
  inherit the colour of the Calphas.  If
  you show the backbone as sticks, the nitrogens will be visible and
  they will have colour. Same goes for backbone oxygens
  which are similarly hidden in your image, but are coloured in the
  side chain at the bottom of the image. 

hth, Marko

On 23/07/2018 18:17, Santrupti Nerli
  wrote:


  
  Hi,
  
  
  I want to color backbone nitrogen atoms together
with side-chain nitrogen atoms. The side-chain nitrogens get the
color, however the backbone nitrogens don’t (see below; I have
selected backbone nitrogens). I tried some options such as
  
  
  select bb, name n
  color by element 
  
  
  
  
  
  But, the backbone nitrogens aren’t getting colored.
Is there a way to color them without showing them as spheres?
  
  
  Thanks a lot.
  
  
  
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Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk
 


  

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[PyMOL] Add to existing selection

[Markus Heller]

Hi,

How can I add a residue to an existing selection?

Example: I'm comparing the binding sites of two superposed protein structures, 
and show the side chains with a certain distance to the ligand.  Sometimes the 
side chain of one protein falls just outside that distance, and thus isn't 
shown, which looks odd.

In essence what I'd like to be able to do is this:

select site, (byres all within 6 of ligand) and polymer
add_to_sel site, resi=666

Is this possible somehow?

Thanks
Markus


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Re: [PyMOL] Add to existing selection

[Jarrett Johnson]

Hello Markus,

Selection algebra (https://pymolwiki.org/index.php/Selection_Algebra) may
be able to help you here. Try doing:

"select site, site or res 666"

Jarrett J.

On Mon, Jul 23, 2018 at 2:02 PM, Markus Heller  wrote:

> Hi,
>
> How can I add a residue to an existing selection?
>
> Example: I'm comparing the binding sites of two superposed protein
> structures, and show the side chains with a certain distance to the
> ligand.  Sometimes the side chain of one protein falls just outside that
> distance, and thus isn't shown, which looks odd.
>
> In essence what I'd like to be able to do is this:
>
> select site, (byres all within 6 of ligand) and polymer
> add_to_sel site, resi=666
>
> Is this possible somehow?
>
> Thanks
> Markus
>
>
> 
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> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Jarrett Johnson,
Schrödinger
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Re: [PyMOL] Add to existing selection

[Markus Heller]

Of course!  Works like a charm.

Thanks Jarrett!

From: Jarrett Johnson 
Sent: Monday, July 23, 2018 11:43 AM
To: Markus Heller 
Cc: Pymol User list 
Subject: Re: [PyMOL] Add to existing selection

Hello Markus,

Selection algebra (https://pymolwiki.org/index.php/Selection_Algebra) may be 
able to help you here. Try doing:

"select site, site or res 666"

Jarrett J.

On Mon, Jul 23, 2018 at 2:02 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:
Hi,

How can I add a residue to an existing selection?

Example: I'm comparing the binding sites of two superposed protein structures, 
and show the side chains with a certain distance to the ligand.  Sometimes the 
side chain of one protein falls just outside that distance, and thus isn't 
shown, which looks odd.

In essence what I'd like to be able to do is this:

select site, (byres all within 6 of ligand) and polymer
add_to_sel site, resi=666

Is this possible somehow?

Thanks
Markus


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Jarrett Johnson,
Schrödinger
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[PyMOL] Unsubscribe pymol user mails

[신현길]

Dear Mr. or Mrs. 
 
I don't want to recieve pymol user mails.
Please remove my account from pymol-user mailing list.
 
Thanks 

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