pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] For set.view(), there's a Wiki example for the GUI, but not the PyMol API

[Thomas H. <tho...@sc...>]

I've added Python syntax examples to https://pymolwiki.org/index.php/set_view

The argument doesn't have to be a string, it can also be a list or tuple of floats. In particular, the return value of cmd.get_view() can be used as input.

Cheers,
  Thomas


> On Apr 29, 2020, at 8:58 PM, <lei...@sb...> <lei...@sb...> wrote:
> 
> Feature request for Wiki: please add an Example below “PyMol API” like:
>  
> cmd.set_view ("-0.219962522,0.763355076,-0.607366502,0.878539860,0.425617725,0.216765702,0.423973948,-0.485916167,-0.764265418, 0.001047601,0.000947788,-48.208724976,-24.094066620,-41.117546082,2.001868963,-84.735671997,181.151062012, -20.000000000")
>  
> and state N.B. that it’s a vector in a string.   The 9-digit decimal precision is probably not needed, as there aren’t a billion pixels in an image.  Even ray-tracing doesn’t need that level of precision.  
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] moving an object and keep others

[杨海滨 <yh...@16...>]

Firstly, select the one that u want to move, then click Action-drag coordinates, click shift without releasing when u move your target.




| |
杨海滨
|
|
邮箱：yh...@16...
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签名由 网易邮箱大师 定制

On 04/30/2020 13:35, C.J. wrote:


Hi,


I'm new to pymol. My pymol version is "PyMOL 2.3.0 Open-Source". After opening two pdb files, how can I keep one object and move another one using mouse? Thank you!


Jianhao

[PyMOL] moving an object and keep others

[C.J. <bi...@gm...>]

Hi,

I'm new to pymol. My pymol version is "PyMOL 2.3.0 Open-Source". After
opening two pdb files, how can I keep one object and move another one using
mouse? Thank you!

Jianhao

Re: [PyMOL] Wait for processing to complete before invoking new commands

[<lei...@sb...>]

Thanks, I was able to resolve the issue by placing refresh before the png
command, and not using sleep.   Sleep used anywhere before or after png
caused a one-ligand lag in the ligand in the image and the ligand name for
the next ligand.   Refresh resulted in very fast image generation and IO to
disk, without the time delay.   Sleep mixed up ligands and image having the
wrong ligand-specific filename.    

 

 

 

 

From: Tamas Hegedus <bio...@gm...> 
Sent: Wednesday, April 29, 2020 10:40 PM
To: pym...@li...
Subject: Re: [PyMOL] Wait for processing to complete before invoking new
commands

 

Something is fishy... as I do not expect this to happen. I have never
experienced this problem.
I made different types of mistakes resulting in such a phenomenon.
* using a for loop and in the command, loading the ligand, I did not
inserted the loop variable into the file name
(e.g. I used lig_1.pdb instead of "lig_%i.pdb" % ix)
* it was not with vina (difficult to imagine this situation), but once I
generated a set of pdb files with the same coordinates

On the other hand:
https://pymolwiki.org/index.php/Sync




On 4/30/20 5:09 AM, lei...@sb...
<mailto:lei...@sb...>  wrote:

I am writing png images for many docked ligands but all the png files have
the same image - even though the file names are different for the
ligand_out.pdbqt files.   So PyMol is getting ahead of itself and quickly
looping through all the code and dumping the same image but with different
files names since the image buffer never caught up.   Thus, I will need to
programatically wait for each png to be generated, and once the png command
is finished, I can move to the next ligand.   

 

What command can be used to instruct PyMol to finish its processing before
taking on new commands, either that or e.g. 5 sec pause? I will need to use
this command right after the png command.






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[PyMOL] Two disparate H-bond methods (docked ligand & receptor)

[<lei...@sb...>]

I located two methods for assessing number of H-bonds between a receptor &
dock ligand.   The first method results in the usual dashed yellow lines for
objects HBA and HBD, depending on what was found.

 

The second method (bottom) shows the # H-bonds if a distance is greater than
a radius.   However, these methods (obviously differ).   For a given ligand
the first shows 2 bonds and the second lists only one (and it's not the 3.2
setting, since raising that to 3.5 didn't make them the same).   

 

The dilemma is that I either need to fetch the total count from the first
method, or draw the bonds that are identified by the second, since the first
method only draws objects and the second only enumerates.

 

cmd.bg_color("white")

cmd.h_add("prot")

cmd.select("don","(elem n,o and (neighbor hydro))")

cmd.select("acc","(elem o or (elem n and not (neighbor hydro)))")

cmd.dist("HBA","(lig and acc)","(prot and don)","3.2")

cmd.dist("HBD","(lig and don)","(prot and acc)","3.2")

cmd.delete("don")

cmd.delete("acc")

cmd.hide("(hydro)")

cmd.hide("labels","HBA")

cmd.hide("labels","HBD")

cmd.show("surface","prot")

 

 

sele1 = "lig & (donors | acceptors)"

sele2 = "prot & (donors | acceptors)"

radius = 3.5

D = cmd.find_pairs(sele1, sele2, mode = 1, cutoff = radius)

print("number of h-bonds: ", len(D)) 

 

Re: [PyMOL] Wait for processing to complete before invoking new commands

[Tamas H. <bio...@gm...>]

Something is fishy... as I do not expect this to happen. I have never 
experienced this problem.
I made different types of mistakes resulting in such a phenomenon.
* using a for loop and in the command, loading the ligand, I did not 
inserted the loop variable into the file name
(e.g. I used lig_1.pdb instead of "lig_%i.pdb" % ix)
* it was not with vina (difficult to imagine this situation), but once I 
generated a set of pdb files with the same coordinates

On the other hand:
https://pymolwiki.org/index.php/Sync



On 4/30/20 5:09 AM, lei...@sb... wrote:
>
> I am writing png images for many docked ligands but all the png files 
> have the same image – even though the file names are different for the 
> ligand_out.pdbqt files.   So PyMol is getting ahead of itself and 
> quickly looping through all the code and dumping the same image but 
> with different files names since the image buffer never caught up.   
> Thus, I will need to programatically wait for each png to be 
> generated, and once the png command is finished, I can move to the 
> next ligand.
>
> What command can be used to instruct PyMol to finish its processing 
> before taking on new commands, either that or e.g. 5 sec pause? I will 
> need to use this command right after the png command.
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Wait for processing to complete before invoking new commands

[<lei...@sb...>]

I am writing png images for many docked ligands but all the png files have
the same image - even though the file names are different for the
ligand_out.pdbqt files.   So PyMol is getting ahead of itself and quickly
looping through all the code and dumping the same image but with different
files names since the image buffer never caught up.   Thus, I will need to
programatically wait for each png to be generated, and once the png command
is finished, I can move to the next ligand.   

 

What command can be used to instruct PyMol to finish its processing before
taking on new commands, either that or e.g. 5 sec pause? I will need to use
this command right after the png command.

Re: [PyMOL] [EXTERNAL] Number of parameters is off for cmd.set_view?

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Your attached Python script was scrubbed by my email server.
It might be best to paste the script into your e-mail message.

You might have picked up hidden codes in your copy and paste operations.

You could try the roundview.py script described 20% of the way down on 
this website https://github.com/MooersLab/EasyPyMOL. It rounds off the
the numbers returned by get_view() and returns them on a single
line to make them easier to reuse at the PyMOL prompt, in pml scripts,
and in python scripts. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: lei...@sb... [lei...@sb...]
Sent: Wednesday, April 29, 2020 1:40 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Number of parameters is off for cmd.set_view?

In the GUI command line, I entered get_view and got the following

set_view (\
    -0.219962522,    0.763355076,   -0.607366502,\
     0.878539860,    0.425617725,    0.216765702,\
     0.423973948,   -0.485916167,   -0.764265418,\
     0.001047601,    0.000947788,  -48.208724976,\
   -24.094066620,  -41.117546082,    2.001868963,\
   -84.735671997,  181.151062012,  -20.000000000 )


However, in my filename.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__filename.py&d=DwQFAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=4zwTbg5t3EDmk7X-dupw3uh7VzTs8TNQZfhZ-kqtd6c&s=Xvp3Zs559FaMsTCNKwCEaX9jhtild2uDUtRerfwI7tM&e=>, use of the command

cmd.set_view (\
    -0.219962522,    0.763355076,   -0.607366502,\
     0.878539860,    0.425617725,    0.216765702,\
     0.423973948,   -0.485916167,   -0.764265418,\
     0.001047601,    0.000947788,  -48.208724976,\
   -24.094066620,  -41.117546082,    2.001868963,\
   -84.735671997,  181.151062012,  -20.000000000 )

Returned the error message:

TypeError: set_view() takes from 1 to 5 positional arguments but 18 were given

[PyMOL] For set.view(), there's a Wiki example for the GUI, but not the PyMol API

[<lei...@sb...>]

Feature request for Wiki: please add an Example below "PyMol API" like:

 

cmd.set_view
("-0.219962522,0.763355076,-0.607366502,0.878539860,0.425617725,0.216765702,
0.423973948,-0.485916167,-0.764265418,
0.001047601,0.000947788,-48.208724976,-24.094066620,-41.117546082,2.00186896
3,-84.735671997,181.151062012, -20.000000000")

 

and state N.B. that it's a vector in a string.   The 9-digit decimal
precision is probably not needed, as there aren't a billion pixels in an
image.  Even ray-tracing doesn't need that level of precision.  

Re: [PyMOL] Number of parameters is off for cmd.set_view?

[Tamas H. <bio...@gm...>]

please see <https://pymolwiki.org/index.php/Set_View>
https://pymolwiki.org/index.php/Set_View

set_view (...)  where ... is 18 floating point numbers
cmd.set_view(string-or-sequence view) !!! you provided 18 floating point 
numbers here and not a string or sequence.

On 4/29/20 8:40 PM, lei...@sb... wrote:
>
> In the GUI command line, I entered get_view and got the following
>
> set_view (\
>
>     -0.219962522,    0.763355076, -0.607366502,\
>
>      0.878539860,    0.425617725, 0.216765702,\
>
>      0.423973948,   -0.485916167, -0.764265418,\
>
>      0.001047601,    0.000947788, -48.208724976,\
>
>    -24.094066620,  -41.117546082, 2.001868963,\
>
>    -84.735671997,  181.151062012,  -20.000000000 )
>
> However, in my filename.py, use of the command
>
> cmd.set_view (\
>
>     -0.219962522,    0.763355076, -0.607366502,\
>
>      0.878539860,    0.425617725, 0.216765702,\
>
>      0.423973948,   -0.485916167, -0.764265418,\
>
>      0.001047601,    0.000947788, -48.208724976,\
>
>    -24.094066620,  -41.117546082, 2.001868963,\
>
>    -84.735671997,  181.151062012,  -20.000000000 )
>
> Returned the error message:
>
> TypeError: set_view() takes from 1 to 5 positional arguments but 18 were given
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Number of parameters is off for cmd.set_view?

[<lei...@sb...>]

In the GUI command line, I entered get_view and got the following

 

set_view (\

    -0.219962522,    0.763355076,   -0.607366502,\

     0.878539860,    0.425617725,    0.216765702,\

     0.423973948,   -0.485916167,   -0.764265418,\

     0.001047601,    0.000947788,  -48.208724976,\

   -24.094066620,  -41.117546082,    2.001868963,\

   -84.735671997,  181.151062012,  -20.000000000 )

 

 

However, in my filename.py, use of the command 

 

cmd.set_view (\

    -0.219962522,    0.763355076,   -0.607366502,\

     0.878539860,    0.425617725,    0.216765702,\

     0.423973948,   -0.485916167,   -0.764265418,\

     0.001047601,    0.000947788,  -48.208724976,\

   -24.094066620,  -41.117546082,    2.001868963,\

   -84.735671997,  181.151062012,  -20.000000000 )

 

Returned the error message:

 

TypeError: set_view() takes from 1 to 5 positional arguments but 18 were
given

 

Re: [PyMOL] Script for drawing docked ligand-active site pics

[Thomas E. <te...@gm...>]

Hi,

I wrote a new PyMOL command a year ago to draw protein-ligand interactions
and create publication-quality images. Not exactly what you are looking for
but may be of help. It is already in the PyMOL script repository, so if you
have it you can load the command directly. For more details look at:

https://github.com/tevang/tutorials/tree/master/show_ligand_interactions

-- 

======================================================================

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic

email: te...@gm..., Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>

website: https://sites.google.com/site/thomasevangelidishomepage/

[PyMOL] vector coordinates within same structure

[Kayce T. <to...@du...>]

Hi all,

I'm hoping someone can help me. I'm trying to chart movement through CX-MS on a structure, and I need to find vectors between one position and another. I saw that rotkit may have had a command that would work, but I received a "module not found error" when I tried. I've also looked into Modevectors, but that seems to be between two different structures and I want to use the same structure for different conformational states to show model consistency.

If anyone has any ideas, please let me know!

Thank you,
Kayce


Kayce Alexandra Tomcho


PhD Candidate

Cascio Research Group

Department of Chemistry and Biochemistry

Duquesne University

Re: [PyMOL] Script for drawing docked ligand-active site pics

[Tamas H. <bio...@gm...>]

Hi,

I do not provide a full solution...
I suggest
* try every particular step in pymol, in the command window
* if one step is successful, then put it (finally everything) into a file
* use python commands (not pymol; e.g. cmd.color("blue", "lig_01"))
* run the file either using "run python.file.py" in pymol; in this case 
you can set "argumuments" as regular python variables before running 
"run ..."
* run the file from the shell "pymol -c python.file.py -- arg1 arg_i 
view1.pkl
* if you have several poses in the vina output, I suggest to split them 
(vina_split) convert to pdb (e.g. openbabel) and then load them 
individually into pymol in a for cycle
* before saving png, try/test "ray x, y"; later this can be set in the 
"png" command
* READ the documentation
* use GOOGLE; e.g. "pymol find polar contacts"

You can save your view:
pickle.dump(cmd.get_view(), open(fname, 'wb'))
Load it back:
cmd.set_view(pickle.load(open(fname, 'rb')))


On 4/29/20 6:29 PM, lei...@sb... wrote:
>
> I have two receptors and their active sites for which I need to draw 
> about 70 separate ligand-active site images (.png).  Both active sites 
> are saved in session files (.pse) based on 3D coordinates from pdbqt 
> files after prepping for Vina docking.   The ligand 3D coordinates are 
> based on *_out.pdbqt files from docking with Vina.
>
> After opening a .pse file to show the surface of the active site, the 
> following automated steps are needed:
>
>  1. Open a ligand docking output file, ligandname_out.pdbqt, and
>     automatically orient the active site (the site coordinates jump a
>     little as soon as each ligand docking output file is opened).   So
>     the same active site orientation is needed so images are consistent.
>  2. Adjust the brightness level (mouse thumbwheel) so that each saved
>     image has a consistent look.
>  3. On the ligand, removes valence.
>  4. Change the color of the ligand using ColoràElementsàGreen (carbon)
>  5. On the ligand, FindàPolar contactsàTo any atom (is there away to
>     get counts of H-bonds)
>  6. Save PNG using ligand name.
>
> (need to also programmatically hit Return after code is pasted into 
> command line)
>
> Once I get something that works after pasting the code for the above 6 
> steps into the command line, and discover that the image is saved, I 
> can then write my own code to clone the commands, and substitute all 
> the ligand file names.
>
> Certainly, someone has already written code to autodraw a docked 
> ligand (from Vina) sitting in an active site?
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Script for drawing docked ligand-active site pics

[<lei...@sb...>]

I have two receptors and their active sites for which I need to draw about
70 separate ligand-active site images (.png).  Both active sites are saved
in session files (.pse) based on 3D coordinates from pdbqt files after
prepping for Vina docking.   The ligand 3D coordinates are based on
*_out.pdbqt files from docking with Vina.  

 

After opening a .pse file to show the surface of the active site, the
following automated steps are needed:

 

1.	Open a ligand docking output file, ligandname_out.pdbqt, and
automatically orient the active site (the site coordinates jump a little as
soon as each ligand docking output file is opened).   So the same active
site orientation is needed so images are consistent.
2.	Adjust the brightness level (mouse thumbwheel) so that each saved
image has a consistent look.
3.	On the ligand, removes valence.
4.	Change the color of the ligand using Color-->Elements-->Green
(carbon)
5.	On the ligand, Find-->Polar contacts-->To any atom (is there away to
get counts of H-bonds)
6.	Save PNG using ligand name.

 

(need to also programmatically hit Return after code is pasted into command
line)

 

Once I get something that works after pasting the code for the above 6 steps
into the command line, and discover that the image is saved, I can then
write my own code to clone the commands, and substitute all the ligand file
names.   

 

Certainly, someone has already written code to autodraw a docked ligand
(from Vina) sitting in an active site?  

 

 

Re: [PyMOL] Extract all phi and psi angles

[Jarrett J. <jar...@sc...>]

Hi Neena,

Is this command sufficient?

https://pymol.org/dokuwiki/doku.php?id=command:phi_psi

Best,
Jarrett J

On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>
> Many thanks,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] Extract all phi and psi angles

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

How to extract all peptide dihedral angles (phi and psi) in PyMOL?

Many thanks,
Neena

Re: [PyMOL] Grid mode problem

[Tamas H. <bio...@gm...>]

alter 3n7h, b=0.0

On 4/24/20 4:09 PM, George Tzotzos wrote:
> Thank you both,
>
> Below are the first 3 lines of my script
>
> select 3n7h
> alter all, b=0.0
> set_color color0, [0.30196078431372547,0.0,0.29411764705882354]
>
> I introduced line 1 for the selection of the protein (similarly in the second script).
> Is this line correct because it didn’t get rid of the problem?
>
>>
>>> On 24 Apr 2020, at 14:39, Tamas Hegedus <bio...@gm...> wrote:
>>>
>>> Use a selection in your commands in your scripts. Set the selection to one of your proteins in one of your script and the selection to the other one in the other script.
>>>
>>>
>>> On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:
>>>> Below is a summary of a task I’m trying to implement in pymol
>>>>
>>>> 1. Load 2 proteins
>>>> 2. Align them (align prt1, prt2)
>>>> 3. Use grid_slot to display the proteins side by side
>>>> 4. Load two different scripts (one for each protein)
>>>>
>>>> Step 4 is where I get stuck. Each script is applied to both proteins.
>>>>
>>>> Is there a way to apply each script to one grid only?
>>>>
>>>> Thanks in advance for any suggestions
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Grid mode problem

[George T. <gtz...@me...>]

Thank you both,

Below are the first 3 lines of my script

select 3n7h
alter all, b=0.0
set_color color0, [0.30196078431372547,0.0,0.29411764705882354]

I introduced line 1 for the selection of the protein (similarly in the second script).
Is this line correct because it didn’t get rid of the problem?

> 
> 
>> On 24 Apr 2020, at 14:39, Tamas Hegedus <bio...@gm...> wrote:
>> 
>> Use a selection in your commands in your scripts. Set the selection to one of your proteins in one of your script and the selection to the other one in the other script.
>> 
>> 
>> On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:
>>> Below is a summary of a task I’m trying to implement in pymol
>>> 
>>> 1. Load 2 proteins
>>> 2. Align them (align prt1, prt2)
>>> 3. Use grid_slot to display the proteins side by side
>>> 4. Load two different scripts (one for each protein)
>>> 
>>> Step 4 is where I get stuck. Each script is applied to both proteins.
>>> 
>>> Is there a way to apply each script to one grid only?
>>> 
>>> Thanks in advance for any suggestions
>>> 
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> 
>> 
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 

Re: [PyMOL] Grid mode problem

[Tamas H. <bio...@gm...>]

Use a selection in your commands in your scripts. Set the selection to 
one of your proteins in one of your script and the selection to the 
other one in the other script.


On 4/24/20 3:02 PM, George Tzotzos via PyMOL-users wrote:
> Below is a summary of a task I’m trying to implement in pymol
>
> 1. Load 2 proteins
> 2. Align them (align prt1, prt2)
> 3. Use grid_slot to display the proteins side by side
> 4. Load two different scripts (one for each protein)
>
> Step 4 is where I get stuck. Each script is applied to both proteins.
>
> Is there a way to apply each script to one grid only?
>
> Thanks in advance for any suggestions
>
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> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Grid mode problem

[George T. <gtz...@me...>]

Below is a summary of a task I’m trying to implement in pymol

1. Load 2 proteins
2. Align them (align prt1, prt2)
3. Use grid_slot to display the proteins side by side
4. Load two different scripts (one for each protein)

Step 4 is where I get stuck. Each script is applied to both proteins.

Is there a way to apply each script to one grid only?

Thanks in advance for any suggestions

[PyMOL] How to get all side-chain torsion angles of a protein structure

[Cavi <cav...@ya...>]

Hi all,
I would like to get all the dihedral angles of a protein structure. I'm most especially interested in the side-chain angles. I've only been able to get the phi and psi angles using PyMOL, which is not exactly what I need. Does anyone have a script to calculate the side-chain dihedral angles?
Thanks in advance!
Cheers,Cavi

Re: [PyMOL] incomplete secondary structure

[Thomas H. <tho...@sc...>]

If you need a convenient method for C-alpha only secondary structure assignment, I can recommend SST:

https://pymolwiki.org/index.php/Sst

Cheers,
  Thomas

> On Apr 16, 2020, at 2:50 PM, hon...@bi... wrote:
> 
> When you look at the coordinate file for 3jav in a text editor, you'll see that for the parts of the structure which give you a "AssignSS-Warning: Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha coordinates only, while in the parts which render the secondary structure properly, you have coordinates for all heavy atoms. The header contains secondary structure information only for those residues where full coordinates are available, and the dss command is unable to assign secondary structure from C-Alpha only.
> 
> If you really want to obtain a cartoon representation for the whole molecule, you either have to use a method to determine the secondary structure from C-alpha atoms only, and assign the secondary structure to the molecule using the "alter" command (laborious), or submit your coordinates to a server capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 1.3, https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, caution: you need to submit each chain separately, since the server cannot deal with multi-chain models.
> 
> Annemarie
> 
> 
> Today's Topics:
> 
>    1. incomplete secondary structure (h. adam steinberg)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 15 Apr 2020 10:51:07 -0500
> From: "h. adam steinberg" <h.a...@gm...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] incomplete secondary structure
> Message-ID: <8B4...@gm...>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them as helices when showing the cartoon. Clearly there is something that is not perfect with the deposited cyro structure.
> 
> If I run the dss command, the cartoon structure isn?t fixed, and I get repeats of the following error for each residue from 1-2750 for each chain: 
>  AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  ?
> 
> Does anyone know how I can fix the secondary structure without having to manually assign it to each helix?
> 
> Thanks!
> 
> 
> Adam
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] incomplete secondary structure

[h. a. s. <h.a...@gm...>]

Wow! I am always amazed at the level of knowledge on this list. Thank you both.

> On Apr 16, 2020, at 8:32 AM, Ali Kusay <aku...@un...> wrote:
> 
> Hi Adam, 
>  
> As Annemarie has mentioned you will need a way of generating the backbone for the regions in the structure that have simply been resolved as Ca atoms. Another way to do this is to simple model 3jav on itself using modeller, modeller can make a reasonable guess as to where helices should be based on where the Ca atoms current are. This is quite simple to do and you can construct all chains at the same time, however, without validation I would only recommend using it for visualisation purposes, I have attached an image of what the protein looks like after modelling if you are interested in taking this route.
>  
> Cheers,
>  
> Ali
>  
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>  
> From: "hon...@bi... <mailto:hon...@bi...>" <hon...@bi... <mailto:hon...@bi...>>
> Date: Thursday, 16 April 2020 at 11:13 pm
> To: "pym...@li... <mailto:pym...@li...>" <pym...@li... <mailto:pym...@li...>>
> Subject: [PyMOL] incomplete secondary structure
>  
> When you look at the coordinate file for 3jav in a text editor, you'll see that for the parts of the structure which give you a "AssignSS-Warning: Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha coordinates only, while in the parts which render the secondary structure properly, you have coordinates for all heavy atoms. The header contains secondary structure information only for those residues where full coordinates are available, and the dss command is unable to assign secondary structure from C-Alpha only.
>  
> If you really want to obtain a cartoon representation for the whole molecule, you either have to use a method to determine the secondary structure from C-alpha atoms only, and assign the secondary structure to the molecule using the "alter" command (laborious), or submit your coordinates to a server capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 1.3, https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, <https://protect-au.mimecast.com/s/1oetC0YKPvi46vD6uWIeGJ?domain=mobyle.rpbs.univ-paris-diderot.fr> caution: you need to submit each chain separately, since the server cannot deal with multi-chain models.
>  
> Annemarie
>  
> 
> Today's Topics:
> 
>    1. incomplete secondary structure (h. adam steinberg)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 15 Apr 2020 10:51:07 -0500
> From: "h. adam steinberg" <h.a...@gm... <mailto:h.a...@gm...>>
> To: pymol-users <pym...@li... <mailto:pym...@li...>>
> Subject: [PyMOL] incomplete secondary structure
> Message-ID: <8B4...@gm... <mailto:8B4...@gm...>>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them as helices when showing the cartoon. Clearly there is something that is not perfect with the deposited cyro structure.
> 
> If I run the dss command, the cartoon structure isn?t fixed, and I get repeats of the following error for each residue from 1-2750 for each chain: 
>  AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  ?
> 
> Does anyone know how I can fix the secondary structure without having to manually assign it to each helix?
> 
> Thanks!
> 
> 
> Adam
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> <modelled_helicies.png>

[PyMOL] incomplete secondary structure

[<hon...@bi...>]

When you look at the coordinate file for 3jav in a text editor, you'll see that for the parts of the structure which give you a "AssignSS-Warning: Ignoring incomplete residue" feedback, the coordinate file contains C-Alpha coordinates only, while in the parts which render the secondary structure properly, you have coordinates for all heavy atoms. The header contains secondary structure information only for those residues where full coordinates are available, and the dss command is unable to assign secondary structure from C-Alpha only.

If you really want to obtain a cartoon representation for the whole molecule, you either have to use a method to determine the secondary structure from C-alpha atoms only, and assign the secondary structure to the molecule using the "alter" command (laborious), or submit your coordinates to a server capable of modelling a full atom structure from the Alpha trace (e.g. SABBAC 1.3, https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::SABBAC, caution: you need to submit each chain separately, since the server cannot deal with multi-chain models.

Annemarie


Today's Topics:

   1. incomplete secondary structure (h. adam steinberg)


----------------------------------------------------------------------

Message: 1
Date: Wed, 15 Apr 2020 10:51:07 -0500
From: "h. adam steinberg" <h.a...@gm...>
To: pymol-users <pym...@li...>
Subject: [PyMOL] incomplete secondary structure
Message-ID: <8B4...@gm...>
Content-Type: text/plain; charset="utf-8"

Hi all,

When I open 3jav the backbone shows many helices, but Pymol doesn?t draw them as helices when showing the cartoon. Clearly there is something that is not perfect with the deposited cyro structure.

If I run the dss command, the cartoon structure isn?t fixed, and I get repeats of the following error for each residue from 1-2750 for each chain: 
 AssignSS-Warning: Ignoring incomplete residue /3jav//D/2750  ?

Does anyone know how I can fix the secondary structure without having to manually assign it to each helix?

Thanks!


Adam
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