Re: [PyMOL] Loading chempy objects into PyMOL 2.4.0

[Thomas H. <th...@th...>]

Hi Raul,

I suggest to use cmd.load_coords() to add trajectory frames to your model.

https://pymolwiki.org/index.php/Load_coords <https://pymolwiki.org/index.php/Load_coords>

Cheers,
  Thomas


> On Nov 30, 2021, at 21:49, R Mera <rau...@us...> wrote:
> 
> Dear all,
> 
> I am trying to implement a reader for a trajectory format.
> I use cmd.get_model to get the "reference" structure, and then iterate over the trajectory frames, everytime replacing the coordinates of my model with the ones from the trajectory, and then loading the modified model back into PyMOL with cmd.load_model, changing the state every time.
> 
> The issue is, I can't get the sequence view to work correctly (i.e. to display the one-letter code of each residue). This happens even if I don't modify the coordinates at all, like here:
> 
> #This doesn't display the sequence
> for i in range(9):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> On the other hand, if I load only one state for the object, the sequence is displayed correctly:
> 
> #this DOES display the sequence
> for i in range(1):
>    m=cmd.get_model("sele")
>    cmd.load_model(m,"sele2",state=i+1)
> 
> 
> 
> I have tried with the Wiki help and even looking at the cmd code, but I can't find any way of getting this to work. The options for load_model, for instance, have no effect. What I _can_ do is to use:
> 
> cmd.set("seq_view_discrete_by_state",0)
> 
> Which will show the sequence correctly (apparently, the first state always gets the sequence, the others don't).  It is not a good solution, though, as you can't use that sequence to select residues (it will only select them on the first state, _and_ it will take you back to that state).
> 
> Is this possible at all to do? Is it an issue with my PyMOL version? (I am using PyMOL on Fedora [Linux], and it i the version from the Fedora 32 repositories, by the way, although I don't think I am doing anything OS-dependent). 
> 
> Thanks!
> 
> Raul
>  
> 
> -- 
> 
> Prof. Dr. Raúl Mera Adasme
> 
> Facultad de Química y Biología ,
> Universidad de Santiago de Chile (USACH).
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