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 <raul.m...@usach.cl> 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). > _______________________________________________ > 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
_______________________________________________ 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
