Copy attribute value from one attribute to another
Hello, I have a question with a probably obvious answer but I cannot figure it out. Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value. Sorry in advance if I miss something obvious.
Hi Sean, If the sharing is for Chimera or ChimeraX users, you can save it as an "attribute assignment file" <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> As for reassigning bfactor with the values of some other attribute, you can do it with a short bit of python, which somebody else on the ChimeraX team can provide (soon). You may lose significant digits writing it out in the bfactor column of a PDB file, however. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2022, at 3:39 AM, Sean Connell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have a question with a probably obvious answer but I cannot figure it out.
Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value.
Sorry in advance if I miss something obvious.
The Python would be: for m in session.models: if hasattr(m, 'residues'): for r in m.residues: r.atoms.bfactors = getattr(r, 'seq_conservation', 0.0) Which you could put into a file with a '.py' suffix, and execute in ChimeraX simply by opening it. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 2, 2022, at 10:17 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Sean, If the sharing is for Chimera or ChimeraX users, you can save it as an "attribute assignment file" <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
As for reassigning bfactor with the values of some other attribute, you can do it with a short bit of python, which somebody else on the ChimeraX team can provide (soon). You may lose significant digits writing it out in the bfactor column of a PDB file, however.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2022, at 3:39 AM, Sean Connell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have a question with a probably obvious answer but I cannot figure it out.
Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value.
Sorry in advance if I miss something obvious.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks so much Elaine and Eric. This is very helpful
On 2 Nov 2022, at 19:56, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
The Python would be:
for m in session.models: if hasattr(m, 'residues'): for r in m.residues: r.atoms.bfactors = getattr(r, 'seq_conservation', 0.0)
Which you could put into a file with a '.py' suffix, and execute in ChimeraX simply by opening it.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 2, 2022, at 10:17 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Sean, If the sharing is for Chimera or ChimeraX users, you can save it as an "attribute assignment file" <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
As for reassigning bfactor with the values of some other attribute, you can do it with a short bit of python, which somebody else on the ChimeraX team can provide (soon). You may lose significant digits writing it out in the bfactor column of a PDB file, however.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 2, 2022, at 3:39 AM, Sean Connell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have a question with a probably obvious answer but I cannot figure it out.
Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value.
Sorry in advance if I miss something obvious.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Sean Connell