Coloring chains from Python
Hi,
In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures.
Best, Jan
Hi Jan! Depending on whether you want to color all atoms with a particular chain ID, or atoms in the peptide/nucleic acid chain with that ID but not waters, etc. there are two routes:
In the code below I am going to assume you have your color in a variable named color, and the model in a variable named m and that you are coloring chain A.
All atoms with that chain ID for a in m.atoms: if a.residue.id http://a.residue.id/.chainId == ‘A’: a.color = color
All polymer atoms in that chain seq = m.sequence(‘A’) for r in seq.residues: if r: for a in r.atoms: a.color = color
Chimera just doesn’t have the data structures to do this efficiently that ChimeraX has. If the chain is being depicted as ribbon, you would actually set the residue’s color rather than the atom colors.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 31, 2020, at 5:54 AM, Jan Kosinski jan.kosinski@embl.de wrote:
Hi,
In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures.
Best, Jan _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Jan, As far as I know, there is no way to use those special characters as chain IDs — there is no #1:12.’@‘. I don’t know if this helps or not, but Chimera reads columns 73-76 as a “segment ID” and assigns that as an atom attribute (really should probably be a residue attribute). Anyway, if you have values in those columns, the atom spec for segment ID “xyzw” would be: @/pdbSegment=xyzw.
—Eric
On Jan 31, 2020, at 3:16 PM, jan.kosinski@embl.de wrote:
Hi Eric,
OK, this way I know if course, I've just thought I'm missing a way that doesn't require iteraitng through the atoms.
For the 'color' command or stom spec, is there a universal way of escaping any special characters as chain ids such as , (comma) , @, =, : etc? Double quote works only for some of them. Yes, we trying to get a PDB file with 80sth chains working in the Xlink Analyzer 😉
Best, Jan
On Jan 31, 2020 10:16 PM, Eric Pettersen pett@cgl.ucsf.edu wrote: Hi Jan! Depending on whether you want to color all atoms with a particular chain ID, or atoms in the peptide/nucleic acid chain with that ID but not waters, etc. there are two routes:
In the code below I am going to assume you have your color in a variable named color, and the model in a variable named m and that you are coloring chain A.
All atoms with that chain ID for a in m.atoms: if a.residue.id http://a.residue.id/.chainId == ‘A’: a.color = color
All polymer atoms in that chain seq = m.sequence(‘A’) for r in seq.residues: if r: for a in r.atoms: a.color = color
Chimera just doesn’t have the data structures to do this efficiently that ChimeraX has. If the chain is being depicted as ribbon, you would actually set the residue’s color rather than the atom colors.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 31, 2020, at 5:54 AM, Jan Kosinski <jan.kosinski@embl.de mailto:jan.kosinski@embl.de> wrote:
Hi,
In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures.
Best, Jan _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi Eric,
OK! I have just tested your "All polymer atoms in that chain” suggestion and actually it is sufficiently fast and we can now use all kind of weird characters, allowing us to use around 80 chains in the good old PDB format in the good old Chimera ;-)
Yes, indeed, the segments would work too but for now it would be too many changes to Xlink Analyzer.
Thanks, it got us going! Jan
On 3. Feb 2020, at 20:19, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Jan, As far as I know, there is no way to use those special characters as chain IDs — there is no #1:12.’@‘. I don’t know if this helps or not, but Chimera reads columns 73-76 as a “segment ID” and assigns that as an atom attribute (really should probably be a residue attribute). Anyway, if you have values in those columns, the atom spec for segment ID “xyzw” would be: @/pdbSegment=xyzw.
—Eric
On Jan 31, 2020, at 3:16 PM, jan.kosinski@embl.de mailto:jan.kosinski@embl.de wrote:
Hi Eric,
OK, this way I know if course, I've just thought I'm missing a way that doesn't require iteraitng through the atoms.
For the 'color' command or stom spec, is there a universal way of escaping any special characters as chain ids such as , (comma) , @, =, : etc? Double quote works only for some of them. Yes, we trying to get a PDB file with 80sth chains working in the Xlink Analyzer 😉
Best, Jan
On Jan 31, 2020 10:16 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Hi Jan! Depending on whether you want to color all atoms with a particular chain ID, or atoms in the peptide/nucleic acid chain with that ID but not waters, etc. there are two routes:
In the code below I am going to assume you have your color in a variable named color, and the model in a variable named m and that you are coloring chain A.
All atoms with that chain ID for a in m.atoms: if a.residue.id http://a.residue.id/.chainId == ‘A’: a.color = color
All polymer atoms in that chain seq = m.sequence(‘A’) for r in seq.residues: if r: for a in r.atoms: a.color = color
Chimera just doesn’t have the data structures to do this efficiently that ChimeraX has. If the chain is being depicted as ribbon, you would actually set the residue’s color rather than the atom colors.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 31, 2020, at 5:54 AM, Jan Kosinski <jan.kosinski@embl.de mailto:jan.kosinski@embl.de> wrote:
Hi,
In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures.
Best, Jan _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Glad something works. :-)
—Eric
On Feb 3, 2020, at 12:25 PM, Jan Kosinski jan.kosinski@embl.de wrote:
Hi Eric,
OK! I have just tested your "All polymer atoms in that chain” suggestion and actually it is sufficiently fast and we can now use all kind of weird characters, allowing us to use around 80 chains in the good old PDB format in the good old Chimera ;-)
Yes, indeed, the segments would work too but for now it would be too many changes to Xlink Analyzer.
Thanks, it got us going! Jan
On 3. Feb 2020, at 20:19, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote:
Hi Jan, As far as I know, there is no way to use those special characters as chain IDs — there is no #1:12.’@‘. I don’t know if this helps or not, but Chimera reads columns 73-76 as a “segment ID” and assigns that as an atom attribute (really should probably be a residue attribute). Anyway, if you have values in those columns, the atom spec for segment ID “xyzw” would be: @/pdbSegment=xyzw.
—Eric
On Jan 31, 2020, at 3:16 PM, jan.kosinski@embl.de mailto:jan.kosinski@embl.de wrote:
Hi Eric,
OK, this way I know if course, I've just thought I'm missing a way that doesn't require iteraitng through the atoms.
For the 'color' command or stom spec, is there a universal way of escaping any special characters as chain ids such as , (comma) , @, =, : etc? Double quote works only for some of them. Yes, we trying to get a PDB file with 80sth chains working in the Xlink Analyzer 😉
Best, Jan
On Jan 31, 2020 10:16 PM, Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> wrote: Hi Jan! Depending on whether you want to color all atoms with a particular chain ID, or atoms in the peptide/nucleic acid chain with that ID but not waters, etc. there are two routes:
In the code below I am going to assume you have your color in a variable named color, and the model in a variable named m and that you are coloring chain A.
All atoms with that chain ID for a in m.atoms: if a.residue.id http://a.residue.id/.chainId == ‘A’: a.color = color
All polymer atoms in that chain seq = m.sequence(‘A’) for r in seq.residues: if r: for a in r.atoms: a.color = color
Chimera just doesn’t have the data structures to do this efficiently that ChimeraX has. If the chain is being depicted as ribbon, you would actually set the residue’s color rather than the atom colors.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 31, 2020, at 5:54 AM, Jan Kosinski <jan.kosinski@embl.de mailto:jan.kosinski@embl.de> wrote:
Hi,
In the “old” Chimera, is there an efficient way of coloring an entire chain with a single defined color from the Python interface without resorting to runCommand(‘color …') and atom_spec ? The runCommand(‘color …atom_spec ’) makes some issues when special characters are used as chain ids in the atom_spec. I guess I could loop through all atoms of chain but that might be slow for big structures.
Best, Jan _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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