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gringer ♦
gringer ♦
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Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I can't do that, because for nglview I need to have a special Object. As I'm a newbie, I'd like to address this question to specialists.

At the moment I'm trying to visualise model (structure), not electron density. But the next step is trying to find a package to visualize electron density also. I've just started becoming familiar with some open packages.

Thank You in Advance!

Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I can't do that, because for nglview I need to have a special Object. As I'm a newbie, I'd like to address this question to specialists.

Thank You in Advance!

Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I can't do that, because for nglview I need to have a special Object. As I'm a newbie, I'd like to address this question to specialists.

At the moment I'm trying to visualise model (structure), not electron density. But the next step is trying to find a package to visualize electron density also. I've just started becoming familiar with some open packages.

Thank You in Advance!

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gringer ♦
gringer ♦
  • 15.1k
  • 5
  • 24
  • 83

Hi everyone (moctlymostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of thea specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I couldn'tcan't do that, because for nglview I need to have a special Object. As beeinI'm a newbie, I decidedI'd like to adressaddress this question to specialists.

Thank You in Advance!

Hi everyone (moctly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of the specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I couldn't do that, because for nglview I need to have a special Object. As beein a newbie, I decided to adress this question to specialists.

Thank You in Advance!

Hi everyone (mostly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I can't do that, because for nglview I need to have a special Object. As I'm a newbie, I'd like to address this question to specialists.

Thank You in Advance!

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kitsune_breeze
kitsune_breeze
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How to visualize electron density of a specific part of the protein residue?

Hi everyone (moctly who are interested in structural bioinformatics). I face the problem that I cannot plot the electron density of the specific part of my protein. For the whole protein it is not a problem:

from Bio.PDB import *
import nglview as nv
import ipywidgets


pdbl = PDBList()
path = pdbl.retrieve_pdb_file('1FAT')
parser = MMCIFParser()
struct = parser.get_structure("1fat", path)
view = nv.show_biopython(struct)
view

But when I tried to pick up residues from 10 till 109 (res_list = Selection.unfold_entities(struct, "R")[10:109]) and plot I couldn't do that, because for nglview I need to have a special Object. As beein a newbie, I decided to adress this question to specialists.

Thank You in Advance!