Questions tagged [3d-structure]
The 3d-structure tag has no usage guidance.
32
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3
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how to add a custom elements into PyMOL visualization?
I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some "holes" in the structure. Say I fetch 1tqn and I want ...
- 165
1
vote
1
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187
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Changing transparency of markers in Chimera X
I am using the software Chimera X to visualize the 3d composition of molecules. I am very new to Chimera and only use it for visualization. The files I'm using are cmm files (xml-formatted) basically ...
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2
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53
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How to analyse qualitatively the penetration ability of particles in spheroids using fluorescent z-stacks?
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I have to establish the penetration profile of particles in tumour spheroids.
For this I have spheroids composed of cells which were exposed to particles, both of which are fluorescently labeled. ...
- 41
3
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2
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47
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Algorithm for counting neighbors
I need an algorithm to process protein chains. The volume size would probably not exceed 30x30x30 angstrom^3.
Say, I have a point cloud of 50,000 points in a 3D space.
I want to count the number of ...
- 624
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1
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49
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Why am I not being able to detect all the bonds in a residue?
Let us consider the first seven atoms of the protein 1CRN.pdb:
...
- 624
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3
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1k
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Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file
As the title summarizes, I am trying to:
Read a PDB file (for example, 1enh.pdb).
Extract the backbone dihedral angles (phi, psi).
Modify the dihedral angles (phi, ...
- 125
2
votes
1
answer
546
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What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?
What is the difference between the I-TASSER, phyre2, and SWISS-model in the 3D tertiary structure?
How do they get the results? When I did a prediction, I got a similar result for the highest template ...
3
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1
answer
90
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How to visualize electron density of a specific part of the protein residue?
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 ...
2
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1
answer
231
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What tool RCSB and AlphaFold use to visualize 3D structures?
I would like to implement on a web page a tool to visualize 3D structures like it is for AlphaFold and RCSB.
A couple of examples:
https://www.rcsb.org/3d-view/7KX9
https://alphafold.com/entry/Q5VSL9
...
- 137
1
vote
1
answer
57
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Site Mutations in a 3D protein structure to locate the core of mutations
I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations to see the hub of ...
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Intrinsically disordered protein
This question has also been asked on Biostars
The position that I have to visualize is in the 2700 position and this position exists in two ranges in https://www.uniprot.org/uniprot/Q12802#...
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0
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3d model of a protein via nucleotide sequence
I really appreciate @Matteo Ferla's detailed answer to my previous question.
I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
- 91
1
vote
1
answer
50
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Best way to dock subset of protein PDB and definition of a ligand
I have extracted residue 45 to 88 from a PDB file (2YRQ).
With that I have a new smaller PDB file. Let's call it 45_88.pdb
And I want to dock it to some other full protein.
My question is what's the ...
- 131
3
votes
2
answers
348
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How to make 3d model of a protein that not exist in PDB?
I'm working on nsSNPs(Non-synonymous single nucleotide polymorphisms) of protein AKAP13 whose PDB not available.
I did one mutation in this protein and I want to show the effect by 3d modeling without ...
- 91
1
vote
1
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179
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Label and labelbox mismatched in Pymol after ray
I would like to ask how to overcome the problem of mismatched boxes and labels (pic). Is there an option focused on this?
thanks
Radim
2
votes
4
answers
663
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How to draw a 3d structure using 3d coordinates from pdb file?
I am trying to create a 3d structure from 3d coordinated from a pdb file.
I am trying to draw 3d coordinates from pdb file "ATOM 1 N VAL A 14 22.692 -27.591 -39.402" and using webgl ...
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6
votes
2
answers
222
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BinaryCIF vs MMTF formats, which one to choose?
Both file formats are advertised as more memory/parsing efficent than old PDB format and its successor mmCIF format, but I can't understand the context (I'm a developer, but pretty new to the field of ...
- 63
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2
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62
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What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?
Since distant homologs often have significant structural changes, meaning the ...
- 21
0
votes
0
answers
189
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Extract only the amino acid residues on the surface of protein structure data
I'd like to use protein structure data from PDBs visualized by Chimera to do two things.
I'd be happy to learn the appropriate tools and methods.
・Mapping information about amino acids present on ...
0
votes
1
answer
43
views
Generating 3D coordinates error
I have been trying to convert a multi entry sdf file to pdb using openbabel. Everytime I check the Generate 3D coordinates box I end up with .ENT files instead of .PDB files. What am I doing wrong.
...
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2
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1
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506
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Where can I visualize Ramachandran plot?
I am using Rampage webserver to obtain a Ramachandran plot. However, the server does not reveal any plot just values (favored, allowed, outlier regions).
Can you recommend other similar web sites?
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1
vote
1
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448
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What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?
I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
- 25
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1
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216
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Reconstruct a protein's 3D structure from a pair-wise distance matrix
What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues?
I think the question is self-explanatory. I know of this method
but it seems that it uses ...
- 111
1
vote
1
answer
136
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Which is the amino acids classification when analyzing the solvent accessibility of a protein?
I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
- 113
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3
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86
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biological fluorescence supervised machine learing
Some general questions...
So it appears with most classification learners one must come up with a series of quantifiable variables to associate with each observation. This might include mean and std ...
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3
votes
1
answer
111
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Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms
I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.
Specifically, I'd like to determine the ...
- 133
2
votes
1
answer
284
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Label protein strucuture residues in Chimera
I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Coulombic electrostatic potential described below where positive charge is blue and ...
- 719
8
votes
2
answers
241
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How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?
I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY.
I ...
- 517
4
votes
1
answer
80
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JSmol - hide "JSmol" logo
I'm using JSmol for my SimRNAweb server. I would like to hide "JSmol" logo from all small visualizations that I have there. I would like to just put information about JSmol under the panel in text.
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Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]
This is an interesting problem - I was wondering if anyone has a creative solution.
So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
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5
votes
2
answers
236
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Tool for predicting interactions in the cell
What tools are available to predict, based on the structure of a certain protein, its interactions within a cell?
For example, I am considering the split GFP protein and I am trying to predict if ...
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5
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Converter between PDB or mmCIF and MMTF
I'd like to test MMTF, a new format for storing biomolecular structures which is promoted by RCSB as a more compact alternative to mmCIF and PDB.
From MMTF FAQ:
How do I convert a PDBx/mmCIF ...
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