Questions tagged [3d-structure]

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Tools and software to visualize the moving cell compartments in 3D

Also asked on biostars I am looking for tools and software that could help me visualize moving cell compartments in 3D where I can go from the cell membrane to the ER, then out with the protein into ...
Saamar's user avatar
  • 9
2 votes
1 answer
79 views

Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?

I was surprised as to how hard it was to find a reference on this among the docs. Does the Protein Data Bank mmcif/pdb-x archival format use Angstrom to specify cartesian x,y,z coordinates of atoms or ...
rtviii's user avatar
  • 364
3 votes
1 answer
85 views

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 ...
jhutar's user avatar
  • 165
1 vote
1 answer
606 views

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 ...
ciru_4011's user avatar
4 votes
2 answers
61 views

How to analyse qualitatively the penetration ability of particles in spheroids using fluorescent z-stacks?

0 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. ...
Timi's user avatar
  • 51
3 votes
2 answers
52 views

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 ...
user366312's user avatar
1 vote
1 answer
51 views

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: ...
user366312's user avatar
7 votes
3 answers
1k views

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, ...
epsilone's user avatar
  • 125
2 votes
1 answer
658 views

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 ...
Sewar Khassawneh's user avatar
3 votes
1 answer
105 views

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 ...
kitsune_breeze's user avatar
2 votes
1 answer
276 views

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 ...
Spartan 117's user avatar
1 vote
1 answer
68 views

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 ...
saamar rajput's user avatar
0 votes
1 answer
36 views

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#...
dachi's user avatar
  • 91
1 vote
0 answers
89 views

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 ...
dachi's user avatar
  • 91
1 vote
1 answer
52 views

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 ...
neversaint's user avatar
3 votes
2 answers
415 views

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 ...
dachi's user avatar
  • 91
1 vote
1 answer
211 views

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
Radim Jaroušek's user avatar
2 votes
4 answers
797 views

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 ...
php.prg's user avatar
  • 33
6 votes
2 answers
245 views

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 ...
ashas's user avatar
  • 63
0 votes
2 answers
62 views

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 ...
TRakesh's user avatar
  • 21
0 votes
0 answers
237 views

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 ...
farinelli's user avatar
0 votes
1 answer
51 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. ...
Shahbaaz's user avatar
2 votes
1 answer
616 views

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?
polonio210's user avatar
1 vote
1 answer
588 views

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 ...
Linda's user avatar
  • 25
1 vote
1 answer
224 views

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 ...
Wise's user avatar
  • 111
1 vote
1 answer
147 views

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 ...
girl101's user avatar
  • 123
1 vote
3 answers
86 views

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 ...
thietpas's user avatar
3 votes
1 answer
120 views

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 ...
Jonathon Byrd's user avatar
2 votes
1 answer
305 views

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 ...
L R Joshi's user avatar
  • 719
8 votes
2 answers
289 views

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 ...
Aalawlx's user avatar
  • 517
4 votes
1 answer
81 views

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.
Marcin Magnus's user avatar
7 votes
0 answers
69 views

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 ...
Noga Aharony's user avatar
5 votes
2 answers
251 views

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 ...
jaslibra's user avatar
  • 524
9 votes
5 answers
1k views

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 ...
marcin's user avatar
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