Questions tagged [3d-structure]

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1answer
22 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
2
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4answers
92 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 ...
4
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1answer
46 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 ...
0
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2answers
44 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 ...
0
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0answers
24 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 ...
0
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1answer
27 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. ...
2
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1answer
109 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?
1
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1answer
53 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 ...
1
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1answer
111 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 ...
1
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1answer
76 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 ...
1
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3answers
83 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 ...
3
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1answer
74 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 ...
2
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1answer
125 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 Columbic electrostatic potential. I have opened them in two separate windows for comparison....
8
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2answers
97 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 ...
4
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1answer
61 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.
7
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0answers
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 ...
5
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2answers
118 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 ...
9
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4answers
757 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 ...