Help with RanCH

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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jennthedukie
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Help with RanCH

#1 Post by jennthedukie » 2018.04.18 16:53

Hi,

I'm new to using RanCH. So after running the program, I saved the output pdb files. I am looking at two domains with a flexible linker region (A - FL - B). The output files show A and B but not FL. Is this normal? For my research, I need to show FL (interaction between FL and B is important). Is there a way I can do this?

Thank you!

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AL
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Re: The output files show A and B but not FL. Is this normal

#2 Post by AL » 2018.04.18 18:34

jennthedukie wrote:The output files show A and B but not FL.
Do you mean the flexible linker is not present in the file if you open it in a text editor (should be only one CA for each residue) or the linker is not visible if you open it with your pdb viewer (pymol, rasmol...)?

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Re: Help with RanCH

#3 Post by jennthedukie » 2018.04.26 06:21

Hello again,

I opened one of the output pdb file on texteditor and there is only CA for each residue on the linker region. For purpose of my research, the identity of each residue is important and I'm afraid that RanCH does not consider the amino acid types of linker residues when generating random structures. I'm trying to figure out if the linker sequence is important in determining conformations of A and B domain (does the linker sequence bias a particular interdomain interaction). So I am trying to understand how RanCH runs exactly. To rephrase my question:

Does RanCH take the sequence of the linker into consideration when generating pdb output files?

I am running RanCH twice. Input pdb files for A and B domains are kept the same for both runs. But for the first run, I'll put in the sequence file with the wild type linker sequence (let's say KADDNA). For the second run, I'll put in the mutated linker sequence of the same length (let's say AAAAAA) instead of KADDNA but other residues are the same as the first sequence file. Will this make a difference to the structures I will generate?

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Re: Help with RanCH

#4 Post by AL » 2018.04.26 12:18

jennthedukie wrote:Does RanCH take the sequence of the linker into consideration when generating pdb output files?
No, it does not take te sequence into account. However you may choose which CA dihedral angle distribution will be used for all linkers (compact-chain, native-like or random-coil).
jennthedukie wrote:For purpose of my research, the identity of each residue is important and I'm afraid that RanCH does not consider the amino acid types of linker residues when generating random structures.
You might be overinterpreting your results. SAXS is a low resolution method.
jennthedukie wrote:I am running RanCH twice. Input pdb files for A and B domains are kept the same for both runs. But for the first run, I'll put in the sequence file with the wild type linker sequence (let's say KADDNA). For the second run, I'll put in the mutated linker sequence of the same length (let's say AAAAAA) instead of KADDNA but other residues are the same as the first sequence file. Will this make a difference to the structures I will generate?
You may try yourself by running ranch twice with the same with --seed option. I bet the generated models will be identical.

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Re: Help with RanCH

#5 Post by jennthedukie » 2018.04.26 17:04

Is there a software that takes the sequence into account?

[/quote]No, it does not take te sequence into account. However you may choose which CA dihedral angle distribution will be used for all linkers

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I-TASSER

#6 Post by AL » 2018.04.27 11:19

Eh... I-TASSER?

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