linker residue representation

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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abeerasz
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Joined: 2017.08.15 11:28

linker residue representation

#1 Post by abeerasz » 2020.03.24 00:21

Hello everybody,

I am doing eom analysis on a two-domain structure with a linker in between. I entered both the sequence file and the pdb files for both the domains.
The problem is that the output pdb file with the linker only displayed as the central carbon atom (i.e. only one atom per residue) which prevents proper visualisation. The linker residues are from 135-160 with the problem being from residue number 139-160.

I attached the sequence, the two input pdb files and the output pdb.

Thanks in advance,
Abeer
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Domain_1.pdb
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fin.seq
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Domain_2.pdb
(315.5 KiB) Downloaded 20 times
Output.pdb
(141.31 KiB) Downloaded 20 times

Alex
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Joined: 2007.08.09 21:10
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Re: linker residue representation

#2 Post by Alex » 2020.05.27 17:29

I am doing eom analysis on a two-domain structure with a linker in between. I entered both the sequence file and the pdb files for both the domains.
The problem is that the output pdb file with the linker only displayed as the central carbon atom (i.e. only one atom per residue) which prevents proper visualisation. The linker residues are from 135-160 with the problem being from residue number 139-160.
it only models Calpha trace for missing parts. sometimes it is quite inaccurate, since it does not take into account clashes with side chains for obvious reasons..
You can convert c-alpha trace to backbone and then add side chains. for that you would use other packages

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