Alignment Problems: check the sequence and the domains

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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2107086a
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Posts: 11
Joined: 2016.04.14 12:57

Alignment Problems: check the sequence and the domains

#1 Post by 2107086a » 2016.08.23 18:47

Hi,

This is my first time using EOM and I want to demonstrate 2 conformers of a protein that fits to the average scattering intensity data. The scattering intensity file that I have for my protein is the data of the protein unbound (Apo) and I have the crystal structure of the protein (bound to cAMP) andThe N-terminal unbound (Apo). When I entered the data for the EOM, I've submitted the N-terminal and C-terminal separately. I've given the full sequence of the protein but the program won't run as it always gives me this response ' Alignment Problems: check the sequence and the domains'

Below is what was written for the whole EOM process. Could anyone see what is wrong? I've checked my sequence and it should be fine.

******* ------------------------------------------------------ *******
******* Advanced Ensemble Optimization Method *******
******* EOM - version 2.1 - (r6759) *******
******* Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2014 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******
Core symmetry? Select one of: (1) p1, (2) p2, (3) p3, (4) p4, (5) p5,
(6) p6, (7) p7, (8) p8, (9) p9, (10) p10, (11) p11, (12) p12, (13)
p13, (14) p14, (15) p15, (16) p16, (17) p17, (18) p18, (19) p19, (20)
p22, (21) p32, (22) p42, (23) p52, (24) p62, (25) p72, (26) p82, (27)
p92, (28) p102, (29) p112, (30) p122, (31) p222 (default: p1) ........ : p2
Overall symmetry? Select one of: (s) Symmetry, (a) Asymmetry, (m) Mix
(default: Mix) ....................................................... : a
Chain type to generate? Select one of: (c) compact-chain, (n)
native-like, (r) random-coil (default: random-coil) .................. : n
Sequence file name? .................................................. : /Users/user/Desktop/bd1971.seq
Number of domains? (max. 50) (default: 0) ............................ : 2
------ Domain 1 ------
PDB file name for the domain ......................................... : /Users/user/Desktop/Ndomain.pdb
Does this PDB contain multiple chains? (default: no) ................. :
Keep the subunit in the original PDB coordinates? (default: no) ...... :
PDB file for D/RNA bound to the subunit (CR for none) ................ :
------ Domain 2 ------
PDB file name for the domain ......................................... : /Users/user/Desktop/Cdomain.pdb
Does this PDB contain multiple chains? (default: no) ................. :
Keep the subunit in the original PDB coordinates? (default: no) ...... :
PDB file for D/RNA bound to the subunit (CR for none) ................ :
Contact conditions file name? ........................................ :
Total number of models to generate (default: 10000) .................. :
File enumeration starting from? (default: 1) ......................... :
Save the generated PDB files? (default: no) .......................... :
Suffix of generated pdb files? (default: eom) ........................ :
Calculate Intensity? (default: yes) .................................. :
Number of harmonics (min. 10, max. 50)? (default: 15) ................ :
Maximum s value (min. 0.1, max. 0.5)? (default: 0.500) ............... : 0.3
Number of points (min. 10, max. 201)? (default: 51) .................. : 100
Run the Genetic Algorithm? (default: yes) ............................ :
How many times (min. 1)? (default: 1) ................................ :
Number of experimental curves to fit? (default: 1) ................... :
Experimental data file name 1? (*.dat) .............................. : /Users/user/Desktop/apo_5mg.dat
Loading values and configuration ...
Number of residues per chain: 400
Alignment Problems: check the sequence and the domains

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Hayds
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Posts: 101
Joined: 2008.05.21 19:01
Location: EMBL, Hamburg

Re: Alignment Problems: check the sequence and the domains

#2 Post by Hayds » 2016.11.17 12:26

Hi,

one typically sees this problem if you have no "flexible" sequence for EOM to generate. There must be some sequence missing between the n-terminal and c-terminal domain PDB files.

So for example, if the sequence is:

AAAAAAAAAABBBBBBBBBBCCCCCCCCCC

and PDB file 1 contains the residues:
AAAAAAAAAA

and PDB file 2 contains the residues:
CCCCCCCCCC

then the missing region:
BBBBBBBBBB

will be built by EOM.

However, if the PDB files contain the following sequence:
PDB 1: AAAAAAAAAABBBBB
PDB 2: BBBBBCCCCCCCCCC

EOM will fail as there is no flexible region definined.

Hope that helps :)

Haydyn

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