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normal martinize error

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11 years 7 months ago #1115 by alex.bjorling
martinize error was created by alex.bjorling
I get the following errors while using the martinize script. First with the dssp binary:
> ./martinize.py -f 209C.pdb -o 209C_cg.top -x 209C_cg.pdb -dssp ~/structure/dssp-2.0.4-linux-amd64 -p backbone
...
DSSP could not be created due to an error:
unknown option -V
INFO       Writing coarse grained structure.
Traceback (most recent call last):
  File "./martinize.py", line 2176, in <module>
    coarseGrained = ci.cg()
  File "./martinize.py", line 1203, in cg
    beads, ids = cgmap(residue)
  File "./martinize.py", line 211, in cgmap
    return zip(*[cgaver(i) for i in q])                                   # Bead positions           #!#        
  File "./martinize.py", line 195, in cgaver
    mwx,ids = zip(*[((m*x,m*y,m*z),i) for m,(x,y,z),i in b])              # Weighted coordinates     #!#
ValueError: need more than 0 values to unpack
Then, considering the dssp message, with a pre-made dssp output file:
> ./martinize.py -f 209C.pdb -o cg.top -x 209C_cg.pdb -ss 209C.ssd -p backbone
...
Traceback (most recent call last):
  File "./martinize.py", line 2176, in <module>
    coarseGrained = ci.cg()
  File "./martinize.py", line 1203, in cg
    beads, ids = cgmap(residue)
  File "./martinize.py", line 211, in cgmap
    return zip(*[cgaver(i) for i in q])                                   # Bead positions           #!#        
  File "./martinize.py", line 195, in cgaver
    mwx,ids = zip(*[((m*x,m*y,m*z),i) for m,(x,y,z),i in b])              # Weighted coordinates     #!#
ValueError: need more than 0 values to unpack

The dssp output file looks fine to me, and it seems the dssp "-V" message just comes from a version check in the script.

The residues in the pdb are numbered from 4 to 322, but the dssp output numbers them from 1 to 319. Looking at some other threads on here, that doesn't seem to be the problem.

Any other ideas?
Thanks,
Alex

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11 years 7 months ago #1116 by djurre
Replied by djurre on topic martinize error
Since the error message is exactly the same with both methods of dssp-input, I don't think it is due to the dssp. To me it more seems as if something is wrong with the atomistic input. Is it possible that one or more residues is missing an atom? Or maybe even one atoms is missing a position?

Why the dssp gives an error I don't understand. But I'll look into it.

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11 years 7 months ago #1118 by xavier
Replied by xavier on topic martinize error
I agree with Djurre ... could it be you have a missing atom?

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11 years 7 months ago #1121 by alex.bjorling
Replied by alex.bjorling on topic martinize error
I didn't think so, but that could well be. I'll check the pdb properly.

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11 years 7 months ago #1122 by alex.bjorling
Replied by alex.bjorling on topic martinize error

xavier wrote: I agree with Djurre ... could it be you have a missing atom?


Ah, yes, it turns out these pdb files are quite informative if you just read them.
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     ASP A   4    CG   OD1  OD2
REMARK 470     ARG A  70    CG   CD   NE   CZ   NH1  NH2
REMARK 470     GLU A 193    CG   CD   OE1  OE2
REMARK 470     HIS A 196    CG   ND1  CD2  CE1  NE2
REMARK 470     ARG A 310    CG   CD   NE   CZ   NH1  NH2

There were also some missing residues, but I'd seen that already. Is it prudent to add these atoms and residues, then minimize the FG structure before running martinize?

Thanks,
Alex

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11 years 7 months ago #1124 by djurre
Replied by djurre on topic martinize error
You could do that. Since there are only a few atoms per residue missing in your case and the amino acids are not close (?). Keep in mind that this will only give an estimate of the final structure, and you will have judge whether this is good enough.

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11 years 7 months ago #1127 by xavier
Replied by xavier on topic martinize error
Oups, I thought I answered to that yesterday ...

It is not only prudent, it is mandatory to complete the structure. The method best to predict missing segments is a lot function of the length of the segment and the type of structure ... atomistic level would be recommended ...

You might want to look for a better resolved structure ... homology modeling is possible ...

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11 years 6 months ago #1169 by alex.bjorling
Replied by alex.bjorling on topic martinize error

djurre wrote: Why the dssp gives an error I don't understand. But I'll look into it.


This seems intentional - martinize is checking for the error via the return value of os.system(), and the message is supposed to be directed to /dev/null. So dssp just doesn't want it's output redirected for some reason, and there's no real problem. It spooked me, but I calmed down after examining the Protein_A.itp header...

Alex

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