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Failure in 1j6t Wattos script 1j6t.wcf reading mmCIF #157

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Read mmCIF for this entry specifically.

Original issue reported on code.google.com by jurge...@gmail.com on 19 Jan 2009 at 2:55

GoogleCodeExporter commented 9 years ago 
Looks like only the first model seems to be missing atoms from PO3 that in the 
last model are listed at the end of the coordinate list as:

HETATM 7111  P P    . PO3 C 3 .   ? -15.470 -2.154  13.306  1.00 0.10 ? ? ? ? ? 
200 PO3 ? P    2
HETATM 7112  O O1   . PO3 C 3 .   ? -15.648 -3.567  13.720  1.00 1.44 ? ? ? ? ? 
200 PO3 ? O1   2
HETATM 7113  O O2   . PO3 C 3 .   ? -14.856 -1.857  12.005  1.00 1.47 ? ? ? ? ? 
200 PO3 ? O2   2
HETATM 7114  O O3   . PO3 C 3 .   ? -15.952 -1.070  14.174  1.00 1.48 ? ? ? ? ? 
200 PO3 ? O3   2

Will not request an update from PDB to sync models because the entry is from 
2002.

It only happens when the first model doesn't contain all atoms in the other 
models.
If atoms are absent in subsequent models it's a whole different story and will 
not generate a bug. It will simply be synced (removed from the models that have 
it).

No easy work around possible.

This is a known bug in Wattos and will not be resolved.

Original comment by jurge...@gmail.com on 19 Jan 2009 at 3:12

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 28 Jan 2009 at 4:00

GoogleCodeExporter commented 9 years ago 
Let's keep this issue open for a while even if it can't be fixed easily.

Original comment by jurge...@gmail.com on 28 Jan 2009 at 4:01

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 28 Jan 2009 at 4:04

GoogleCodeExporter commented 9 years ago 
Entries with this issue can be found using the following one-liner:

/star/ find . -name "[0-9][a-z0-9][a-z0-9][a-z0-9].log" | xargs grep "NRG issue 
157" | cut -c3-6

./1j6t/1j6t.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./1jtw/1jtw.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./1dx1/1dx1.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./1f8h/1f8h.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./1vrc/1vrc.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./2con/2con.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157
./2exg/2exg.log:ERROR: This was found in for instance entry 1j6t for the PO3 
group and was reported in NRG issue 157

These kind a errors are now annotated to:
http://code.google.com/p/nmrrestrntsgrid/source/browse/trunk/nmrrestrntsgrid/dat
a/problemEntryList.csv

Original comment by jurge...@gmail.com on 28 Jan 2009 at 5:54

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 29 Jan 2009 at 12:38

GoogleCodeExporter commented 9 years ago 
Issue 225 has been merged into this issue.

Original comment by jurge...@gmail.com on 23 Sep 2009 at 2:02

GoogleCodeExporter commented 9 years ago 
Asking PDB for help.

Original comment by jurge...@gmail.com on 1 Dec 2009 at 2:01

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 1 Dec 2009 at 2:04

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 1 Dec 2009 at 2:08

GoogleCodeExporter commented 9 years ago 
Chris said: Entry 2k9y has this problem as well.

Original comment by jurge...@gmail.com on 1 Dec 2009 at 2:42

GoogleCodeExporter commented 9 years ago 
From PDB:
No, unfortunately, this is not something can be fixed. Authors deposited 
inhomogeneous models in the early 
days. Now, since 2008, we have implemented a new rule that all new NMR entries 
must have homogeneous 
models (same atoms and same residues), but we cannot go back and fix these 
older ones.

I guess I'll need to recode Wattos for this issue.

Original comment by jurge...@gmail.com on 3 Dec 2009 at 8:46

GoogleCodeExporter commented 9 years ago 
I will recode for this issue soon.

Original comment by jurge...@gmail.com on 5 Jan 2010 at 12:38

GoogleCodeExporter commented 9 years ago 
Real soon.

Original comment by jurge...@gmail.com on 20 Sep 2010 at 9:11

GoogleCodeExporter commented 9 years ago 
Fixed in Wattos revissssion 137. Update and compile to Wattos.jar.
I've tested with 1j6t (and 1ai0 2hgh).
Please rerun with: 1j6t 1jtw 1dx1 1f8h 1vrc 2con 2exg 2k9y

Original comment by jurge...@gmail.com on 20 Sep 2010 at 12:29

GoogleCodeExporter commented 9 years ago 
Is the change in there where amber files are read as xxx_ambr.pdb instead of 
xxx_amber.pdb?

Original comment by schulte....@gmail.com on 20 Sep 2010 at 1:51

GoogleCodeExporter commented 9 years ago 
Nop because you made that change right? ;-) You can still have to commit it?

Original comment by jurge...@gmail.com on 20 Sep 2010 at 3:01

GoogleCodeExporter commented 9 years ago 
That's what I thought. It's a quick change though. I tried to commit it, but 
wasn't allowed to because I had changed something (eyes roll). I asked Dimitri 
about it, but we couldn't get it going. We'll keep trying, but we don't have a 
whole lot of spare time either.

I'll process this week's entries, update wattos, and get it working.

Original comment by schulte....@gmail.com on 20 Sep 2010 at 3:11

GoogleCodeExporter commented 9 years ago 
1j6t 1jtw 1f8h 1vrc 2con 2exg 2k9y all processed well. 1f8h (*REVDAT   1   
30-JUN-02 1F8H- before my time) was already processed but needed some presets 
work. There also seem to be more experimental residues than are in the 
structure, but the violations are good and there is now good conversion.

I'm closing this one.

Thanks, Jurgen!

Original comment by schulte....@gmail.com on 22 Sep 2010 at 3:43

GoogleCodeExporter commented 9 years ago 
FYI for completeness: 1dx1 has been obsoleted.

Original comment by schulte....@gmail.com on 22 Sep 2010 at 3:50