Closed GoogleCodeExporter closed 9 years ago
- reformat: whatif.RAMCHK.valueList: 0.17999999999999999 (+- .)
Happens for 1brv_1model pro 172
Fixed by adding another formatting to NTvalue() called self.fmt2 and updated
code through out with revision
335.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 7:37
- link to residues should not have #top in url because it obscures the header
which is needed for
the SUPER fast navigation.
Finding bug in html.py#_navigateHtml->HTMLfile#insertHtmlLink->findHtmlLocation
Fixing by reenabling test_classes.py#test_HTMLfile and looking at results.
Looks like we need to point to the header instead of _top tag:
<body>
<div id="container">
<div id="header">
<h1>1brv_1model.A.PRO172</h1>
<a href="../../../index.html#_top">Home</a>
<a href="../VAL171/index.html#_top">1brv_1model.A.VAL171</a>
<a href="../index.html#_top">UP</a>
<a href="../CYS173/index.html#_top">1brv_1model.A.CYS173</a>
<a href="../../../help.html">Help</a>
<!-- end header --> </div>
<div id="main">
<a id="_top" name="_top"></a>
<div id="left">
<h2 id="PHI">PHI</h2>
<img src="PHI.png" alt=""/>
<p>PHI : average: -47.1 cv: 0.000 || outliers: 0 (models [])</p>
<h2 id="PSI">PSI</h2>
<img src="PSI.png" alt=""/>
...
<!-- end left --> </div>
<!-- end main --> </div>
<br style="clear: both;"/>
<!-- end container --></div>
Fixed by changing the navigation to the header in revision 336.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 8:30
- link to residues should not have #top in url because it obscures the header
which is needed for
the SUPER fast navigation.
Finding bug in html.py#_navigateHtml->HTMLfile#insertHtmlLink->findHtmlLocation
Fixing by reenabling test_classes.py#test_HTMLfile and looking at results.
Looks like we need to point to the header instead of _top tag:
<body>
<div id="container">
<div id="header">
<h1>1brv_1model.A.PRO172</h1>
<a href="../../../index.html#_top">Home</a>
<a href="../VAL171/index.html#_top">1brv_1model.A.VAL171</a>
<a href="../index.html#_top">UP</a>
<a href="../CYS173/index.html#_top">1brv_1model.A.CYS173</a>
<a href="../../../help.html">Help</a>
<!-- end header --> </div>
<div id="main">
<a id="_top" name="_top"></a>
<div id="left">
<h2 id="PHI">PHI</h2>
<img src="PHI.png" alt=""/>
<p>PHI : average: -47.1 cv: 0.000 || outliers: 0 (models [])</p>
<h2 id="PSI">PSI</h2>
<img src="PSI.png" alt=""/>
...
<!-- end left --> </div>
<!-- end main --> </div>
<br style="clear: both;"/>
<!-- end container --></div>
Fixed by changing the navigation to the header in revision 336.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 8:30
- Don't include an orange critique when a red critique is present: e.g. 1brv
omega 176: ORANGE:
violMax: 5.774, RED: fractionAbove: 1.000
Simplified the setMaxColor code but that wasn't the problem.
Fixed bugs in #criticize of DistanceRestraint and DihedralRestraint in revision
337.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 8:59
- Don't include an orange critique when a red critique is present: e.g. 1brv
omega 176: ORANGE:
violMax: 5.774, RED: fractionAbove: 1.000
Simplified the setMaxColor code but that wasn't the problem.
Fixed bugs in #criticize of DistanceRestraint and DihedralRestraint in revision
337.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 8:59
- For the above residue why is CHI1 red? No critique present or so...
Not reproduced.
- for 2hgh rearrange the restraint list to bubble up the red restraints.
In 1brv the red one is on top but the orange are at the bottom.
Solution: use same sorting algorithm as Geerten coded in:
ResidueHTMLfile#_generateRestraintsHtml and use
an extra method for it.
sortListByRogAndKey
While fixing this; also fixed the annotation of the dihedrals in the dihedrals
list in revision 338.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 9:36
- split the chain A for 2hgh; it looks stupid.
40-49 RGUA40 RGUA41 RADE42 RADE43 URA44 RADE45 RCYT46 RCYT47 RADE48 RGUA49
50-59 RGUA50 URA51 RGUA52 RCYT53 RCYT54 RCYT55 MET104 TYR105 VAL106 CYS107 HIS10
8 PHE109
110-119 GLUH110 ASN111 CYS112 GLY113 LYS114 ALA115 PHE116 LYS117 LYS118 HIS119
There's a cut needed between RCYT55 and MET104. The data came from CYANA
dealing only with single chains per molecule.
Fixed in revision 339.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 9:54
- When no atom list (cs) critiques; show no critiques instead of an empty list.
Fixed by adding check:
tableSelection = table.rows(critiqued)
if len(tableSelection.getRows()):
- remove from atom list the link from the critique because it links to
nowhere...
atom.rogScore.createHtmlForComments(self.main)
Recoded from:
<a href="" class="orange">xxx</a>
to:
<font color="orange">xxx</font>
for where there are no refs which is always for now.
While we are here:
A) The columns have been narrowed to all cs values be 50px.
B) I've abbreviated the messages where possible. Geerten please check these
mods; you might not find them
descriptive enough.
Fixed in revision 340.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 11:19
- When no atom list (cs) critiques; show no critiques instead of an empty list.
Fixed by adding check:
tableSelection = table.rows(critiqued)
if len(tableSelection.getRows()):
- remove from atom list the link from the critique because it links to
nowhere...
atom.rogScore.createHtmlForComments(self.main)
Recoded from:
<a href="" class="orange">xxx</a>
to:
<font color="orange">xxx</font>
for where there are no refs which is always for now.
While we are here:
A) The columns have been narrowed to all cs values be 50px.
B) I've abbreviated the messages where possible. Geerten please check these
mods; you might not find them
descriptive enough.
Fixed in revision 340.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 11:19
- enable the cys checks again by refining the cys residue selection in 2 places.
Fixed but left duplication in code in revision 341.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 11:36
- enable the cys checks again by refining the cys residue selection in 2 places.
Fixed but left duplication in code in revision 341.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 11:36
- fails to read 1y4o_1model test case
No model read from pdb:
WARNING: in #PDB2Molecule: CYANA, model 1 incompatible record (ATOM 3049 HZ3
LYS B 283 0.440 20.753 -0.381 1.00 0.00 H )
WARNING: in #PDB2Molecule: CYANA, model 1 incompatible record (ATOM 3188 HZ3
LYS B 292 -13.442 -7.198 0.819 1.00 0.00 H )
WARNING: Total number of warnings: 56
==> PDB2Molecule: new Molecule <Molecule "1y4o_1model" (C:2,R:208,A:3904,M:0)>
from /Users/jd/workspace34/cing/Tests/data/cyana/1y4o_1model/1y4o_1model.pdb
DEBUG: Parsed PDB file
"/Users/jd/workspace34/cing/Tests/data/cyana/1y4o_1model/1y4o_1model.pdb",
molecule <Molecule "1y4o_1model" (C:2,R:208,A:3904,M:0)>
Bug was in example data's lack of ENDMDL record.
Added in revision 342.
WATCH OUT THIS HAPPENS OFTEN WITH HAND EDITED FILES.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 12:15
- skip dssp and shiftx when there are only nucleic acids.
Testing for entry 1a4d. Fixed by adding a check on method
molecule.hasAminoAcid()
- correct nucleic acid data (e.g. for wi) because all get's flagged.
E.g. there is ANGCHK data for this piece of RNA. O wait, that data present is
shown. Voiding this bug item.
Fixed the above in revision 343.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 12:47
That just leaves:
- speed up calculation of dihedrals again.
which I'll create a separate less important issue for.
Original comment by jurge...@gmail.com
on 17 Oct 2008 at 12:53
Original issue reported on code.google.com by
jurge...@gmail.com
on 2 Oct 2008 at 2:35