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PiRSquared17 / cing

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What if bugs #175

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Original data plotted at:

http://nmr.cmbi.ru.nl/NRG-CING//data/br/1brv/1brv.cing
(Then go to the molecule view and select the plot labelled:
QUA/RAM/BBC/C12

The new plot looks like attached.
http://nmr.cmbi.ru.nl/~jd/viavia/service/gert/1brv.cing
The script is at:
http://nmr.cmbi.ru.nl/~jd/viavia/service/gert/1brv.cing/1brv/Whatif/check_000.db
The output at:
http://nmr.cmbi.ru.nl/~jd/viavia/service/gert/1brv.cing/1brv/Whatif/DO_WHATIF.ou
t0

-1- The values for BBCCHK are all zero. I bet the database needs to be 
regenerated which is something Gert needs to do for 
me. Relaying this issue per email to Gert now. 
-2- The following messages hint to a bad install:

The file MUTDB.IND can not be read. Installation problem?
No NQA database found.
 SPCATM:           1 1H  
 SPCATM:           2 2H  
 SPCATM:           3 3H  
 SPCATM:           4  O  
 SPCATM:           5  OXT
 SPCATM:           6  O  
 SPCATM:           7 1H  
 SPCATM:           8 2H  
 SPCATM:           9 1HD 
 SPCATM:          10 1HE 
 SPCATM:          11 2H  
 SPCATM:          12 3H  
ERROR reading CCONFI setup file.

-3- The topology probably needs some fixing too for the hydrogens. Below is the 
relevant output section.
SCRIPT<<<< Give the name of the coordinate file :
SCRIPT>>>> model_000.pdb
SCRIPT<<<< Give the set-name (model_000.pdb) :
SCRIPT>>>> xxx
ERROR. HG11 (HG11) does not belong in VAL ( 171) A   0
ERROR. HG12 (HG12) does not belong in VAL ( 171) A   0
ERROR. HG13 (HG13) does not belong in VAL ( 171) A   0
ERROR. HG21 (HG21) does not belong in VAL ( 171) A   0
ERROR. HG22 (HG22) does not belong in VAL ( 171) A   0
ERROR. HG23 (HG23) does not belong in VAL ( 171) A   0
ERROR. HG21 (HG21) does not belong in THR ( 175) A   0
ERROR. HG22 (HG22) does not belong in THR ( 175) A   0
ERROR. HG23 (HG23) does not belong in THR ( 175) A   0
     1 -   10   VAL PRO CYS SER THR  CYS GLU GLY ASN LEU
ERROR. HG21 (HG21) does not belong in ILE ( 188) A   0
ERROR. HG22 (HG22) does not belong in ILE ( 188) A   0
ERROR. HG23 (HG23) does not belong in ILE ( 188) A   0
ERROR. HG12 (HG12) does not belong in ILE ( 188) A   0
ERROR. HG13 (HG13) does not belong in ILE ( 188) A   0
    11 -   19   ALA CYS LEU SER LEU  CYS HIS ILE GLU
Hydrogens/deuteriums skipped in protein: 113

-4- What's the meaning of this section?

Atom too bad for validation  CA
Atom too bad for validation  C
Atom too bad for validation  CB
Atom too bad for validation  N
Atom too bad for validation  CA
Atom too bad for validation  C
Atom too bad for validation  CA
Atom too bad for validation  C
Atom too bad for validation  CA

Ok, I stop debugging here because these bugs might disappear with adding a db.
....

Original issue reported on code.google.com by jurge...@gmail.com on 2 Jun 2009 at 9:34

GoogleCodeExporter commented 9 years ago 
Created another bug report to Gert directly. Db is indeed not functioning.

Original comment by jurge...@gmail.com on 3 Jun 2009 at 7:27

GoogleCodeExporter commented 9 years ago 
Gert promised to make new db tomorrow.

Original comment by jurge...@gmail.com on 8 Jun 2009 at 1:23

GoogleCodeExporter commented 9 years ago 
wi install on G.'s machine itself broke so need to wait for that fix.

Original comment by jurge...@gmail.com on 16 Jun 2009 at 1:48

GoogleCodeExporter commented 9 years ago 
Got a new revision_7040 of WI now for testing.

Original comment by jurge...@gmail.com on 27 Nov 2009 at 8:40

GoogleCodeExporter commented 9 years ago 
Fails because topology file couldn't be found.
Lots of /home/vriend problems still.

Original comment by jurge...@gmail.com on 27 Nov 2009 at 9:08

GoogleCodeExporter commented 9 years ago 
admin/WHATIF.FIG
replace /home/vriend with new location.

dbdata/CCONFI.FIG 
last line should start with 30 or so spaces

Still a problem with:
SCRIPT>>>> %fulchk
ERROR. Validating with protons requires them present

Gert's looking into it.

Original comment by jurge...@gmail.com on 27 Nov 2009 at 1:36

GoogleCodeExporter commented 9 years ago 
Now runs to completion.
> -1- The values for BBCCHK are all zero.
Is no longer a problem.

-2- The following messages hint to a bad install:
# 75 # Warning: Abnormal packing environmesh: 
/Users/vriend/whatif/scatter/scatter: cannot execute binary file
sh: /Users/vriend/whatif/scatter/scatter: cannot execute binary file
sh: /Users/vriend/whatif/scatter/fig2dev: cannot execute binary file
cat: SCATTER.fig: No such file or directory

The current summary changed again dramatically. Of course this might be due to 
a change of the reference database but look at the omega e.g.

To:
 Structure Z-scores, positive is better than average:
  1st generation packing quality :  -3.167
  2nd generation packing quality :  -1.134
  Ramachandran plot appearance   :  -3.073 (poor)
  chi-1/chi-2 rotamer normality  :  -5.091 (bad)
  Backbone conformation          :  -2.676

 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.561 (loose)
  Bond angles                    :   1.371
  Omega angle restraints         :   1.368 (loose)
  Side chain planarity           :   1.296
  Improper dihedral distribution :   1.677 (loose)
  Inside/Outside distribution    :   1.117

from:
 Structure Z-scores, positive is better than average:
  1st generation packing quality :  -3.167
  Ramachandran plot appearance   :  -4.044 (bad)
  chi-1/chi-2 rotamer normality  :  -5.036 (bad)
  Backbone conformation          :  -3.271 (poor)

 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.561 (loose)
  Bond angles                    :   1.371
  Omega angle restraints         :   0.249 (tight)
  Side chain planarity           :   1.296
  Improper dihedral distribution :   1.679 (loose)
  Inside/Outside distribution    :   1.117

Original comment by jurge...@gmail.com on 3 Dec 2009 at 1:47