[modeller_usage] error STDEV < 0 (no lig in second template)

[Jacques Zylberg <>]

I have read and understood the problem and the answer.
I have a similar problem : in one template there is a ligand and in the
second
there is no ligand, and thus i think this error is generated... (the
relevant ligand
is an ATP and MG which are present in one template and absent in the
other).
I use gaps to compensate the missing ligands and I still get the error
messages



Dynamically allocated memory at        amprmcns [B,kB,MB]:
16912855   16516.461    16.129
make_re_417_> Restraint type to be calculated:  distance
r_dista_644W> Two basis restraints have means too far apart:
              ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2
NEW_SD1 NEW_SD2
r_dista_644W> Two basis restraints have means too far apart:
              ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2
NEW_SD1 NEW_SD2
r_dista_644W> Two basis restraints have means too far apart:
              ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2
NEW_SD1 NEW_SD2
.....

r_dista_644W> Two basis restraints have means too far apart:
              ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2
NEW_SD1 NEW_SD2
r_dista_644W> Two basis restraints have means too far apart:
              ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2
NEW_SD1 NEW_SD2
stdevs__397E> STDEV < 0:       -0.2287
              Set to 1E-5.
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:
16912855   16516.461    16.129
Starting time                                            : 2004/07/22
14:48:09.689
Closing time                                             : 2004/07/22
14:48:45.264
Total CPU time [seconds]                                 :       0.00


This error message is usually encountered when two residues in the
target
sequence are aligned with two or more template distances that are very
different, so that the corresponding combined restraint cannot be
reproduced
accurately by a cubic spline. Almost invariably, this error occurs when
there is an error in the alignment (ie, one template 'says' a particular

target distance should be close to 10A and the other template says it
should
be 20A). But in your case, it seems something else may be wrong, because

stdev is less than 0. Would you please modify file
$MODINSTALL6v2/modlib/messages.lib from

M 644  3 1
Two basis restraints have means too far apart:
ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2

To (add @S1 in the fourth line, and keep a blank line after the @S1):

M 644  3 1
Two basis restraints have means too far apart:
ICSR  MEAN1   MEAN2   STDEV1  STDEV2  R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2
@S1

And email me the log file output.


I know the message should be more informative and it should print what
the
violating distance is, and some day we will get there ;-)

I hope this helps.

Best, Andrej


--
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry,
and
    California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier)
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232,  4233, 4239
Email ; Web http://salilab.org


> -----Original Message-----
> From: 
> [">">mailto:] On Behalf Of Guittet,
Muriel
> Sent: Friday, March 21, 2003 12:32 PM
> To: 
> Subject: error STDEV < 0:
>
>
> Dear Modellers,
>
> I saw that someone already encoutered that error in the
> modeller digest .. but unfortunately there was no answer (or
> just to use the "output='long'" command what I did without
> any answer) I try to model a protein structure, using 4
> different templates with about 30% of sequence identity with
> the target.
>
> Modeller always send me the same error message:
> r_dista_644W> Two basis restraints have means too far apart:
>
> ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2
>
> stdevs__397E> STDEV < 0: -0.1509
>
> Set to 1E-5.
>
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
>
>
> Could someone explain me the meaning of this and how to fix it?
>
> thanks a lot for your help.
>
> Muriel
>
>




--
Jacques Zylberg - Prof. B. Fischer's lab
Chemistry Department
Bar-Ilan University
Ramat-Gan, Israel

e-mail: 
Phone:  +972-3-5317785