Hi John,
Thanks again. PH was 5.2. I've tested it as you suggested. All tables are read
in, and the format of the observed chemical shift is correct. Here is part of
the output:
--------------- cycle= 1 --------------------------------------------------
| Etotal =8430.601 grad(E)=5.111 E(CARB)=8430.601 |
-------------------------------------------------------------------------------
X-PLOR>
X-PLOR> carbon print threshold = 0.0 end
The following Ca or Cb delta secondary
shifts are greater than the cutoff:
(Ca) (obsCa) (rcoilCa) (obsdeltaCa) (calcdeltaCa) (deltadeltaCa)
(obsCb) (rcoilCb) (obsdeltaCb) (calcdeltaCb) (deltadeltaCb)
class ALL
A 2 CYS CA 59.40************ -0.72****** 26.70************ 2.39******
A 4 LEU CA 56.75 55.10 1.65************ 44.05 42.30 1.75************
A 5 VAL CA 62.40 62.30 0.10 -0.31 -0.41 34.97 32.10 2.87 0.72 -2.15
A 6 ALA CA 50.50 52.30 -1.80************ 21.65 19.00 2.65************
A 7 SER CA 56.90 58.20 -1.30 -1.27 0.03 66.10 63.20 2.90 1.38 -1.52
A 8 ASN CA 55.50 52.90 2.60************ 37.10 37.90 -0.80************
A 9 LEU CA 57.90 55.10 2.80 2.98 0.18 42.40 42.30 0.10 -0.29 -0.39
A 10 ASN CA 53.60 52.90 0.70************ 38.40 37.90 0.50************
A 11 LEU CA 55.90 55.10 0.80 -1.85 -2.65 44.00 42.30 1.70 1.91 0.21
A 15 GLU CA 56.80 56.40 0.40 -1.63 -2.03 33.70 29.70 4.00 1.89 -2.11
... etc.
It seems that in some cases the program cannot determine calcdeltaCa/Cb. Why
and what should I do about it?
Also, how should I deal with Cys and His?
Thank you,
Irina.
----- Original Message -----
From: John Kuszewski
To: Irina Nesmelova
Sent: Thursday, January 17, 2008 9:46 PM
Subject: Re: [Xplor-nih] carbon chemical shift error
Hi Irina,
Are you sure you read in the random coil shift table and the 13C shift
expectation table? It's lines 106-124 of sa_mef_dipo.inp.
Also, make sure your observed shift table's format follows the example for
mef--
ASSIgn <five selections, for C(i-1), N(i), CA(i), C(i), and N(i+1), in that
order> <Ca shift in ppm> <Cb shift in ppm>
Finally, are you samples taken at some extreme pH? That would throw off the
random coil values a bit, which would prevent the code from determining the
observed secondary shifts correctly.
You should be able to create a small script that tests all of this:
struct @myprot.psf end
carb
phistep 180
psistep 180
nres <a number bigger than the number of residues>
class all
force 0.5
potential harmonic
@C13SHIFTS:rcoil_c13.tbl
@C13SHIFTS:expected_edited_c13.tbl
@myobservedshifts.tbl
end
flags exclude * include carb end
energy end
stop
The output from this should be small enough for you to notice any error
messages that pop up.
Hope this helps. Let me know if it doesn't!
--JK
On Jan 17, 2008, at 8:54 PM, Irina Nesmelova wrote:
Hi John,
Thank you for your reply. That is exactly what I have asked. And the reason
for this question is that I don't see the difference in CARB energy term if I
change the potential from harmonic to square. The energy is very high
(~9000-10000). I am using the script from mef-dna example (sa_mef_dipo.inp) Is
there some other parameters I have to change?
Thank you,
Irina.
----- Original Message -----
From: John Kuszewski
To: Irina Nesmelova
Cc: xplor-nih at nmr.cit.nih.gov
Sent: Thursday, January 17, 2008 4:37 PM
Subject: Re: [Xplor-nih] carbon chemical shift error
Hi,
I presume you're asking about the CARBonshift energy term.
Do you mean you want to define an error in your observed Ca or Cb
chemical shifts? If so, you can't. The term's accuracy in predicting carbon
shifts from backbone torsion angles is rather low (~ 1ppm, if I remember
correctly) compared to the accuracy of measurement of Ca and Cb chemical
shifts, so there's no point in defining a squarewell that way.
Rather, the carbonshift's squarewell potential works by comparing the
difference between observed and expected shift values relative to the known
accuracy of the prediction surface at each point. These accuracies are
recorded in the same table as the expected secondary chemical shifts.
So all you need to do is turn on the square well potential shape by
calling CARBon SQUArewell, and you're all set.
If I've misunderstood your question, forgive me.
--JK
On Jan 17, 2008, at 5:00 PM, Irina Nesmelova wrote:
Hello,
How can I input the error for carbon chemical shift?
Thank you,
Irina.
_______________________________________________
Xplor-nih mailing list
Xplor-nih at nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
_______________________________________________
Xplor-nih mailing list
Xplor-nih at nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20080118/7f09eb1d/attachment-0001.html
