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Evgeny A. Fadeev | 3 Feb 2004 23:28
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nested loop question

Hello,

i am a little confused about the difference between
 <at>  and  <at>  <at> . according to the online manual (i know it
is not maintained by nih, but still...)  when  <at>  is
used, content of the file is run only once on the
fist pass of the loop containing the  <at>  statement
while  <at>  <at>  would make the included file to be rerun on
each pass. but i had a strange behavior with the
nested loop structure (example attached)

whenever i run the variant with the inner loop (my
example is with a double loop) included from an
external file as  <at>  <at>  (and keeping the comments like
they are now in loop1.inp) xplor complains ("for" -
unexpected command or something like that) - it
actually includes the file, but cannot parse it
however, the included file gets successfully parsed
and run if it does not contain a loop.(i could
include some benign statement like 'display' in the
loop2.inp and it would work fine)

but when i run the same file with the inner loop in
loop1.inp uncommented and line  <at>  <at> loop2.inp removed
the program runs fine, which shows that there is
nothing wrong with the logic, but the inclusion
mechanism fails for some reason.

finally, when i run the inner loop file with  <at>  it
works. and  seems to run the included file on _each_
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Evgeny A. Fadeev | 4 Feb 2004 00:19
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syntax question

hi,
i wonder if somebody could explain what does this
statement do.

 vector show element (resid) ( id $id )

is (resid) clause a selection? if it is, what would
it select?

thank you.

e.
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John Kuszewski | 4 Feb 2004 00:34
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Re: syntax question

Section 2.16.3 of the old xplor 3.1 manual (the printed one,
p. 23) will tell you all about the vector show statement.  

Briefly, your example will cause xplor to spit out the
residue number of the atom that has the internal ID number
of $id.  The (resid) clause is not a selection--it's a 
vector-expression, in the manual's terminology.

--JK

"Evgeny A. Fadeev" wrote:
> 
> hi,
> i wonder if somebody could explain what does this
> statement do.
> 
>  vector show element (resid) ( id $id )
> 
> is (resid) clause a selection? if it is, what would
> it select?
> 
> thank you.
> 
> e.
> 
> _______________________________________________
> Xplor-nih mailing list
> Xplor-nih <at> nmr.cit.nih.gov
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
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kchandra | 5 Feb 2004 17:10
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vmd-xplor

Dear Professor,

   I would like to use VMD-XPLOR
program for simulation and analysis
of our NMR data of sod1 and its
mutants in als. I will be glad
to receive for usage in linux platform.

With thanks

Dr.C.Karunakaran
Postdoc
Biophysics
Medical college of wisconsin
Milwaukee
wi-53226
phone:414-456-4006
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Charles | 5 Feb 2004 17:16

Re: vmd-xplor


> 
>    I would like to use VMD-XPLOR
> program for simulation and analysis
> of our NMR data of sod1 and its
> mutants in als. I will be glad
> to receive for usage in linux platform.
> 

please follow the download and install instructions at
http://nmr.cit.nih.gov/xplor-nih/
and proceed to the example scripts contained in the eginputs
subdirectory. The protG example is probably the simplest.

best regards--
Charles
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Klara Briknarova | 9 Feb 2004 18:42

Is the rdc calculation in xplor-nih correct?

Hello,
I have been using a standard annealing script with TAD from CNS 1.0 that
included sani restraints (only 1 class, HN). Most of the structures had
no sani violations larger than 1 nor 0.1, as listed in the header of pdb
file. However, when I loaded the structures in vmd-xplor and displayed
the dipolar couplings (using the same DFS, Da and R values as for the
calculations), there were usually several violations larger than 1 or
even 2. I was quite surprised by this discrepancy. :( I listed all the
rdc, as calculated by CNS, using the sani print statement (with
threshhold = 0) and indeed, the values differed quite a bit between CNS
and vmd-xplor. I thought that this was perhaps some peculiarity of CNS,
but a sani print statement in xplor-nih (version 2.9.2) gave me
calculated values of rdcs identical to those from CNS, and different
from vmd-xplor!!!
This does not look quite right, does it? Since I was getting two
different sets of calculated rdcs, I wrote my own program to calculate
them from pdb files with ANI residue. My calculated values agree very
well with vmd-xplor values. This suggests that rdcs calculated by the
sani statement in xplor are not quite correct - which makes my very
suspicious about any sani calculations!!! If calculated rdcs are not
quite correct in xplor, then the whole sani energy term may not be doing
a good job! Or how else would it be possible to get different calculated
rdc values from the same Da, R and coordinates?
Please help,
Klara
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Charles | 9 Feb 2004 19:39

Re: Is the rdc calculation in xplor-nih correct?


Hi--

Well I'm glad we seem to get the right answer some of the time...

> I have been using a standard annealing script with TAD from CNS 1.0 that
> included sani restraints (only 1 class, HN). Most of the structures had
> no sani violations larger than 1 nor 0.1, as listed in the header of pdb
> file. However, when I loaded the structures in vmd-xplor and displayed
> the dipolar couplings (using the same DFS, Da and R values as for the
> calculations), there were usually several violations larger than 1 or
> even 2. I was quite surprised by this discrepancy. :( I listed all the
> rdc, as calculated by CNS, using the sani print statement (with
> threshhold = 0) and indeed, the values differed quite a bit between CNS
> and vmd-xplor. I thought that this was perhaps some peculiarity of CNS,
> but a sani print statement in xplor-nih (version 2.9.2) gave me
> calculated values of rdcs identical to those from CNS, and different
> from vmd-xplor!!!

the SANI code in Xplor-NIH and CNS is pretty much identical, so it's
not surprising that they give the same answer.

> This does not look quite right, does it? Since I was getting two
> different sets of calculated rdcs, I wrote my own program to calculate
> them from pdb files with ANI residue. My calculated values agree very
> well with vmd-xplor values. This suggests that rdcs calculated by the
> sani statement in xplor are not quite correct - which makes my very
> suspicious about any sani calculations!!! 

Another option for you would be to use the DIPO term in Xplor-NIH- you
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Charles | 10 Feb 2004 01:36

Re: Is the rdc calculation in xplor-nih correct?


Hello Klara--

> 
> Thank you very much for the prompt response. I put a file named m341.tar
> on the ftp site - please let me know if there is any problem with the
> file. It contains the following:
> 

I figured out the problem with your files: the axis atoms do not
define an orthogonal coordinate system. Using the orthogonalized
coordinates:
ATOM   2440  X   ANI   500       0.489  -7.608  -6.902  1.00  0.00          
ATOM   2441  Y   ANI   500       0.479  -6.591  -7.884  1.00  0.00          
ATOM   2442  Z   ANI   500       0.902  -7.898  -8.223  1.00  0.00          
ATOM   2443  OO  ANI   500       1.166  -7.226  -7.531  1.00  0.00          

I find that vmd-xplor and the SANI term agree well. Here are the
results for the first few residues

                                                SANI   VMD-XPLOR
           8    GLU  HN        8    GLU  N    -18.682  -18.684   
           9    LEU  HN        9    LEU  N      6.192  6.18938   
           11   VAL  HN        11   VAL  N      7.440  7.43588   
           12   ALA  HN        12   ALA  N      8.758  8.7578	   
           13   VAL  HN        13   VAL  N     18.308  18.3081   
           14   GLU  HN        14   GLU  N     16.207  16.2066   
           15   THR  HN        15   THR  N     10.320  10.3172   
           16   LEU  HN        16   LEU  N      7.267  7.26662   
           17   ALA  HN        17   ALA  N     18.766  18.7661
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Evgeny A. Fadeev | 12 Feb 2004 03:57
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noe <R-3> averaging

Hi,
i just have a small question about the use of
<R-3> noe distance averaging option.

i understand that this option calculates
the distance between a proton and another *one* that
is jumping through several sites a lot faster then overall tumbling. (i
emphasised *one* because that follows from the description of analogous
<R-6>
option in the manual
http://atb.slac.stanford.edu/xplor/manual/node358.html#noeaveraging
)

now if i have a methyl group that is rotating through its three minimum
energy sites i have three such protons. should i therefore use scaled
distance restraint

d_scaled = d_raw * N^(-1/6), with N=3 for the three methyl protons.
where d_raw = (cal_const/cross_peak_intensity)^(-1/6)
(or in other words use scaled noe signal to get a contribution from an
individual 'jumping' atom)

or XPLOR does that scaling automatically and i could just use the 'raw'
distance restraint?

Thank you.
Evgeny.
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Evgeny A. Fadeev | 27 Feb 2004 05:34
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%READC-ERR

hi,

in my output i often encounter
 %READC-ERR: multiple coordinates for N atoms

is there a way to avoid it?

thank you

evgeny
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