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John Kuszewski | 1 Dec 2006 02:34
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Re: PASD for structure determination of proteins from solid state data


On Nov 23, 2006, at 8:23 AM, jtn <at> chem.au.dk wrote:

> Dear Xplor-NIH developers,
>
> For some time ago I posted some questions regarding using the PASD/ 
> MARVIN
> facility to determine the structure of a protein from solid state  
> data. Thanks
> a lot, your answers helped a lot. I am now ready to start the  
> calculations, but
> I have some more specific questions for you regarding data formats  
> and specific
> (non-existing) options in PASD. I wondered if there is some  
> documentation out
> there on PASD, alternatively, I hope you can help me...
>
> I think PASD is a very elegant and robust method to handle  
> ambiguous data and
> false peaks and I would prefer using this method. However, for the  
> solid state
> data I work with the ambiguity is very pronounced. I.e. for your  
> case of
> cyanovirin-N you have and assignment degeneracy of >=5 in 5% of the  
> cases and
> degeneracy >= 10 in less than 2% of the cases (as judged from  
> output from
> “initialMatch3dC.tcl”) whereas for my case with solid state data I  
> have
> degeneracy>=5 in ca. 2/3 of the cases and degeneracy>=10 in 1/3 of
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Blanton Tolbert | 6 Dec 2006 02:16
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RNA refinement

Hello,

I would like to refine an RNA molecule using only NOE and scalar
coupling data.  I have searched the egin directory, but the only
stripped down refinement protocol I've found is for protG.  Does
anyone know of a similar protocol that can be used for RNA?  I am new
to xplor-nih having used CNS in the past.  In CNS, there were
significantly less refinement protocols to select from.  Any advice
that can be given will be greatly appreciated.

Thanks,

--

-- 
Blanton Tolbert, Ph.D
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Charles | 6 Dec 2006 15:33

Re: RNA refinement


Hello Blanton--

> I would like to refine an RNA molecule using only NOE and scalar
> coupling data.  I have searched the egin directory, but the only
> stripped down refinement protocol I've found is for protG.  Does
> anyone know of a similar protocol that can be used for RNA?  I am new
> to xplor-nih having used CNS in the past.  In CNS, there were
> significantly less refinement protocols to select from.  Any advice
> that can be given will be greatly appreciated.

You might start with rna_refi/rna_database_refine.inp and strip out the
RDC stuff. You will probably need the database potentials to get
far. Another approach would be to start from dna_refi/refine_full.py,
(again removing rdc stuff).

best regards--
Charles
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gil sal | 8 Dec 2006 11:33
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volume peak calibration

Hello,
I need some help in the following problem.

How can we calibrate the peak volumes to proton-proton distances in xplor-NIH?
The output data from sparky does not have such calibration...prople from sparky forum recommended me to use Aria or Cyana....but I only have xplor-NIH.

please let me know if any of you know how to do in combining sparky data treatment with xplor calculations.
cheers

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Wenyong Tong | 8 Dec 2006 16:55
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Re: volume peak calibration


Hi , 

This is what I also want to know. 

Also there is a Sparky tool-noe2xplor.py  which can
output the Xplor-NIH distance restrains on the website
of Sparky. I dont know whether it is helpful. I am
going to try.

Wenyong

--- gil sal <gil_salgado <at> yahoo.com> wrote:

> Hello,
> I need some help in the following problem.
> 
> How can we calibrate the peak volumes to
> proton-proton distances in xplor-NIH?
> The output data from sparky does not have such
> calibration...prople from sparky forum recommended
> me to use Aria or Cyana....but I only have
> xplor-NIH.
> 
> please let me know if any of you know how to do in
> combining sparky data treatment with xplor
> calculations.
> cheers
> 
>  
> ---------------------------------
> Want to start your own business? Learn how on Yahoo!
> Small Business.>
_______________________________________________
> Xplor-nih mailing list
> Xplor-nih <at> nmr.cit.nih.gov
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
> 

 
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John Kuszewski | 12 Dec 2006 23:31
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Re: volume peak calibration

Hi,

In xplor-nih's marvin code, I just divide the peaks into distance  
bins, based on their relative intensities.
Specifically, the most intense 20% of peaks get distance bounds of  
1.8 - 2.7 A.
The next most intense 30% of peaks get bounds of 1.8 - 3.3 A.
The next most intense 30% of peaks get bounds of 1.8 - 5.0 A.
The least-intense 20% of peaks get bounds of 1.8 - 6.0 A.

Dan Garrett provided this method to me.

Hope this helps.

--JK

On Dec 8, 2006, at 10:55 AM, Wenyong Tong wrote:

>
> Hi ,
>
> This is what I also want to know.
>
> Also there is a Sparky tool-noe2xplor.py  which can
> output the Xplor-NIH distance restrains on the website
> of Sparky. I dont know whether it is helpful. I am
> going to try.
>
> Wenyong
>
> --- gil sal <gil_salgado <at> yahoo.com> wrote:
>
>> Hello,
>> I need some help in the following problem.
>>
>> How can we calibrate the peak volumes to
>> proton-proton distances in xplor-NIH?
>> The output data from sparky does not have such
>> calibration...prople from sparky forum recommended
>> me to use Aria or Cyana....but I only have
>> xplor-NIH.
>>
>> please let me know if any of you know how to do in
>> combining sparky data treatment with xplor
>> calculations.
>> cheers
>>
>>
>> ---------------------------------
>> Want to start your own business? Learn how on Yahoo!
>> Small Business.>
> _______________________________________________
>> Xplor-nih mailing list
>> Xplor-nih <at> nmr.cit.nih.gov
>> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
>>
>
>
>
>
> ______________________________________________________________________ 
> ______________
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> Access over 1 million songs.
> http://music.yahoo.com/unlimited
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RMB Hoffman | 19 Dec 2006 02:48
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How do I know when AtomSel (doesn't) work?

Hello Xplorers:

I'm using version 2.16.0 on the Mac OS X platform.

I've been trying to (completely) restrain a subset of the atoms in a  
(portion of a) single-conformer simulation. Parroting an example from  
Charles' intro presentations:

ivm.fix( AtomSel( '''
                     (name ca or name c or name o or name n or name  
hn) and resi 2:88
                   '''))
....doesn't seem to produce the desired results. While  
troubleshooting this, I found that it was hard to get any kind of  
indication a selection was bogus:

AtomSel("name xxxx")
--produces no error messages in the log file

AtomSel("name xxxx").apply( SetProperty("fric",10.) )
--no errors

AtomSel("").apply( SetProperty("fric",10.) )
--no errors

AtomSel("name xxxxxx")
--does produce error messages in the log file:
%COPYST-ERR: ST2MAX too small. Check input file.
            Offending string:"XXXXXX"
                 with length=    6
            Max allowed length of string=    4

My questions are: am I using the "fix" member correctly? Should I  
expect error messages for my bogus test selections?

Thanks,

ry
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R.M. van der Werf | 19 Dec 2006 15:19
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RDC-refinement with floating alignment tensor

Hi,

I am doing a RDC-refinement of an RNA molecule.
I predicted the axial component and the rhombicity of the alignment
tensor by relating to the gyration tensor.
[Wu, B.; Petersen, M.;Girard, F.; Tessari, M.;Wijmenga S.S. (2006):
J.Biomol. NMR, 35, pp. 103-115]

In Xplor I incorporated these values:
sani coef 0.0 -51.72 0.14 
(first number is addition (a0), second number anisotropy, and third
rhombicity)

In my refinement script I have a floating alignment tensor.
After refinement I do a backcalculation, and see a correlation between
the experimental and backcalculated values of 0.997 !

If I look at the structures, I see the Ayy is along the longest axis of
the molecule (mine is 'rod'-shaped).

What happens? And how can I fix this ?
Azz should be along the longest axis of the molecule. And the
backcalculation should also see this 'error'.

Greetings,
Ramon

--

-- 
R.M. van der Werf
E-mail: R.vanderWerf <at> nmr.ru.nl

Radboud university of Nijmegen
Dept. Biophysical Chemistry (NMR)
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Charles | 19 Dec 2006 15:57

Re: How do I know when AtomSel (doesn't) work?


Hi Ryan--

> 
> AtomSel("name xxxxxx")
> --does produce error messages in the log file:
> %COPYST-ERR: ST2MAX too small. Check input file.
>             Offending string:"XXXXXX"
>                  with length=    6
>             Max allowed length of string=    4
> 
> My questions are: am I using the "fix" member correctly? Should I  
> expect error messages for my bogus test selections?

the maximum length of an atom name string is 4 characters- your's here
is 6 characters- hence the error. For instance, 

AtomSel("name xxxx")

should work fine.

regards--
Charles
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Charles | 19 Dec 2006 16:04

Re: RDC-refinement with floating alignment tensor


Hello Ramon--

> 
> I am doing a RDC-refinement of an RNA molecule.
> 
> In Xplor I incorporated these values:
> sani coef 0.0 -51.72 0.14 
> (first number is addition (a0), second number anisotropy, and third
> rhombicity)
> 
> In my refinement script I have a floating alignment tensor.
> After refinement I do a backcalculation, and see a correlation between
> the experimental and backcalculated values of 0.997 !
> 

that does seem a bit too good to be true.

This is most likely caused by an unphysical configuration of the tensor
atoms. Please make sure that the pseudo-atoms representing the tensor
orientation make up an orthogonal set of axes. i.e.
  (X-O) dot (Y-O) = 0
and so on. 

By the way, this type of error is not possible if the Python interface
is used (correctly).

regards--
Charles
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