Paul Hanson | 11 May 17:18 2005

phosphoserine and phosphotyrosine

Hi,
  Is there a way to incorporate phosphoserine (and others) into a structure?  Thanks in advance!

always basic,
pH

Paul Hanson, Ph.D.
Assistant Professor, JFAP
Department of Chemistry
University of New Orleans
New Orleans, LA. 70148

office:  504-280-7336
lab:      504-280-6855
fax:      504-280-6860

Charles | 11 May 23:22 2005

Re: phosphoserine and phosphotyrosine


Hi--

>     Is there a way to incorporate phosphoserine (and others) into a
>    structure?  Thanks in advance!

It certainly has been many times- you may wish to contact a group which
has published XPLOR work which includes phosphoserine. I noticed that
parameters can be generated from this site:
  http://xray.bmc.uu.se/hicup/SEP/

If you find something which works, or which almost works, we would be
very interested in including it in the Xplor-NIH distribution for others
to use.

thanks--

Charles
Charles | 12 May 15:33 2005

Re: phosphoserine and phosphotyrosine


Hi Again--

> 
> >     Is there a way to incorporate phosphoserine (and others) into a
> >    structure?  Thanks in advance!
>  
> It certainly has been many times- you may wish to contact a group which
> has published XPLOR work which includes phosphoserine. I noticed that
> parameters can be generated from this site:
>   http://xray.bmc.uu.se/hicup/SEP/
> 

It turns out that Marius is just now working on a system with
phosphoserine and phosphocysteine. No phosphotyrosine yet. Input files
for topology and parameters can be found at
  http://nmr.cit.nih.gov/xplor-nih/updates/2.10/

We'll probably modify these slightly, but it's a start.

regards--
Charles

--

-- 
Charles Schwieters     email:   Charles <at> Schwieters.org
		       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt

Yufeng | 18 May 21:02 2005
Picon

Python/Tk in Xplor-NIH

Hi Xplorers,

A question about python/Tk interface of Xplor-NIH.

I am testing xplor-nih v.2.10. Installation follows the instructions 
in the INSTALL file. After installation, testDist
gives positive results, claiming all the 145 tests of xplor, 
21 tests of python and 5 tests of tcl passed. But when I run

  xplor -py -pydoc -g 

It gives an ImportError for module Tkinter, which apparently is
the problem of search path setting, which again is a list of

['', '/home/tong/calxplor','/usr/local/xplor/bin.Linux_2.4_i686',
'/usr/local/xplor/python',
'/usr/local/xplor/python/wrappers',
'/usr/local/xplor/python/dist', 
'/usr/local/xplor/python/bin.Linux_2.4_i686', 
'/usr/local/xplor/python/dist/lib/python23.zip', 
'/usr/local/xplor/python/dist/lib/python2.3',
'/usr/local/xplor/python/dist/lib/python2.3/plat-linux2',
'/usr/local/xplor/python/dist/lib/python2.3/lib-tk', 
'/usr/local/xplor/python/dist/lib/python2.3/lib-dynload']

To my supprise, I didn't see .../python/disk/lib/...
directories in the xplor package I installed, which is downloaded
freshly from NIH site. And I am not sure why there should be 
a empty search path as the first element of the list.

For xplor v2.9.4a, it does not gives the same error messege
when I invoke the command, but Tkinter is still not avaible
in the search paths.

So my two questions:
1. How to fix it? Or how to setup in xplor the python distribution
already installed in the system?
2. Should the testDist include a routine to test the graphics interface?

Yufeng

			
Yufeng Tong
Dept. Physiol. & Biophys.
Case Western Reserve Univ.
Cleveland, Ohio 44106
Tel: (216)368-8654 (O)

Charles | 18 May 21:27 2005

Re: Python/Tk in Xplor-NIH


Hi--

> 
>   xplor -py -pydoc -g 
> 
> It gives an ImportError for module Tkinter, which apparently is
> the problem of search path setting, which again is a list of

oops.

> 
> 
> So my two questions:
> 1. How to fix it? Or how to setup in xplor the python distribution
> already installed in the system?

I'll fix it for the next release, and see if there's a simple way to
update the existing package.

> 2. Should the testDist include a routine to test the graphics interface?
> 

indeed. 

sorry about this.
Charles
Charles | 23 May 17:21 2005

Re: D-amino acid


Hi--

> 
> Can anyone help me create a template for a D-amino acids in xplornih, to be 
> more specific a D-CYS. 
> 

Sorry for taking a while to reply- I was waiting for someone with actual
practical experience.

The standard topology file includes the patch LtoD, which changes an L-amino
acid to D-

An example of using the patch is:
  patch LtoD 
      reference=nil=( resid 8 )        ! change to match the correct resid
  end

In the Python interface, I've updated psfGen by adding a new function
dAmino which will change a specified residue form L- to D-. I've placed
this in the updates section of the web site:
http://nmr.cit.nih.gov/xplor-nih/updates/2.10/

Be careful with coordinates- starting with L- coordinate will not
usually work. However, starting from random coordinates as in the
eginput/protG example should work fine.

best regards--
Charles

--

-- 
Charles Schwieters     email:   Charles <at> Schwieters.org
		       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


Gmane