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how to get started

Tony Pemberton pemberaj at sgisw.bham.ac.uk
Thu May 8 03:03:19 EST 1997

On 7 May 1997, Matthias Jank wrote:

> Hi,
> I would like to start using x-plor for determining nmr solution structures (ok, one to start with  ;-)  ). All I have is the handbook (rather confusing) and an installed version of x-plor 3.1 (whether correctly installed or not I dont know, there is no
> Currently I have two major problems:
> 1. Is there a possibility to figure out, if the program is correctly 
>    and completely installed. (I have some doubts about that, as files    
>    like the "generate_inp" or "generate_template_inp" etc. are nowhere   
>    to be found in the working directory - but everyone in this newsgroup 
>    is talking about them (and if I understood it correctly, they are 
>    using them for generating a file that contains the input parameters.
>    Still there is a file called "xgenerate.inp" but neither I can open
>    it directly nor could I figure out any other way.)

I assume you have the printed manual - X-PLOR version 3.1 A System for
X-ray Crystallography and NMR by Axel T. Brunger

Are you using a UNIX system? If so look at page 355 and check that you
have the minimal directory structure as shown. You will note the


These benchmark tests are useful if you want to quickly check your
installation. One of these tests runs fairly quickly as I remember. There
is also a test directory containing a whole bunch of pretty exhuastive
tests for the program, the runtests.com file runs all these tests.

As regards getting started on NMR structures see chapters 20 & 21 in the
manual and follow the protocols described there.
> 2. Is there any tutorial/handbook/description that gives a step-by-step  
>    instruction on how to start the program, write the first simple      
>    sequence, introduce restraints and define the necessary calculation 
>    protocols? Lets say, some example structure and files, containing all 
>    intermediate results, so that I can run a tutorial of the programm
>    and see, if I come up whith the correct result?

see http://www.NMR.EMBL-Heidelberg.DE/nilges/XplorPrimer/

This is Michael Nilges' primer on X-PLOR. Also see the subdir 


under your installation directory. These contain all the scripts refered
to in chapters 20 & 21 of the manual.

I know all this seems daunting at the outset but stay with it!!


Tony Pemberton

Mr. A.J.Pemberton
c/o Dept. Rheumatology,        Tel:  +44 121-414-3388
Medical School,                Fax:  +44 121-414-6794
The University of Birmingham,  Email: A.J.Pemberton at bham.ac.uk
Birmingham B15 2TT.            www: http://sgisw.bham.ac.uk/~pemberaj/

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