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
directories:
benchmark1
benchmark2
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
tutorial/nmr
tutorial/nmr_relaxation
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!!
Regards,
Tony Pemberton
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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/
U.K.
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