To answer this for myself!:
Anybody know if there's a way to force the block size in topspin?
topspin has a parameter xdim which you can set for each dimension (just type xdim on the command line) to set the block size.
Than xfb, ft3, ftnd, etc take it as an argument e.g.
ftnd 0 xdim
so setting xdim to something like 64 8 8 for a typical triple resonance expt should give decent performance in analysis I think.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
________________________________________
From: CcpNmr software mailing list [[log in to unmask]] On Behalf Of Brian Smith [[log in to unmask]]
Sent: 26 February 2014 15:24
To: [log in to unmask]
Subject: Re: bruk2ucsf issue in linux mint 64-bit - contouring speed.
Hi Wayne,
We've found that using topspin processed 3rrr data the contouring in
analysis can be very slow. We think this is due to the small block size
that topspin uses in the acquisition dimension (4 points per block)
compared to say AZARA. We can fix this by unblocking the data and
reblocking it, but it's a bit of a faff. So:
Anybody know if there's a way to force the block size in topspin?
Any chance you could look at the contouring code to see if it can be made
less sensitive to the acquisition dimension block size?
Ta,
Brian
On Wed, 26 Feb 2014, Wayne Boucher wrote:
> Hello,
>
> You should not need to run bruk2ucsf at all because you should be able to load up 3rrr files directly in Analysis. (So unless you are also wanting to run Sparky on the data.) In Analysis you select the Bruker option in the "File format" and you select the procs file but you don't have to navigate down into the directory which contains this because it is looked for three levels down, so you should be able to click on the procs file in the file selection table when you navigate into the top Bruker directory for the experiment.
>
> Wayne
>
> On 26 Feb 2014, at 14:37, Fowler, Andrew wrote:
>
>> Hi Dave,
>>
>> Did you make a copy of the bruk2ucsf program - which comes with Sparky -
>> in the pdata/1 directory? That's what you're telling it to run when you
>> type ./bruk2ucsf. I'd try it without the dot (if you have Sparky's bin
>> directory in your path), or type in the full path which is probably
>> something like /usr/local/Sparky/bin/bruk2ucsf or
>> $HOME/Sparky/bin/bruk2ucsf.
>>
>> Cheers,
>> Andrew
>>
>>
>>
>>
>> On 2/26/14 6:36 AM, "L. David Finger" <[log in to unmask]> wrote:
>>
>>> I have recently partitioned my hard drive to add linux mint 64-bit to my
>>> computer. I have downloaded CCPNMR linux 64-bit, and it runs beautifully.
>>> However, when I run the bruker2ucsf conversion program on my 3rrr files,
>>> I receive an error. The following is what I have entered into the
>>> terminal in the pdata/1/ directory of the data set (please bear in mind
>>> that I have copied the program into this directory).
>>>
>>> ./bruk2ucsf 3rrr hf336_trhnca.ucsf
>>> bash: ./bruk2ucsf: No such file or directory
>>>
>>> I have tried to look at the program using the nano and gedit command,
>>> but it is jibberish. I was able to run this program on a 32-bit computer
>>> running ubuntu, but linux mint 64 bit will not. Is there something I must
>>> download to run a script like this? Sorry to take your time with what is
>>> likely a novice problem, but I am pretty new to this linux and CCPNMR
>>> stuff.
>>>
>>> Thanks,
>>> Dave
>>
>>
>>
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--
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
