Subject: Re: Moving assignment from CCPN to sparky
From: nichtverstehen
Date: Feb 8, 2013

Previous: 873

Youre welcome. When you open Sparky there should be a Pointer mode window that pops up. There are shortcuts for each of the modes using the Function keys on your keyboard, but you can also choose them from that window. F11 will put you in zoom mode which will let you zoom in on a selected area. I usually just drag the scroll bars to move, but I dont know of a way to move without using the scroll bars (except for 3D data, and then you can use zu and zd to go through the planes). You can also adjust the Aspect ratio by typing vt and then editing it. This can help if your proton dimension is more squished than you would like it to be, relative to your other dimensions.

~ Kari

--- In nmr_sparky@yahoogroups.com , Martin Ballaschk wrote:

Hi Kari,

thanks for the help. There is some flexibility in the CCPN export routines, and I could easily reverse the order of the column. Now after using rp everything looks pretty. :)

Is there actually a different way of moving around and zooming than using the scroll bars and zo/zi?

Regards
Martin

On 08.02.2013, at 19:02, nichtverstehen wrote:

That peak list looks close to what Sparky will want. The only problems you might have is that Sparky will expect w1 to be 15N and w2 to be 1H, which is more of a problem of ordering the columns than to do with the header. Also, Sparky generally will write the assignment as T31N-HN instead of having the residue assignment twice, but Im not sure that will cause you any problems. Try using the command rp to read in the peak list, and this should generate the peaks on your spectra. If they look like the axes are flip-flopped you will probably need to reverse the order of the columns of 15N and 1H. You can do this through command line with:

gawk {print $1, $3, $2} Nhsqc.list newName.list

You many also then need to at least change the order of the assignment in the name, so that it expects the N assignment first, or else the labeling will certainly be reversed.

Hopefully that helps.

~ Kari

--- In nmr_sparky@yahoogroups.com , Martin Ballaschk wrote:

Dear Sparky users,

after assigning a protein in CCPN I want to move the NH/N assignment of my root spectrum (HSQC) to Sparky. What does it need for that?

* the HSQC spectrum itself: a ucsf file ï¿½ that was easy to import.
* a resonance list: Im not sure what that is for.
* a peak list?

I managed to load the spectrum and also a resonance list, but the assigned peaks did not (magically) appear in my spectrum. Can I generate peaks from the resonance list? I did not find a function to import a peak list, I guess thatd be all I need. And it would suit me better than generating peaks from the resonance list.

I generated peak lists from CCPNs format converter which have the format:

Assignment w1 w2 Height Volume
T31HN-T31N 9.879 125.768 1.70E+05 1.42E+06
.
.
.

Does that look right?

Any help (also some kind of FAQ/HOWTO) would be heavily appreciated, as Im pretty new to Sparky and dont really know where to start.

Regards,
Martin