because the hcch_tocsy spectrum's different H-H record order, it has to change the axis order which conversion from NMRPipe to Sparky, the post before this...
Hi, Nice to know that we have a NMR group for sparky. I'm a new user learning the NMR assignment. I'm doing the assignment of a 13KDa protein. My questions...
Hi sandra, You are welcome! A suggestion: you can read the sparky's manual, "Automated Protein Backbone Assignment" part. In this part, the author says we can ...
Hello group, Has anyone here used the chimera extension (accelerator = km) to map residue assignments from NOESY spectra onto a structure using chimera? I...
I didn't use the chimera extension before. I can have a try and share with you the success or failure. By the way, there is another extension called peak...
I have tried the chimera extension. I believe you have edited the sparky startup file to include the correct chimera full path name. When I finished, I start...
That is similar to my experience so far. According to the manual, setting the environment variable CHIMERA to the chimera install directory either in the...
Hi all! Any ideas how I can do peak peaking in a cross correlation spectra? I want to have the intensity ratio of the doublets in the spectrum. It's the first...
Hello all! I just found this site and am as green as I could be when it comes to sparky. I've been given a research project - NMR data of a protein - and looks...
I don't know anything about Felix, but it sounds like you have gotten a rather bad deal. If you still have the original raw data from the spectrometer, I...
Thanks, Josh! I emailed the guy about nmr pipe. I'd actually heard of it already just from reading about about all this stuff. You're not kidding about the ...
So, what kind of data are you looking at exactly? I am assuming you are working on backbone/NOESY assignments from the sounds of things. Oh, and rereading...
the sparky startup file is a c-shell script, which setup the envrionment variables for sparky. my chimera is the beta, version 1 build 2065 and is install in :...
Wow! Thanks Josh! I'm gonna look into the book and websites you mentioned. Yes, I'll eventually be trying to do a backbone assignment. It's a protein that's...
As if you are using sparky and python on windows system, I recommend you to do it on a linux system, on which I use sparky with python well. The RedHat linux 9...
It should be starightforward to do. Just set the cursor to find peaks (F8) and pick each peak individually. Use the 'at' accelerator to label each peak...
Thanks Tieying, I know that the uscfdata is what I'm after, the problem I'm having is that when sparky opens the python window, it says it's not running python...
What experiments are you looking at and what exactly is wrong with the spectra? Did they enter enter the sweepwidth incorrectly, or was it referenced...
Hi, Josh! We have a mess of different spectra. We have the raw data and are also figuring that it needs to be re-Fourier transformed. Redtape is currently...
hi all, I've written/adapted some extensions for sparky that might be useful to people on this list. * atomnames.py: some corrections in the atomnames ...
Thanks Eiso, I have uploaded these files to this group "Files" pages. Any adaption about the sparky extension is welcome! Tieying Zhang at SIBS ... ...
The file(MBA2.tar.gz) attached in "File" section is the code and a (minimal) documentation. Note that the program requires large computational resources. We...
Hello all. I have been unable to get sparky to accept an RNA sequence. Using atomnames.py as a guide I input the one-letter residues codes. When I click OK...
Sorry for my less experience, I didn't use the atomnames.py extension before. But as I know, sparky don't check the protein/DNA/RNA name. While you do the...
Has anyone complied sparky from the source? I recently install a new computer with Fedora Core 4, and the prebuild package cann't be installed. I try to...
I got sparky working with fedora core 4. I first had problems with it (just install as normal, extract to a directory) but i managed to get it to work. Firstly...
thank you James! Here's the thing: our lab buy a new computer with cpu is intel P630(p4 3.0GHz, 2M cache, 800MHz bus frequency, HT). When I install Red Hat 9 ...
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