Hi. Okay, it has been awhile since I thought about this stuff, but I am trying to re-learn the origin of what I always called the "anti-diagonal"; i.e. the...
Hi, all, I am looking for the nomenclature for the n-terminal acetyl and C-terminal amine group in TALOS and DYNAMO program. For example, I have a peptide that...
Hi, Frank, Thanks for your reply. I just created a script "act" by modifying the "dynamo/params/protein/gly" script to the following, proc add_act {seg resID}...
Yes, you should be able to add N-terminal acid and C-terminal amine to a DYNAMO structure as custom residue types. However, TALOS will not be able to account...
Dear Frank, Thank you so very much for your quick response. I really appreciate it. I feel pretty ignorant to ask you this: 1) How do I extract the NOE...
Dear Frank, Thank you so very much for your quick response. I really appreciate it. I feel pretty ignorant to ask you this: 1) How do I extract the NOE...
Hi, Frank, Thanks for your reply. I just created a script "act" by modifying the "dynamo/params/protein/gly" script to the following, proc add_act {seg resID}...
Hi Everyone, My name is Marc. I am a graduate student just getting started with biomolecular NMR. I am working on a 6 amino acid peptide that binds to DNA....
I¹m not an expert yet either (I¹m a graduate student too), but I might be able to help with a few things. ... Re: [nmrpipe] my first post Im not an expert...
Hi Marc, If you are running VnmrJ, you can use BioPack to calibrate all the parameters for the triple resonance experiments. Start by running ghn_co and...
DeRose, Eugene (NIH/N...
derose@...
Mar 26, 2009 12:55 am
1879
As fellow Pipers know, "RTFM" means "Read through Frank's Manuals". Some day, they will all be in one place, and well organized. Until then ... * There is a...
Hi, I have used Sparky to assign and integrated the cross peaks from NOE spectra. Now I am looking for the extraction of NOE distances from NOESY. Does anyone...
Oh, by the way, when I said "they will all be in one place, and well organized" ... I meant the manuals, not the Pipers. Pipers are already perfect as they...
Hi, Has anyone added any custom residue into a DYNAMO structure successfully? I am trying to add N-terminal Acetyl group and C-terminal Amide group to DYNAMO...
Here's a crude example that adds a chlorinated alanine residue ... In the directory dynamo/params/protein, I created a new file "ALC", which has the following...
Hi, I have a protein (1LVE.pdb) where part of the sequence numbering uses alphanumeric values. For example, the numbering goes like this: 1,2,3,4 .......
Hi Marc, If you only have 6 residues, you may be able to assign them from the HNCACB only. After all, you don¹t have that many possible combinations! It¹ll...
Hi Sujoy ... this is a good question. Those letters are actually not part of the residue ID field, they are pdb "ICODE" values, used for "insertion" of...
Hi Marc, Since you only have 6 residues there is a pretty good chance you can assign it with only the HNCA. Maybe an additional HN(CO)CA just to be sure about...
The nmrWish code to renumber residues and reset the ICODE to blanks would look something like this: set t [gdbRead table -in 1lve.pdb -pdb] set eList...
Dear Pipers, I wish to simulate 1D spectra using simTimeND. Frank's manual seems straightforward, and I thought I had the necessary params and commands, but...
Mark Foster
foster.281@...
Apr 3, 2009 7:05 pm
1891
Oh No! What have I done? Your usage more or less correct, assuming you have a peak table which includes INDEX X_AXIS XW and HEIGHT columns. ... BUT ... ...
Hello All- I'm wondering if anyone has run into conversion issues for standard Bruker 4D code/acquisitions. I ran a carbon-carbon 4D noesy in TS 2.1 PL3. I...
Greetings ... If conversion is performed via -yMODE Echo-AntiEcho then every pair of adjacent 1D vectors from the original data will be recombined to generate...
Hi, all, I have a gCOSY spectrum taken by Varian 500 MHz. I am following acme.tar instruction to extract the couplings. After extracting the spectrum from the...
Hey, isn't a Varian gCOSY experiment a magnitude-mode one, not phase-sensitive? If so, this surely won't work for either ACME or for diagonal suppression. As...
Hi all, I am a first year graduate student just getting my grips on NMRPipe. I have this H1-N15 HSQC RNA spectrum acquired using a Varian 700Mhz machine. It...
Try changing States-TPPI to echo-antiecho. Â In some cases you may need to reverse the indirect dimension in addition to that. Â Good luck, -David Rovnyak ... ...
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