thesisandpapers

Few tips that will save your time when using Relax* ( https://www.nmr-relax.com ). *d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR , 40 (2), 107-119. *d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR , 40 (2), 121-133.  FILES to load:    NOE, R1, R2, pdb Format of NOE/Rs: name of protein / number / residue / number / atom (N) / value / error COMT    1    GLN    1    N    1.055199602    0.047908918 COMT    2    GLY    2    N    0.628859626    0.020470979 C...

In case of some formatting problems, you can easily change formats on bmrb website: http://www.bmrb.wisc.edu/software/starch/ Usually it's easy even to "make" Sparky format in excel (if you don't know how to do it in terminal), use "Concatenate" command to add text together, for example: Q1N-HN-CA-CB-C, then Sparky format looks like: Assignment w1 w2 w3 w4 w5 Q1N-HN-CA-CB-C 123.046 8.298 53.18113 26.51555 175.4883 G2N-HN-CA-CB-C 103.031 5.632 41.25012 80.24249 176.281 BMRB asks for: Input file must contain column names in the first line. First column must contain residue sequence numbers, second column: residue labels (pref.  PDB Ligand Expo  Component Identifiers). Names of the first two columns are ignored, names of subsequent columns are used for atom names. Data lines (starting from the 2nd line) must contain residue sequence number, label, followed by shift values. ...

Recently I was looking for a software that will give me a nice picture of secondary structure in a single line, that I can use to illustrate residues. I have found: Polyview-2D:  http://polyview.cchmc.org/ That one was quick and what I finally got was: Not really that nice as I wanted. But I didn't have time to create that picture by myself, so then I tried: PDB Sum Click "generate" on the left if you want to upload your own pdb file. For results I had to wait, program runs every hour. That was what I got: And this is great! :-) You can also easily change colour and number of residue per line. Perfect.

I had a problem with Origin recently.. When trying to make a nice column graph with few y values for one x value it automatically gave me a stacked columns like that: And what I wanted were groups. It took me some time to find the solution. Go to > Graph > Layer Contents Highlight all y and group. Apply. Voilà !!!

Firstly, save your movie as png images. You can set_view/get_view to have the right orientation. To save scenes go to > scene > store > F 1/2/3... then > Movie > Program > Scene Loop I use usually: Nutate > 30 deg. over 4 sec. > file > save movie as png images then for 300 images you can easily use http://gifmaker.me/ (quite slow even with highest speed) or https://ezgif.com/maker up to 2000 files (delay time 1 makes a nice speed) or it's easy to find some png to gif conventer online

Useful tip for journal format of thesis. If you want to have multiple reference lists (for example after every chapter), you go to your EndNote > Edit >  Output Styles > New Style/Edit "xxx" then on the left you have "Sections" and you can click "create a bibliography for each section". Then in your Word documents make section page breaks after each References in each chapters. > Page Layout > Breaks > Next Page Go to EndNote in Word and update citations and bibliography with the right style. Works!

Are you exporting peak height from ccpn peak list? Be careful! I think the error is connected with peak picking - if you do that in the program, then should be all right, but if you are importing peaks then you can get a random number in peak height.. That's what I had vs. what should be there:   How to avoid the error: Select all in peak list. Recalc Fit. Parabolic. No. Done.