Perl Scripts & Pulse Sequences

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Please note: The following perl scripts & pulse sequences are offered as is. We hope they are useful to you, but all the standard disclaimers apply. They can and may need to be modified to suit your needs. If you have questions or suggestions contact us and we will try and help!


Perl Scripts:

phe_cent_3.pdb: This perl script outputs the coordinates of the centroid of every phenylalanine ring in a pdb file, and the distances between each pair of centroids. This version works for pdb files that contain a chain specifier (e.g. A, B, C,...) and needs to be modified for some older pdb files that contain no chain specifier.

download phe_cent_3.pl



2D X-Nucleus Decoupled Bruker Avance Pulse Sequences:

The following pulse sequences are standard Bruker 2D homonuclear pulse sequences modifed to decouple an X nucleus in both t1 & t2 dimensions (hence the "xcpd" in thier names). We use these pulse sequences to take 2D DQFCOSY, TOCSY, and NOESY spectra of 15N-labeled proteins. We add a hard 180 degree pulse centered in the t1 delay, and composite pulse decoupling during t2. The modification is pretty trivial, but the pulse sequences are quite useful.

cosydfxcpd.mck X-nucleus decoupled double-quantum filtered COSY, with presaturation and TPPI quadrature detection.

mlvprtpxcpd.mck X-nucleus decoupled TOCSY, with presaturation and TPPI quadrature detection.

noeprtpxcpd.mck X-nucleus decoupled NOESY, with presaturation and TPPI quadrature detection.

mlev19xcpd.mck X-nucleus decoupled TOCSY, with Watergate and TPPI quadrature detection.

noegsf319xcpd X-nucleus decoupled NOESY, with Watergate and TPPI quadrature detection.

Last Revised 01/22/01

©2000 Jamie McKnight