My software notes

July 19, 2012

[Xplor-NIH] modified residues (protein)

Filed under: xplor/xplor-nih/cns — kpwu @ 1:02 am
Tags: , , ,

I searched the Xplor-NIH mailing list to know how many modified amino acids are supported in Xplor-NIH.

So far, I can see N-terminal acetylation and spin labeled (MTSL) cysteine are documented in the mailing list. I wonder to know if acetylated lysine, phosphorylated serine, threonine and methylation are also supported in Xplor-NIH.

Here is the example of N-terminal acetylation and MTSL-labeled cysteine:

code: ACE = N-terminal acetylation. Xplor-NIH set it as an individual residue
CYSP = spin labeled cysteine.

Steps to do:

  1.  edit your sequence file: (3-letter code, residues are separated by space), add ACE as the first residue and change the desire CYS to CSYP
  2. in typical xplor-nih anneal.py (see such example scripts in xplor-nih home/eginputs), around line 35-45, change to:
    # generate PSF data from sequence and initialize the correct parameters.
    #
    from psfGen import seqToPSF
    #seqToPSF(open(‘xyza.seq’).read())
    seqToPSF(“xyza.seq”, seqType=’prot’, startResid=0)

    –> The original script was marked off and a similar script was shown here. I also alter the number start residue to “0”.  That will be easier for me while doing NOESY assignment without shifting my residue numbers

  3. Then, run “xplor -py anneal.py” to check if the generated template PDB have correct residue numbers and the modified amino acids.

Here is the snapshot of my generated template PDB. (ACE as residue 0, CYSP as residue 2)

December 24, 2010

Install Xplor-NIH 2.26 on new iMac (10.6)

Filed under: mac,softwares and scripts,xplor/xplor-nih/cns — kpwu @ 9:52 am
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A short note for installation of xplor-nih 2.26 on iMac.

Few months ago, I downloaded XPLOR-NIH 2.26 for Mac OS and installed it on my new iMac (core i3, 3.06 GHz). The default configuration script does not include “Intel Core i3”  in the processor list (at xplor-nih-xxx/arch/getDarwinCPU).

The solution to make the configuration is to edit “getDarwinCPU” script. I replaced i5 by i3 at line 21 and keep everything else unchaged.  The configuration script works and an extensive test were performed, no interruption occurred.

Second note on 2/5/2011.
For version of Xplor-NIH 2.27, same edition has to be done to make it run well on my iMac. Some Mac users may have the same problem.
 

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