Hello Mingxuan-- My apologies- we are overdue in delivering a new version of Xplor-NIH, where this issue is fixed. You might grab a (linux) snapshot from
https://bit.niddk.nih.gov/out/toMingxuan-20250304 while I am preparing a proper new release. I believe the snapshot above will also fix your SEP residue issues. Please do let me know if you have further problems. Charles On Mon, 03 Mar 2025 18:35:51 -0500, Mingxuan Jiang wrote: > > [1 <multipart/related (7bit)>] > [1.1 <multipart/alternative (7bit)>] > [1.1.1 <text/plain; Windows-1252 (qu soted-printable)>] > [1.1.2 <text/html; Windows-1252 (quoted-printable)>] > Dear Xplor-NIH team, > > > > I encountered a bug with readNEF from nefTools.py > > > > from nefTools import readNEF > > nef = readNEF(input.nef) # generates PSF information > > > > Creates a chain double the supposed length of the sequence. > * > > (lyr_gen_nef.pdb) > > > > When the sequence is supposed to be: > > 1 A 5 GLU start . . > > 2 A 6 LYS middle . . > > 3 A 7 LEU middle . . > > 4 A 8 PRO middle . . > > 5 A 9 PRO middle . . > > 6 A 10 GLY middle . . > > 7 A 11 TRP middle . . > > 8 A 12 GLU middle . . > > 9 A 13 LYS middle . . > > 10 A 14 ARG middle . . > > 11 A 15 MET middle . . > > 12 A 16 SER middle . . > > 13 A 17 ARG middle . . > > 14 A 18 SER middle . . > > 15 A 19 SER middle . . > > 16 A 20 GLY middle . . > > 17 A 21 ARG middle . . > > 18 A 22 VAL middle . . > > 19 A 23 TYR middle . . > > 20 A 24 TYR middle . . > > 21 A 25 PHE middle . . > > 22 A 26 ASN middle . . > > 23 A 27 HIS middle . . > > 24 A 28 ILE middle . . > > 25 A 29 THR middle . . > > 26 A 30 ASN middle . . > > 27 A 31 ALA middle . . > > 28 A 32 SER middle . . > > 29 A 33 GLN middle . . > > 30 A 34 TRP middle . . > > 31 A 35 GLU middle . . > > 32 A 36 ARG middle . . > > 33 A 37 PRO middle . . > > 34 A 38 SER middle . . > > 35 A 39 GLY middle . . > > 36 A 40 ASN middle . . > > 37 A 41 SER end . . > > 38 B 42 GLY start . . > > 39 B 43 LEU middle . . > > 40 B 44 TYR middle . . > > 41 B 45 ARG middle . . > > 42 B 46 SEP middle . . > > 43 B 47 PRO middle . . > > 44 B 48 PRO middle . . > > 45 B 49 LEU middle . . > > 46 B 50 PRO middle . . > > 47 B 51 GLY end . . > > I took a brief look at the python script in neftools.py, and I think the ‘end’ > marker does not stop the code from continuing and making the chain twice as > long every time readNEF is called. > > > > How should we resolve this in the code? > > > > > > Thank you. > > > > Best wishes, > > Mingxuan Jiang > > > > Postgraduate > > Creixell Lab > > CRUK Cambridge Institute > > University of Cambridge > > > > A black background with a black square > > Description automatically generated with medium confidence > > > > > > > > > ------------------------------------------------------------------------------- > > To unsubscribe from the XPLOR-NIH list, click the following link: > Bad URL Removed - see why - > https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1 > [1.2 image001[38].png <image/png (base64)>] > [1.3 image002[88].png <image/png (base64)>] > [2 running_scripts.zip <application/zip (base64)>] > [3 script.sh <application/octet-stream (base64)>] > [4 runTalos.sh <application/octet-stream (base64)>] > [5 input.nef <application/octet-stream (base64)>] > [6 lyr_gen_nef.pdb <application/octet-stream (base64)>] ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
