I’m trying to run contact on a protonated pdb file and want to ignore
hydrogens, but when I use the HEXCLUDE keyword I still get hydrogen contacts.
Is it a bug, or am I doing it wrong? Pasting the top of the log file below.
Thanks
Kevin
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### CCP4 8.0.017: CONTACT version 8.0.017 : ##
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User: kjude Run date: 30/ 8/2024 Run time: 12:02:24
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
************** PROGRAM CONTACT *********
Data line--- mode isub
Data line--- limits 0 4.0
Data line--- HEXCLUDE
Data line--- from residue all chain A 1 to 60
Data line--- to residue all chain B 1 to 60
Data line--- end
Atoms of all types will be used.
Intersubunit contacts will be printed
Atom-atom search will be done within the limits of 0.00 to 4.00 angstroms
Logical name: XYZIN File name: 8da3.pdb1
PDB file is being opened on unit 1 for INPUT.
MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
RF RO
0.028 -0.000 -0.000 -0.000 35.546 0.000 0.000 -0.000
-0.000 0.024 -0.000 0.000 0.000 42.449 0.000 0.000
0.000 -0.000 0.013 -0.000 0.000 0.000 74.288 -0.000
-0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
Xmin Xmax Ymin Ymax Zmin Zmax : 7.32 40.92 -8.96 33.26 29.29 77.18
NX NY NZ boxes 8 11 10
LIST OF CONTACTS :
==================
source atoms target atoms distance angle
Asn 3A C ... Phe 32B CZ ... 3.74
Asn 3A O ... Phe 32B CZ ... 3.71
... Phe 32B CE1 ... 3.77
Asn 3A ND2 ... Trp 35B CZ3 ... 3.91
... Trp 35B CH2 ... 3.84
Asn 3A HB2 ... Phe 32B CZ ... 3.96
Asn 3A HB3 ... Phe 32B CZ ... 3.30
... Phe 32B CE1 ... 3.18
... Trp 35B CZ3 ... 3.86
Asn 3A HD21 ... Trp 35B CH2 ... 3.85
Asn 3A HD22 ... Asp 36B OD1 ... 3.80
... Trp 35B CZ3 ... 3.54
... Trp 35B CH2 ... 3.72
Etc…
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
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