Hello, you could run pdbset with the "exclude hydrogens" card or pdbcur with "delhydrogen". What contacts are you looking for e.g. crystallographic or intramolecular?
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android -------- Original Message -------- On 30/08/2024 20:04, Dr. Kevin M Jude wrote: > 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 > > ############################################################### > > ############################################################### > > ############################################################### > > ### CCP4 8.0.017: CONTACT version 8.0.017 : ## > > ############################################################### > > 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 > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
