Hello all - Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize comma-separated chain IDs with the source or target keyword.
I'm trying to use NCONT to determine contacts between antibody chains and their bound epitope as part of a programmatic workflow. I'm using a Biopython Bio.Application.AbstractCommandline subclass to generate the command to be executed. It ends up looking something like this: ncont xyzin /path/to/xxxx.pdb <<eof source L,H target P maxdist 4 eof The problem is, the output only identifies the contacts between chains L and P. If I switch the order of the source to "H,L" it only identifies contacts between H and P. Similarly, if I switch the source and target selections (i.e. "source P", "target L,H") I see the same behavior. I'm using NCONT from CCP4 v6.2.0 on Mac OS 10.7.3 installed via Fink. A quick archives search produced a 2006 discussion about having the wrong ncont in the user's path, but mine appears to be correct: $ which ncont /sw/share/xtal/ccp4-6.2.0/bin/ncont Any suggestions on what might be going on here? I've pasted the full NCONT output below in case that might shed any light on the issue. Of course, I could work around this by running each pair of chains separately, but I'd prefer to do it in one fell swoop. Many thanks, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329/398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ Here's the full output from NCONT with a test antibody-peptide complex from 1Q1J, first with "L,H" then with "H,L" as the source selections. $ ncont xyzin 1Q1J.pdb <<eof > source P > target L,H > maxdist 4 > eof ############################################################### ############################################################### ############################################################### ### CCP4 6.2: NCONT version 6.2 : ## ############################################################### User: jared Run date: 1/ 3/2012 Run time: 14:22:07 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. ------------------------------------------------------------------------------ PDB file 1Q1J.pdb has been read in. ------------------------------------------------------------------------------ Input cards Data line--- source P Data line--- target L,H Data line--- maxdist 4 ------------------------------------------------------------------------------ Selected 73 source atoms Selected 1611 target atoms ------------------------------------------------------------------------------ 23 contacts found: SOURCE ATOMS TARGET ATOMS DISTANCE /1/P/ 309(ILE). / CG2[ C]: /1/L/ 91(TRP). / CH2[ C]: 3.78 /1/L/ 32(TYR). / CG [ C]: 3.93 /1/L/ 32(TYR). / CD1[ C]: 3.47 /1/L/ 32(TYR). / CE1[ C]: 3.86 /1/P/ 312(GLY). / N [ N]: /1/L/ 91(TRP). / CH2[ C]: 3.97 /1/P/ 312(GLY). / CA [ C]: /1/L/ 91(TRP). / CH2[ C]: 4.00 /1/P/ 313(PRO). / N [ N]: /1/L/ 91(TRP). / CD2[ C]: 3.96 /1/P/ 313(PRO). / CA [ C]: /1/L/ 91(TRP). / CD1[ C]: 3.94 /1/P/ 313(PRO). / CB [ C]: /1/L/ 91(TRP). / CB [ C]: 3.82 /1/L/ 95(ALA).B/ O [ O]: 3.49 /1/L/ 91(TRP). / CG [ C]: 3.93 /1/P/ 313(PRO). / CG [ C]: /1/L/ 96(TRP). / NE1[ N]: 3.57 /1/L/ 91(TRP). / CB [ C]: 3.95 /1/L/ 96(TRP). / CD2[ C]: 3.73 /1/L/ 96(TRP). / CE2[ C]: 3.27 /1/L/ 96(TRP). / CZ2[ C]: 3.39 /1/L/ 96(TRP). / CH2[ C]: 3.90 /1/P/ 313(PRO). / CD [ C]: /1/L/ 91(TRP). / CE3[ C]: 3.91 /1/L/ 96(TRP). / CE2[ C]: 3.95 /1/L/ 96(TRP). / CZ2[ C]: 3.51 /1/L/ 96(TRP). / CH2[ C]: 3.65 /1/L/ 91(TRP). / CD2[ C]: 3.90 /1/P/ 314(GLY). / N [ N]: /1/L/ 95(ALA).B/ CB [ C]: 3.91 Total 23 contacts -------------------------------------------------------------------------- NCONT: Normal termination Times: User: 0.0s System: 0.0s Elapsed: 0:00 $ ncont xyzin 1Q1J.pdb <<eof > source P > target H,L > maxdist 4 > eof ############################################################### ############################################################### ############################################################### ### CCP4 6.2: NCONT version 6.2 : ## ############################################################### User: jared Run date: 1/ 3/2012 Run time: 14:22:26 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. ------------------------------------------------------------------------------ PDB file 1Q1J.pdb has been read in. ------------------------------------------------------------------------------ Input cards Data line--- source P Data line--- target H,L Data line--- maxdist 4 ------------------------------------------------------------------------------ Selected 73 source atoms Selected 1756 target atoms ------------------------------------------------------------------------------ 98 contacts found: SOURCE ATOMS TARGET ATOMS DISTANCE /1/P/ 305(LYS). / O [ O]: /1/H/ 100(ASP).F/ N [ N]: 3.95 /1/H/ 100(ASP).F/ CB [ C]: 3.59 /1/P/ 305(LYS). / CB [ C]: /1/H/ 100(GLU).E/ OE1[ O]: 3.70 /1/H/ 100(GLU).E/ OE2[ O]: 3.74 /1/P/ 306(ARG). / N [ N]: /1/H/ 100(GLU).E/ OE1[ O]: 3.95 /1/P/ 306(ARG). / CA [ C]: /1/H/ 100(ASP).F/ O [ O]: 3.46 /1/P/ 306(ARG). / C [ C]: /1/H/ 100(ASP).F/ O [ O]: 3.53 /1/P/ 306(ARG). / CB [ C]: /1/H/ 100(TYR).H/ CE1[ C]: 3.77 /1/P/ 306(ARG). / CG [ C]: /1/H/ 100(TYR).H/ CE1[ C]: 3.62 /1/P/ 306(ARG). / CD [ C]: /1/H/ 100(TYR).H/ CE1[ C]: 3.44 /1/H/ 100(TYR).H/ CZ [ C]: 3.69 /1/H/ 100(TYR).H/ OH [ O]: 3.45 /1/P/ 306(ARG). / NE [ N]: /1/H/ 100(TYR).H/ CZ [ C]: 3.97 /1/H/ 100(TYR).H/ OH [ O]: 3.21 /1/P/ 306(ARG). / CZ [ C]: /1/H/ 100(TYR).H/ OH [ O]: 3.30 /1/P/ 306(ARG). / NH1[ N]: /1/H/ 100(TYR).H/ OH [ O]: 3.54 /1/P/ 306(ARG). / NH2[ N]: /1/H/ 100(TYR).H/ OH [ O]: 3.88 /1/P/ 307(ILE). / N [ N]: /1/H/ 100(ASP).F/ O [ O]: 2.63 /1/H/ 100(ASP).F/ C [ C]: 3.84 /1/P/ 307(ILE). / CA [ C]: /1/H/ 100(ASP).F/ O [ O]: 3.51 /1/P/ 307(ILE). / C [ C]: /1/H/ 100(TYR).H/ N [ N]: 3.88 /1/H/ 100(ASP).F/ O [ O]: 3.91 /1/P/ 307(ILE). / O [ O]: /1/H/ 100(TYR).H/ CA [ C]: 3.53 /1/H/ 100(TYR).H/ O [ O]: 3.78 /1/H/ 100(TYR).H/ CB [ C]: 3.41 /1/H/ 100(TYR).H/ CG [ C]: 3.85 /1/H/ 100(TYR).H/ CD1[ C]: 3.38 /1/H/ 100(TYR).G/ CA [ C]: 3.55 /1/H/ 100(TYR).G/ C [ C]: 3.54 /1/H/ 100(TYR).H/ N [ N]: 2.68 /1/H/ 100(ASP).F/ O [ O]: 3.40 /1/P/ 307(ILE). / CB [ C]: /1/H/ 100(ASP).F/ O [ O]: 3.57 /1/P/ 307(ILE). / CG1[ C]: /1/H/ 100(ASP).F/ O [ O]: 3.88 /1/H/ 100(GLU).E/ OE1[ O]: 3.76 /1/H/ 100(GLU).E/ CB [ C]: 3.75 /1/P/ 307(ILE). / CD1[ C]: /1/H/ 100(GLU).E/ OE1[ O]: 3.42 /1/P/ 308(HIS). / CA [ C]: /1/H/ 100(TYR).H/ O [ O]: 3.62 /1/P/ 308(HIS). / C [ C]: /1/H/ 100(TYR).H/ O [ O]: 3.55 /1/P/ 308(HIS). / ND1[ N]: /1/H/ 100(TYR).J/ CE1[ C]: 3.62 /1/H/ 100(TYR).J/ CZ [ C]: 3.79 /1/H/ 100(TYR).J/ OH [ O]: 3.03 /1/H/ 100(TYR).H/ CB [ C]: 3.78 /1/H/ 100(TYR).H/ CG [ C]: 3.96 /1/P/ 308(HIS). / CE1[ C]: /1/H/ 100(TYR).J/ OH [ O]: 3.50 /1/P/ 309(ILE). / N [ N]: /1/H/ 100(TYR).H/ C [ C]: 3.84 /1/H/ 100(TYR).H/ O [ O]: 2.61 /1/P/ 309(ILE). / CA [ C]: /1/H/ 100(TYR).H/ O [ O]: 3.44 /1/P/ 309(ILE). / C [ C]: /1/H/ 100(TYR).H/ O [ O]: 3.89 /1/P/ 309(ILE). / O [ O]: /1/H/ 100(TYR).J/ CA [ C]: 3.97 /1/H/ 100(TYR).J/ CB [ C]: 3.96 /1/H/ 100(TYR).J/ CD1[ C]: 3.70 /1/H/ 100(TYR).H/ O [ O]: 3.64 /1/H/ 100(TYR).I/ CA [ C]: 3.70 /1/H/ 100(TYR).I/ C [ C]: 3.82 /1/H/ 100(TYR).J/ N [ N]: 3.01 /1/P/ 309(ILE). / CB [ C]: /1/H/ 100(TYR).H/ O [ O]: 3.44 /1/P/ 309(ILE). / CG1[ C]: /1/H/ 100(TYR).H/ O [ O]: 3.63 /1/P/ 313(PRO). / O [ O]: /1/H/ 33(TRP). / CZ3[ C]: 3.17 /1/H/ 33(TRP). / CH2[ C]: 3.95 /1/P/ 313(PRO). / CB [ C]: /1/H/ 50(ARG). / NH1[ N]: 3.85 /1/P/ 314(GLY). / C [ C]: /1/H/ 33(TRP). / CH2[ C]: 3.80 /1/P/ 314(GLY). / O [ O]: /1/H/ 52(LYS). / NZ [ N]: 3.94 /1/H/ 33(TRP). / CH2[ C]: 3.41 /1/P/ 315(ARG). / CD [ C]: /1/H/ 33(TRP). / CZ3[ C]: 3.81 /1/H/ 33(TRP). / CH2[ C]: 3.72 /1/P/ 315(ARG). / NE [ N]: /1/H/ 33(TRP). / CE3[ C]: 3.72 /1/H/ 33(TRP). / CZ3[ C]: 3.51 /1/H/ 100(TYR).J/ CG [ C]: 3.78 /1/H/ 100(TYR).J/ CD1[ C]: 3.88 /1/H/ 100(TYR).J/ CD2[ C]: 3.94 /1/H/ 33(TRP). / CH2[ C]: 3.86 /1/P/ 315(ARG). / CZ [ C]: /1/H/ 33(TRP). / CE3[ C]: 3.31 /1/H/ 33(TRP). / CZ3[ C]: 3.53 /1/H/ 100(TYR).J/ CG [ C]: 3.93 /1/H/ 100(TYR).J/ CD2[ C]: 3.61 /1/H/ 100(TYR).J/ CE2[ C]: 3.72 /1/H/ 33(TRP). / CD2[ C]: 3.44 /1/H/ 33(TRP). / CE2[ C]: 3.78 /1/H/ 33(TRP). / CH2[ C]: 3.87 /1/P/ 315(ARG). / NH1[ N]: /1/H/ 33(TRP). / CG [ C]: 3.84 /1/H/ 33(TRP). / CE3[ C]: 3.60 /1/H/ 33(TRP). / CZ3[ C]: 3.77 /1/H/ 100(TYR).J/ CE2[ C]: 3.82 /1/H/ 33(TRP). / CD2[ C]: 3.27 /1/H/ 33(TRP). / NE1[ N]: 3.64 /1/H/ 33(TRP). / CE2[ C]: 3.14 /1/H/ 33(TRP). / CZ2[ C]: 3.38 /1/H/ 33(TRP). / CH2[ C]: 3.67 /1/P/ 315(ARG). / NH2[ N]: /1/H/ 33(TRP). / CB [ C]: 3.94 /1/H/ 95(ASP). / CG [ C]: 3.66 /1/H/ 95(ASP). / OD2[ O]: 3.28 /1/H/ 95(ASP). / CB [ C]: 3.17 /1/H/ 33(TRP). / CG [ C]: 3.77 /1/H/ 33(TRP). / CE3[ C]: 3.38 /1/H/ 100(TYR).J/ CG [ C]: 3.88 /1/H/ 100(TYR).J/ CD2[ C]: 3.39 /1/H/ 100(TYR).J/ CE2[ C]: 3.82 /1/H/ 33(TRP). / CD2[ C]: 3.49 Total 98 contacts -------------------------------------------------------------------------- NCONT: Normal termination Times: User: 0.0s System: 0.0s Elapsed: 0:00 ------------------------------------------------------------ This email message, including any attachments, is for the 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