From: Sampson, Jared
Date: 1 March 2012 20:08
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From: Eleanor Dodson
Thats why I love distang!
Eleanor
--
Date: 1 March 2012 20:08
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 <<eofsource L,Htarget Pmaxdist 4eof
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
-
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
----------
From: Eleanor Dodson
Thats why I love distang!
Eleanor
----------
From: Sampson, Jared
Thanks to Pius for the tip that I can use more than one "source" keyword.
ncont xyzin my.pdb <<eof
source L
source H
target P
eof
works like a charm!
--
On Mar 1, 2012, at 4:47 PM, Pius Padayatti wrote:
what if you add as follows
ncont xyzin /path/to/xxxx.pdb <<eof
source L,Htarget Pmaxdist 4source H,Lwill it run? and give both?target Pmaxdist 4eof
just a thought
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