Thats why I love distang!
Eleanor
On Mar 1 2012, Sampson, Jared wrote:
>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
>
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--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
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