PISA question

From: Zhou, Tongqing 
Date: 23 August 2011 17:16
To: CCP4BB@jiscmail.ac.uk

Dear CCP4bb,

We are trying to get some detailed interface information from an antibody:antigen complex, PDBePISA used to have an option to select atomic level details, now the new web interface only gives residue level information. Is there a way to run PISA (in the CCP4 package) with a different configuration to get the detailed information?

Thanks,

Tongqing

Tongqing Zhou, Ph.D.

Staff Scientist

Structural Biology Section

Vaccine Research Center, NIAID/NIH

Building 40, Room 4607B

40 Convent Drive, MSC3027

Bethesda, MD 20892

(301) 594-8710 (Tel)

(301) 793-0794 (Cell)

(301) 480-2658 (Fax)

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From: <eugene.krissinel
Date: 23 August 2011 17:50
To: CCP4BB@jiscmail.ac.uk


Dear Tongqing

No there is no such option in CCP4's PISA, but I put this on the list for further developments. Regrettably PDBe changed the interface after I moved out and I cannot help you with that. However, you may ask them to put that option back.

Sorry,

Eugene.

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From: MARTYN SYMMONS
Date: 24 August 2011 11:35
To: CCP4BB@jiscmail.ac.uk


Dear All

I may not have understood but if I run PDBe PISA
and go Interface>Details
then I get a table of the form eg for H-bonds

Hydrogen bonds
 1       A:GLN 213[ NE2]         3.52    A:SER   3[ O  ]
 2       A:ASN 112[ ND2]         2.77    A:SER   3[ O  ]
 3       A:GLN 213[ NE2]         2.99    A:SER   4[ O  ]
 4       A:LYS 154[ NZ ]         2.74    A:ILE   5[ O  ]
 5       A:ARG 214[ NH2]         2.75    A:GLU  16[ OE2]
 6       A:TYR 168[ N  ]         2.86    A:LYS  31[ O  ]
 7       A:TYR 168[ OH ]         3.00    A:ASN  34[ OD1]
 8       A:LYS 175[ NZ ]         2.95    A:ASP  36[ OD2]
 9       A:ARG 129[ NH1]         3.22    A:ASP 127[ O  ]
 10      A:ARG 129[ NH2]         2.90    A:ASP 127[ O  ]
 11      A:HIS 363[ ND1]         3.47    A:GLN 132[ O  ]
 12      A:HIS 363[ ND1]         3.41    A:GLN 132[ OE1]
 13      A:TYR 350[ OH ]         2.71    A:LEU 179[ O  ]

which seems to include atom details (not Hs however).

In the new pages there is no longer a pulldown for atomic detail but this now is the default.

Hope that helps
       Martyn



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From: Tom Oldfield
Date: 24 August 2011 14:22
To: CCP4BB@jiscmail.ac.uk


Tongqing

Thank you for highlighting an issue with a recent release of the PDBePisa service.  The  option to return the atom detail as well as the residue detail within the PISA service was accidentally missed from the production service during a major update of features.  I am sorry that this has effected your work.

We are have identified and fixed the problem and are currently testing the change and should have the  fix in production  by the end of the week.

Regards
Tom Oldfield
PDBe