Thread: [Apbs-users] chain support in APBS
Biomolecular electrostatics software
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From: <ho...@br...> - 2006-03-22 17:03:25
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Are there any plans to add support for Chain IDs to apbs? My understanding was that the pqr format would allow for Chain IDs by that they weren't implemented in the pdb2pqr program yet. It would be very nice to have the Chain ID support in both pdb2pqr and apbs os that structures for complexes could be used. Thanks in advance for any clarifications. Jack |
From: Todd D. <to...@cc...> - 2006-03-22 18:11:54
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Hi Jack - Adding chain IDs to APBS presents something of a problem, since the chain IDs can cause columns to merge, messing up the C-based parser within APBS. As you mentioned, PDB2PQR currently strips chain IDs so as to ensure that they are not present before using APBS. As it stands now, an upcoming release of PDB2PQR will give users the option of including or excluding chain ids, but APBS will still be unable to handle chain IDs. In the future we're looking to potentially suppor other input formats, and that should allow us to include chain IDs and other useful information. Thanks! Todd On 3/22/06, Jack Howarth <ho...@br...> wrote: > Are there any plans to add support for Chain IDs to apbs? My understan= ding > was that the pqr format would allow for Chain IDs by that they weren't > implemented in the pdb2pqr program yet. It would be very nice to have > the Chain ID support in both pdb2pqr and apbs os that structures for > complexes could be used. Thanks in advance for any clarifications. > Jack > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting langua= ge > that extends applications into web and mobile media. Attend the live webc= ast > and join the prime developer group breaking into this new coding territor= y! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |
From: Robert K. <ro...@uc...> - 2006-03-22 18:25:59
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Hi Jack, since APBS keeps order of input atoms during the calculation, any per-atom information which was stripped from the original PDB file can be recovered during post-processing of the APBS output. Admittedly, this is not as pretty as having a native support for alternative input formats in APBS but this should work in the meantime. robert On Wed, Mar 22, 2006 at 01:11:45PM -0500, Todd Dolinsky wrote: > Hi Jack - > > Adding chain IDs to APBS presents something of a problem, since the > chain IDs can cause columns to merge, messing up the C-based parser > within APBS. As you mentioned, PDB2PQR currently strips chain IDs so > as to ensure that they are not present before using APBS. > > As it stands now, an upcoming release of PDB2PQR will give users the > option of including or excluding chain ids, but APBS will still be > unable to handle chain IDs. In the future we're looking to > potentially suppor other input formats, and that should allow us to > include chain IDs and other useful information. > > Thanks! > > Todd > > On 3/22/06, Jack Howarth <ho...@br...> wrote: > > Are there any plans to add support for Chain IDs to apbs? My understanding > > was that the pqr format would allow for Chain IDs by that they weren't > > implemented in the pdb2pqr program yet. It would be very nice to have > > the Chain ID support in both pdb2pqr and apbs os that structures for > > complexes could be used. Thanks in advance for any clarifications. > > Jack > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking scripting language > > that extends applications into web and mobile media. Attend the live webcast > > and join the prime developer group breaking into this new coding territory! > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting language > that extends applications into web and mobile media. Attend the live webcast > and join the prime developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd_______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users |