PHENIX atom selection language
Hi, Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks. -- Jianghai
Hi Jianghai, there is no dedicated documentation. Most of what one can need is in phenix.refine documentation (and this is probably I know without looking at the source code). What exactly you need it for? Pavel On 10/6/11 3:06 PM, Jianghai Zhu wrote:
Hi,
Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks.
-- Jianghai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I have a fragment with two conformations. I want to select one of the conformations of this fragment. -- Jianghai On Oct 6, 2011, at 6:11 PM, Pavel Afonine wrote:
Hi Jianghai,
there is no dedicated documentation. Most of what one can need is in phenix.refine documentation (and this is probably I know without looking at the source code). What exactly you need it for?
Pavel
On 10/6/11 3:06 PM, Jianghai Zhu wrote:
Hi,
Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks.
-- Jianghai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Example: sel = chaina A and resseq 123 and resname LIG and altloc A "resseq 123" and "resname LIG" are probably redundant, so you can just do sel = chaina A and resseq 123 and altloc A Another example: sel = chaina A and resseq 123 and name C1 and altloc A Pavel On 10/6/11 3:12 PM, Jianghai Zhu wrote:
I have a fragment with two conformations. I want to select one of the conformations of this fragment.
-- Jianghai
On Oct 6, 2011, at 6:11 PM, Pavel Afonine wrote:
Hi Jianghai,
there is no dedicated documentation. Most of what one can need is in phenix.refine documentation (and this is probably I know without looking at the source code). What exactly you need it for?
Pavel
On 10/6/11 3:06 PM, Jianghai Zhu wrote:
Hi,
Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks.
-- Jianghai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Cool. Thanks, Pavel. It would be nice to have a list of all selection keywords and corresponding definitions somewhere. -- Jianghai On Oct 6, 2011, at 6:16 PM, Pavel Afonine wrote:
Example:
sel = chaina A and resseq 123 and resname LIG and altloc A
"resseq 123" and "resname LIG" are probably redundant, so you can just do
sel = chaina A and resseq 123 and altloc A
Another example:
sel = chaina A and resseq 123 and name C1 and altloc A
Pavel
On 10/6/11 3:12 PM, Jianghai Zhu wrote:
I have a fragment with two conformations. I want to select one of the conformations of this fragment.
-- Jianghai
On Oct 6, 2011, at 6:11 PM, Pavel Afonine wrote:
Hi Jianghai,
there is no dedicated documentation. Most of what one can need is in phenix.refine documentation (and this is probably I know without looking at the source code). What exactly you need it for?
Pavel
On 10/6/11 3:06 PM, Jianghai Zhu wrote:
Hi,
Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks.
-- Jianghai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Of course it is "chain" and not "chaina", sorry for the typo. Pavel On 10/6/11 3:12 PM, Jianghai Zhu wrote:
I have a fragment with two conformations. I want to select one of the conformations of this fragment.
-- Jianghai
On Oct 6, 2011, at 6:11 PM, Pavel Afonine wrote:
Hi Jianghai,
there is no dedicated documentation. Most of what one can need is in phenix.refine documentation (and this is probably I know without looking at the source code). What exactly you need it for?
Pavel
On 10/6/11 3:06 PM, Jianghai Zhu wrote:
Hi,
Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks.
-- Jianghai
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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