AUTOBUILD: sequence file for multiple chains
Hi All, my model contains multiple chains and I would like Autobuild to build them all. What is the correct way to give multiple sequences (in FASTA format) to Autobuild? In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other? Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Terwilliger, Thomas C [[email protected]] Sent: Saturday, February 02, 2013 9:55 PM To: PHENIX user mailing list Subject: Re: [phenixbb] autosol MIR with more than one native? Hi Ed, Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Edward A. Berry [[email protected]] Sent: Saturday, February 02, 2013 10:39 AM To: PHENIX user mailing list Subject: [phenixbb] autosol MIR with more than one native? Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Gino, One blank line between chains is fine, also a line starting with ">" will indicate a start of a new chain All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Gino Cingolani [[email protected]] Sent: Sunday, February 03, 2013 8:18 AM To: PHENIX user mailing list Subject: [phenixbb] AUTOBUILD: sequence file for multiple chains Hi All, my model contains multiple chains and I would like Autobuild to build them all. What is the correct way to give multiple sequences (in FASTA format) to Autobuild? In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other? Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Terwilliger, Thomas C [[email protected]] Sent: Saturday, February 02, 2013 9:55 PM To: PHENIX user mailing list Subject: Re: [phenixbb] autosol MIR with more than one native? Hi Ed, Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Edward A. Berry [[email protected]] Sent: Saturday, February 02, 2013 10:39 AM To: PHENIX user mailing list Subject: [phenixbb] autosol MIR with more than one native? Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab _______________________________________________ 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
Thanks Tom !! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Terwilliger, Thomas C [[email protected]] Sent: Sunday, February 03, 2013 11:31 AM To: PHENIX user mailing list Subject: Re: [phenixbb] AUTOBUILD: sequence file for multiple chains Hi Gino, One blank line between chains is fine, also a line starting with ">" will indicate a start of a new chain All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Gino Cingolani [[email protected]] Sent: Sunday, February 03, 2013 8:18 AM To: PHENIX user mailing list Subject: [phenixbb] AUTOBUILD: sequence file for multiple chains Hi All, my model contains multiple chains and I would like Autobuild to build them all. What is the correct way to give multiple sequences (in FASTA format) to Autobuild? In my 'seq.dat' file, shall I leave one (or two) spaces in between one sequence and the other? Thanks, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Terwilliger, Thomas C [[email protected]] Sent: Saturday, February 02, 2013 9:55 PM To: PHENIX user mailing list Subject: Re: [phenixbb] autosol MIR with more than one native? Hi Ed, Unfortunately, autosol only has a way to deal with one native, so you'd need to average them together or run 2 runs, one with each. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Edward A. Berry [[email protected]] Sent: Saturday, February 02, 2013 10:39 AM To: PHENIX user mailing list Subject: [phenixbb] autosol MIR with more than one native? Is it possible to run phenix.autosol MIR problem with two "native" datasets? And does this make sense, or would it be better to scale the two natives together to make a single dataset before running autosol? eab _______________________________________________ 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
participants (2)
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Gino Cingolani -
Terwilliger, Thomas C