Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca
Hi Rebecca, The sequence file should be able to contain any number of separate sequences. You can tell how many have been read in for actual model-building when running AutoSol by looking at /net/sigma/raid1/scratch1/terwill/misc/junk/wt056/AutoSol_run_1_/TEMP0/build_xxx/initial_build_cycle_1.log (xxx=solution number) which if I put in 3 dummy sequences to seq.dat gives me: Read 3 chains from file TEMP_seq.dat CHAIN 1 with 7 residues: starting at residue 1 QLMDMRD CHAIN 2 with 8 residues: starting at residue 1 APPTTTTA CHAIN 3 with 10 residues: starting at residue 1 QFRTAAWWWW All the best, Tom T
Dear phenix community:
I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure.
So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit.
Thanks in advance, Rebecca _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Recently was mentioned a command to run autobuild automatically after autosolve- could someone remind me the syntax? Thanks. Ed
Hi Ed, You should be able to say phenix.autobuild after_autosol however I see that with the current version that does not work (it asks for a sequence file). Perhaps that is the reason for your question. I'll fix this. All the best, Tom T On Dec 12, 2011, at 8:13 AM, Edward A. Berry wrote:
Recently was mentioned a command to run autobuild automatically after autosolve- could someone remind me the syntax?
Thanks. Ed _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Hi Ed, Thanks again for the question! The command phenix.autobuild after_autosol works if you have run autosol all the way through and obtained a model (as in your case); if you had no model (as in the test I ran to see if it worked), it would have stopped. I have fixed the problem so it should work in either case (starting tomorrow). All the best, Tom T On Dec 12, 2011, at 8:49 AM, Tom Terwilliger wrote:
Hi Ed,
You should be able to say
phenix.autobuild after_autosol
however I see that with the current version that does not work (it asks for a sequence file). Perhaps that is the reason for your question. I'll fix this.
All the best, Tom T
On Dec 12, 2011, at 8:13 AM, Edward A. Berry wrote:
Recently was mentioned a command to run autobuild automatically after autosolve- could someone remind me the syntax?
Thanks. Ed _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
participants (4)
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Edward A. Berry -
Page, Rebecca -
Thomas C. Terwilliger -
Tom Terwilliger