Thank you Geoff, but the problem is still there. provide copies of the commands, list of generated files, and an output file below. What I unfortunately see -- the output contains one molecule. The connectivity is established as needed, but fragments are not separated in different records. I want to see records for molecule1, molecule2, etc. in one file or in separate files.
Do you think it is possible? Thank you, Dmitri babel --separate -ixyz movie_last.xyz -opdb last.pdb babel --separate -m -ipdb last.pdb -opdb last1.pdb $babel --separate -m -ipdb last.pdb -ohin last1.hin 1 molecule converted $ ls -lt | head total 3528 -rw-r--r-- 1 kilin staff 1548 Dec 8 11:39 last11.hin -rw-r--r-- 1 kilin staff 3783 Dec 8 11:38 last11.pdb -rw-r--r-- 1 kilin staff 3783 Dec 8 11:38 last1.pdb -rw-r--r-- 1 kilin staff 3809 Dec 8 11:37 last.pdb -rw-r--r-- 1 kilin staff 1214 Dec 8 09:42 last.xyz On Thu, Dec 8, 2011 at 10:26 AM, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> But babel reports "1 molecule", see below >> Please advise, > > This is more of a wording question. "1 molecule converted" really means "I > read in one molecular system 'record', where a record may contain more than > one fragment." > > Obviously the latter is a little too long to print easily. :-) > > Hope that helps, > -Geoff
last11.pdb
Description: Protein Databank data
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