Hi Bryan, mmaker is a command for use in Chimera's "internal" command line (shown with the Favorites...Command Line menu option), not directly on the Unix command line. It can be included inside scripts that are run from the Unix command line though. If you briefly outlined what you want to do, I could provide better advice about your best approach. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On May 2, 2005, at 6:32 PM, Bryan W. Lepore wrote:

i'm confused about the command "mmaker".

`chimera --nogui mmaker` causes a "no such file or directory" error, so i tried `chimera --nogui --mmaker` which isnt' right either. also tried just `mmaker` even though its not in bin/ lib/.

so do i make a heredoc script? i suspect i am missing a fundamental point (that i didn't find with `google: mmaker site:www.cgl.ucsf.edu/chimera`).

i've tried both the latest official release and the lastest snapshot.

-bryan

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On May 2, 2005, at 7:25 PM, Bryan W. Lepore wrote:

hi Eric

On Mon, 2 May 2005, Eric Pettersen wrote:

...

mmaker is a command for use in Chimera's "internal" command line...

ok,...

...

It can be included inside scripts that are run from the Unix command line though.

so like this?:

#!/bin/bash chimera --nogui << eof mmaker file1.pdb file2.pdb eof

this fails, but there's no output, hence the email.

Chimera can handle two kinds of script files: those containing Chimera command-line commands (file name ending in .com or .cmd or preceded with cmd: or com: on the Unix Chimera startup command-line) and Python files (.py ending or py: prefix). So if you had a file named "domatch" that contained: open file1.pdb open file2.pdb mmaker #0 #1 pair bb write #1 transformed.pdb and executed chimera as "chimera --nogui cmd:domatch" then file2 would be superimposed on file1 and the transformed coordinates of file2 would be written out to transformed.pdb

...

If you briefly outlined what you want to do, I could provide better advice about your best approach.

take a list of .ent files and generate a superposition-based sequence alignment. i can do this ok with the gui.

There are no Chimera commands that write sequence alignments, so this can only be done using Chimera's Python layer. I've appended a Python script that does the following: 1) reads a file named "structList" that has lines consisting of 3 file names: 2 PDB files and an output alignment file 2) uses MatchMaker to superimpose the structures 3) uses the "iterate match" capability of Multalign Viewer to improve the superposition by pruning off long residue pairings and rematching 4) creates a superposition-based sequence alignment using Match->Align 5) uses Multalign Viewer again to write out the alignment Now, the script can't be run in nogui mode since Multalign Viewer is gui-only at this point. Nonetheless, it does run without user intervention, so you can just leave it running on a display you aren't using. There are comments in the script about what the code is doing and what various options are. Let me know if you have questions. I should also note that the script is using Needleman-Wunsch to do the initial sequence alignment. If your structures have low sequence identity, you might want to switch to Smith-Waterman instead. I am working on an improvement for MatchMaker that will make it much better at matching low sequence identity structures (it will consider secondary structure in addition to residue type). I could send you the new version when it's ready in a few days if the current MatchMaker has trouble on your data. --Eric