See this message: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-June/010017.html> —Eric
On May 7, 2019, at 10:45 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
That will work. So the question now is how to assign the Multialign Viewer to a variable when opening a file with pre-aligned sequences. Eg after running the following command
runCommand('open myseqalignment.fas')
the multialign window opens and the sequence-structure associations are made. How can I access this Multialign viewer instance? Is there something equivalent to
mav = the_multialign_viewer_created_when_opening_a_file
Thanks again
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Tuesday, May 07, 2019 1:04 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info
Ah, in that case if your Multalign Viewer instance is in a variable named ‘mav', call:
mav.saveAssocInfo(“save-file-path”)
—Eric
On May 7, 2019, at 8:00 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Hi Eric,
I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script.
Here is sample of an association file produced by the Multialign viewer
struct1 associates with seq1 chain K 1 - GLU 390.K 2 - ASN 391.K 3 - SER 392.K 4 - GLN 393.K 5 - VAL 394.K .. .. .. struct2 associates with seq2 chain K 1 - ALA 5.K 2 - GLU 6.K 3 - SER 7.K 4 - ASN 8.K 5 - ILE 9.K 6 - LYS 10.K 7 - VAL 11.K 8 - MET 12.K 9 - CYS 13.K 10 - ARG 14.K .. .. ..
The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds with S392 in struct1). This is the info I need.
Thanks
Hernando
From: Eric Pettersen [mailto:pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>] Sent: Monday, May 06, 2019 5:39 PM To: Hernando J Sosa Cc: Chimera Subject: Re: [Chimera-users] Association info
Hi Hernando, If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If not, let me know exactly what you want to save.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 6, 2019, at 11:43 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu <mailto:hernando.sosa@einstein.yu.edu>> wrote:
Dear Chimera,
How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info).
Thanks
Hernando
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