Problem with MSF alignment file

[sanjana.vasanth@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Unable to open .msf file in sequence viewer

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Show Sequence Viewer"

> show # target m

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> open "D:/Thesis/Data/Skanda/Sequence alignment/Sequences -
> Copy/muscle_aligned.msf"

Summary of feedback from opening D:/Thesis/Data/Skanda/Sequence
alignment/Sequences - Copy/muscle_aligned.msf  
---  
notes | Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> select

Nothing selected  

> ui tool show "Show Sequence Viewer"

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> ~hbonds

> hbonds reveal true

Atom specifier selects no atoms  

> interfaces ~solvent

No atoms specified  

> color bynucleotide

> color bfactor

No atoms specified  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> close #

Expected a models specifier or a keyword  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show "Blast Protein"

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msf

Summary of feedback from opening D:\Thesis\Data\Skanda\Sequence
alignment\Sequences - Copy\muscle_aligned.msf  
---  
notes | Destroying pre-existing alignment with identifier muscle_aligned.msf  
Alignment identifier is muscle_aligned.msf  
Showing conservation header ("seq_conservation" residue attribute) for
alignment muscle_aligned.msf  
  
Opened 21 sequences from muscle_aligned.msf  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format fasta

No sequences found in FASTA file 'muscle_aligned.msf'!  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format afas

Invalid "format" argument: Should be one of 'aln', 'amber', 'amira', 'apbs',
'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'clustal', 'cmap', 'cmd', 'cod',
'collada', 'compiled python', 'corecif', 'cube', 'dcd', 'defattr', 'delphi',
'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol',
'gro', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap',
'ims', 'iupac', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mole',
'mrc', 'msf', 'netcdfmap', 'nifti', 'nrrd', 'obj', 'pcod', 'pdb', 'pdbqt',
'pfam', 'photo', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds',
'psf', 'python', 'rsf', 'schrodinger maestro', 'sdf', 'segger', 'session',
'sff', 'situs', 'smallcif', 'smiles', 'spider', 'stl', 'stockholm', 'storm',
'swc', 'swissdock', 'tom_em', 'trr', 'uhbd', 'uniprot', 'viperdb', 'vtk', 'web
fetch', 'xplor', 'xtc', or 'zdock'  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format aln

Cannot open files: Syntax error in ALN file 'muscle_aligned.msf': First non-
blank line does not start with 'CLUSTAL'  

> open "D:\Thesis\Data\Skanda\Sequence alignment\Sequences -
> Copy\muscle_aligned.msf" format msn

Invalid "format" argument: Should be one of 'aln', 'amber', 'amira', 'apbs',
'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'clustal', 'cmap', 'cmd', 'cod',
'collada', 'compiled python', 'corecif', 'cube', 'dcd', 'defattr', 'delphi',
'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol',
'gro', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap',
'ims', 'iupac', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mole',
'mrc', 'msf', 'netcdfmap', 'nifti', 'nrrd', 'obj', 'pcod', 'pdb', 'pdbqt',
'pfam', 'photo', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds',
'psf', 'python', 'rsf', 'schrodinger maestro', 'sdf', 'segger', 'session',
'sff', 'situs', 'smallcif', 'smiles', 'spider', 'stl', 'stockholm', 'storm',
'swc', 'swissdock', 'tom_em', 'trr', 'uhbd', 'uniprot', 'viperdb', 'vtk', 'web
fetch', 'xplor', 'xtc', or 'zdock'  




OpenGL version: 3.3.0 NVIDIA 546.26
OpenGL renderer: NVIDIA GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP Pavilion Laptop 15-cs1xxx
OS: Microsoft Windows 10 Home Single Language (Build 19045)
Memory: 8,471,760,896
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: en-US

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[pett]

Hi Sanjana,

I guess I don't understand the problem. Are talking about the "muscle_aligned.msf" file? When you opened it normally, it said it opened 21 sequences. Only when you tried to open it as some format that it isn't (such as fasta) was there a problem. When you opened it normally, didn't a sequence-alignment viewer window come up?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[sanjana.vasanth@…]

Hi Eric,

My problem is that I was unable to open the .msf file using the ChimeraX
sequence viewer. I wanted to see the conserved residues and consensus
sequence, but despite multiple attempts following the tutorial, I was
unable to complete the action. The sequence viewer was open, but I was
unable to select the sequences on the .msf file that I wanted to view. I
essentially wanted an output like the attached image. Please let me know if
I'm doing something wrong.

Thanks,
Sanjana

[image: image.png]

On Thu, Mar 7, 2024 at 10:29 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[sanjana.vasanth@…]

Added by email2trac

[pett]

Hi Sanjana,

The conservation header should be shown by default initially. To show the consensus header, right click on the sequence viewer and in the resulting popup menu select Headers→Consensus. Let me know if you have further questions.

--Eric