Hi,

so I've recently been trying to align some protein sequences in VMD (V1.9.3) using the Multiseq extension.

The procedure I use and the .pdb files I'm using come from the VMD introductory tutorial that details the step by step instructions to do this yet I cannot get it to work and continue to get an "unkown option" error (see attachment for a screenshot).

I'll include a caption of the instruction to do this below:

"5.1 Structure Alignment with MultiSeq

Very often comparing structures of different proteins reveal many important information. For example, proteins with similar functions tend to be found with similar structural features. MultiSeq structure alignment is useful for this reason. We will compare the structures of four aquaporin proteins, whose coordinate files can all be found in the vmd-tutorial-files directory.

PDB code

1fqy (Murata et al., Nature, 407:599, 2000) Human AQP1

1rc2 (Savage et al., PLoS Biology, 1:E72, 2003) E. coli AqpZ

1lda (Tajkhorshid et al., Science, 296:525, 2002) E. coli Glycerol Facilitator (GlpF)

1j4n (Sui et al., Nature, 414:872, 2001) Bovine AQP1

Table 8: The four aquaporins used in this section.

5.1.1 Loading aquaporin structures

1. Start a new VMD session. Open the Molecule File Browser window bychoosing the File ! New Molecule... menu item in the VMD Main window.In the Molecule File Browser window, use the Browse... button to find andselect the file 1fqy.pdb in the directory vmd-tutorial-files. Press Loadto load the molecule.

2. Load the remaining aquaporins, 1rc2, 1lda, and 1j4n. Make sure thateach PDB is loaded into a new molecule. Close the Molecule File Browserwindow when you finished loading all four molecules. Your VMD Mainmenu should look like Fig. 28 when all four aquaporins are loaded.

5.2.1 Aligning molecules and coloring molecules by degree of conservation

1. In the MultiSeq window, select Tools ! Sequence Alignment window. In the Sequence Alignment Options window, choose ClustalW under Alignment Program and make sure the Align All Sequences option is checked, and go to the bottom of the window and select OK. Now the four aquaporins have been aligned according to their sequence using the ClustalW tool (Thompson et al., Nucl. Acids Res., 22:4673, 1994)."

After selecting "OK" (see the bold instruction above) I get the error.

If anyone has even the slightest idea as to why I'm seeing this please let me know, I'd really appreciate any and all guidance on the matter!

I look forward to hearing from you.

Best,