[Chimera-users] rna model

Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in at nrl.navy.mil
Tue Apr 6 05:33:26 PDT 2021

Hi Elaine

Sorry, I should have been clearer. This was my command:
rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0
rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0 start 40 length 8

Both return the same error.

Divita Mathur, PhD

Research Assistant Professor
George Mason University &
Center for Bio/Molecular Science and Engineering

Naval Research Laboratory
(202) 767-0687 (Office)

On 4/5/21, 8:26 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Divita,
    Is “rna model sequence  #0” actually the command you gave?  In the command usage, the word "sequence" (shown in italics) is supposed to be pathname of the file with the sequence in it (not literally the word "sequence"), and you are also required to either give the "path" option or the "pairs" option.  You cannot omit both.

    "rna model" help

    how to read command usage in help pages

    So if you had  the path markers as #0 then your command could be something like

    rna model /Users/divita/Documents/blahblah.fasta path #0

    (of course, change the pathname as appropriate for the detailed location and filename of your fasta file.)

    I hope this helps,
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco

    > On Apr 5, 2021, at 9:38 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
    > Hello Chimera community
    > I am trying to run the “rna model sequence  #0” code but it is returning the following error:
    > IndexError: list index out of range
    > File “…path/RNALayout/rna_layout.py”, line 393, in place_residues
    >   rprev = rlist[0]
    > See reply log for Python traceback.
    > Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder.
    > Regards,

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