[Chimera-users] rna model

[Elaine Meng]

Hi Divita,
It is not possible to tell what is happening without the data.  Instead of sending e-mail here, please use menu: Help... Report a Bug, attach a session file, and enter a description of steps needed to reproduce the problem.  Also include your email address for feedback.  I guess the bugreport form only allows attaching one thing, but somebody may ask for your fasta file later.

Only other thoughts are that maybe the path model doesn't have the right number of markers in it for your sequence, or maybe your fasta file isn't plain text.
Best,
Elaine

> On Apr 6, 2021, at 5:33 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in at nrl.navy.mil> wrote:
> 
> Hi Elaine
> 
> Sorry, I should have been clearer. This was my command:
> rna model /Users/dmathur/Documents/gapB-sfGFP-mRNA.fasta path #0
> and
> 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
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    how to read command usage in help pages
>    <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html#model>
> 
>    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
>    -----
>    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,