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, -- Divita Mathur, PhD Research Assistant Professor George Mason University & Center for Bio/Molecular Science and Engineering Naval Research Laboratory (202) 767-0687 (Office)
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@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,
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@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@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,
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@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@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@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,
The rna error message is because the command was not able to construct any nucleotides. The reason why is very likely because your input data has a problem. As Elaine says we can't determine what is wrong with your input data without seeing it. So use Help / Report a Bug... as Elaine suggests if you want help figuring it out. Tom
On Apr 6, 2021, at 5:33 AM, Divita Mathur, Contractor Code 6910, FN <divita.mathur.ctr.in@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@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@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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participants (3)
-
Divita Mathur, Contractor Code 6910, FN -
Elaine Meng -
Tom Goddard