Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like MidasError: Dunbrack rotamer library does not support ASX File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible *With Regards,* *J Johnson Paul.*
Dear J Johnson Paul, This is not a bug -- the rotamer libraries only include standard amino acid residues. ASX is not a standard amino acid residue. It is used in some structures where it was not possible to identify whether the residue was ASP or ASN. <https://www.rcsb.org/ligand/ASX> You didn't say exactly what you did to get this error. Since the Rotamers graphical interface does not have ASX as a choice and you cannot use ASX in the "swapaa" command, I can only guess that you used "swapaa" with the "same" option to keep the same residue types as in your current structure and that one or more of the specified residues in your current structure is the type ASX. If you want to use "swapaa" with the "same" option, you can only apply it to standard amino acid residues. E.g. if you want to apply "swapaa same" to "sel" (selected residues), you should first remove (deselect) any nonstandard residues such as ASX from your selection. Also note that as mentioned in the "swapaa" help page, "swapaa" is not recommended for predicting the conformations of multiple sidechains in an interacting cluster. For that purpose, you should instead use something like the SCWRL4 program available from the Dunbrack group: <http://dunbrack.fccc.edu/lab/scwrl> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2023, at 8:49 AM, Johnson Paul via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like
MidasError: Dunbrack rotamer library does not support ASX
File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible With Regards, J Johnson Paul.
Thank you for the clarification. With regards, J Johnson Paul. On Thu, 4 May 2023, 00:20 Elaine Meng, <meng@cgl.ucsf.edu> wrote:
Dear J Johnson Paul, This is not a bug -- the rotamer libraries only include standard amino acid residues. ASX is not a standard amino acid residue. It is used in some structures where it was not possible to identify whether the residue was ASP or ASN. <https://www.rcsb.org/ligand/ASX>
You didn't say exactly what you did to get this error. Since the Rotamers graphical interface does not have ASX as a choice and you cannot use ASX in the "swapaa" command, I can only guess that you used "swapaa" with the "same" option to keep the same residue types as in your current structure and that one or more of the specified residues in your current structure is the type ASX.
If you want to use "swapaa" with the "same" option, you can only apply it to standard amino acid residues. E.g. if you want to apply "swapaa same" to "sel" (selected residues), you should first remove (deselect) any nonstandard residues such as ASX from your selection.
Also note that as mentioned in the "swapaa" help page, "swapaa" is not recommended for predicting the conformations of multiple sidechains in an interacting cluster. For that purpose, you should instead use something like the SCWRL4 program available from the Dunbrack group: <http://dunbrack.fccc.edu/lab/scwrl>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2023, at 8:49 AM, Johnson Paul via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Sir, I am J Johnson Paul, I have recently used your software for my study and research purposes after usage of your software in the area of peptide build structure area I have got an error like
MidasError: Dunbrack rotamer library does not support ASX
File "C:\Program Files\Chimera 1.17.1\share\Rotamers\__init__.py", line 680, in useBestRotamers raise MidasError("%s rotamer library does not support %s" %(lib, rType)) This type of error is soon to me,So please kindly reply to my mail to solve the problem as soon as possible With Regards, J Johnson Paul.
participants (2)
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Elaine Meng -
Johnson Paul