Chains with symbol ID such as % and $ cause errors
I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get: show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Hi Ahmad, Those special characters are not allowed as chain IDs. It is not just a Chimera(X) requirement, but part of the PDB/mmCIF format description, for example described in: <https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> "Each polymer chain must have a unique chain ID. Permissible characters are uppercase letters A-Z, lowercase letters a-z, and numbers 0-9. PDB format allows only single-character chain IDs, while PDBx/mmCIF can accommodate chain IDs of up to four characters.” I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2020, at 8:11 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get:
show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Hi Elaine, The chain IDs were assigned by Coot. Perhaps Paul or some Coot people can give some input regarding that. Regards. On Wed, Jan 8, 2020 at 12:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, Those special characters are not allowed as chain IDs. It is not just a Chimera(X) requirement, but part of the PDB/mmCIF format description, for example described in:
<https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files>
"Each polymer chain must have a unique chain ID. Permissible characters are uppercase letters A-Z, lowercase letters a-z, and numbers 0-9. PDB format allows only single-character chain IDs, while PDBx/mmCIF can accommodate chain IDs of up to four characters.”
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 8, 2020, at 8:11 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get:
show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
participants (2)
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Ahmad Khalifa -
Elaine Meng