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#202 Chain creation problems

3.0.0
closed
nobody
None
3
2017-07-28
2017-07-18
Fogh
No
  • We need some good documentation of the residue type codes and how they work. Basically all residues are given by atype string that is unique across all types. So the one-letter code 'A' corresponds to 'A' for RNA, 'DA' for DNA, and 'ALA' for protein. E.g. 'GUA' is not recognised as wither RNA or DNA.
  • When and how one-letter codes are used and recognised needs checking and documentation. You can certainly create a protein chain from a string of one-letter codes. But I think that otherwise chain creation is given as a sequence of full codes, which would mean that 'ACGT' and 'A C G T' both gave you RNA chains. The interplay between the molecule type pulldown and the value of the sequence needs to be checked, decided on, and documented.
  • We must remember in all contexts that sequences can contain non-standard residues (with no one-letter code), can be of mixed type, and can contain non-polymer residues like glucose, calcium, or NADP.
  • There seems to be no button for cloning an existing chain or making a chain from a substance.
  • The Chain code box in Create Chain defaults to A; it should default to the next free chaincode.

Discussion

  • Fogh

    Fogh - 2017-07-18
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -2,4 +2,4 @@
 * When and how one-letter codes are used and recognised needs checking and documentation. You can certainly create a protein chain from a string of one-letter codes. But I think that otherwise chain creation is given as a sequence of full codes, which would mean that 'ACGT' and 'A C G T' both gave you RNA chains. The interplay between the molecule type pulldown and the value of the sequence needs to be checked, decided on, and documented.
 * We must remember in all contexts that sequences can contain non-standard residues (with no one-letter code), can be of mixed type, and can contain non-polymer residues like glucose, calcium, or NADP. 
 * There seems to be no button for cloning an existing chain or making a chain from a substance.
-* I do not b3lieve you can enter a chain name up front when creating a chain.
+* I do not believe you can enter a chain name up front when creating a chain.
     

  • Fogh

    Fogh - 2017-07-18
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -2,4 +2,4 @@
 * When and how one-letter codes are used and recognised needs checking and documentation. You can certainly create a protein chain from a string of one-letter codes. But I think that otherwise chain creation is given as a sequence of full codes, which would mean that 'ACGT' and 'A C G T' both gave you RNA chains. The interplay between the molecule type pulldown and the value of the sequence needs to be checked, decided on, and documented.
 * We must remember in all contexts that sequences can contain non-standard residues (with no one-letter code), can be of mixed type, and can contain non-polymer residues like glucose, calcium, or NADP. 
 * There seems to be no button for cloning an existing chain or making a chain from a substance.
-* I do not believe you can enter a chain name up front when creating a chain.
+* The Chain code box in Create Chain defaults to A; it should default to the next free chaincode.
     

  • wb104

    wb104 - 2017-07-20

    Clone now added to right mouse menu of SideBar for chains.
    The New Chain dialog now defaults the chain code to the "next" available one.

     

  • wb104

    wb104 - 2017-07-28
     

  • wb104

    wb104 - 2017-07-28

    Last two parts resolved so close and open new ticket for remaining items.

     

  • wb104

    wb104 - 2017-07-28
    • status: open --> closed
     

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