[chimerax-users] Morphing with ligands

[Elaine Meng]

Thanks for the correction, Tom! I will fix the documentation today.  So to include any specific ADP, ATP, and/or MG residues in the morph trajectory, Volodymyr would need to "manually" add them to any input structures from which they are missing.

Alternatively, if they are just going to appear in static positions at certain times in the trajectory, that can be done by keeping the input models present in the session (but hidden), and then just displaying those specific residues from those models at the appropriate times in the morph trajectory playback.  This can be done by using "coordset" commands to play specific segments (frame ranges) of the trajectory interleaved with "show/hide" commands.

Best,
Elaine

> On Aug 10, 2021, at 2:31 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Elaine,
> 
>  For a morph of 3 conformations only the atoms common to all 3 structures will be included.  Each of the two segments of the morph cannot have different sets of atoms because the morph is a single trajectory and trajectories have the same set of atoms at every frame.
> 
> 	Tom
> 
> 
>> On Aug 10, 2021, at 11:19 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi Volodymyr,
>> Looking at #1 6rdc, #2 6rep, #3 6rd9
>> 
>> chain V: ATP 1001 and MG 1002 in #1 and #2, ATP 1000 and MG 1001 in #3
>> 
>> chain Y:  ADP 601 and MG 602 in #1 and #3, not present in #2
>> 
>> chain T: ATP 1001 and MG 1002 in all three models
>> 
>> chain X: ATP 601 and MG 602 in #2 and #3, not present in #1
>> 
>> chain U: ATP 1001 and MG 1002 in all three models
>> 
>> chain Z: ADP 601 and MG 602 in #1 and #2, not present in #3
>> 
>> So to make the chain V residue numbers match up, may need to make a manually edited copy of #3 in which ATP and MG are renumbered to match the others and use it instead of the original #3, as well as the "same true" morph option.
>> 
>> The next issue I wasn't sure about was whether you'd need same residue in all 3 structures to be in a morph of all 3 structures, but at least according to the documentation link sent by Tom (and probably written by me), sounds like only the two endpoint structures for each segment of the morph that are important for what atoms show up in that segment.   So it depends what order you are visiting the 3 structures as to which nucleotide and ion residues will be present.
>> 
>> If you wanted ALL of those residues to be present in the whole morph, you may need to make manually edited versions of the models that contain them where they are missing (e.g. 6rd9 does not have ADP601 and MG 602 in chain Z).  I realize that is not accurate to display along with the structures that did not originally contain them, but these atoms could be present in the morph and then only displayed at the appropriate times in conjunction with the states of the complex that do actually contain them.
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Aug 10, 2021, at 9:21 AM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Maybe the morph command option "same true" is needed.  The rules for pairing up ligands for morphing are described in the documentation
>>> 
>>> 	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing
>>> 
>>> If it is not behaving according to these rules then use ChimeraX menu Help / Report a Bug and attach two example structures that demonstrate the problem.
>>> 
>>> Tom
>>> 
>>> 
>>>> On Aug 10, 2021, at 7:18 AM, Volodymyr Dvornyk via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>>> 
>>>> Dear Colleagues,
>>>> Tried to do morphing of the following structures: 6rdc, 6rep, and 6rd9. All three have the same ligands: ADP, ATP, Mg, and Zn. However, the resulting model lacks all of them. Any thoughts and/or suggestions? 
>>>> Thank you.
>>>> Volodymyr
>> 
>> 
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> 
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