[chimerax-users] Morphing with ligands

[Volodymyr Dvornyk]

Dear Elaine,

Thanks  lot for so detailed explanations. Sorry, the algorithm seems too complex to me. I just added 'same t' and it seems working.

Best,

Volodymyr

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, August 10, 2021 21:20
To: Volodymyr Dvornyk <vdvornyk at alfaisal.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Morphing with ligands

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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