[chimerax-users] Morphing with ligands

[Elaine Meng]

Before creating the morph, I used matchmaker to superimpose the three structures by matching each chain to the others with the same chain ID:

mm #2/t,u,v,x,y,z to #1/t,u,v,x,y,z pair ss
mm #3/t,u,v,x,y,z to #1/t,u,v,x,y,z pair ss

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

Elaine


> On Aug 10, 2021, at 3:03 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Volodymyr,
> It's not really complex: only the ligand and ion residues that are in all 3 structures (with same residue numbers and names and atom names) will be in the morph.  So if you didn't manually edit anything, as per what I sent before, the resulting morph will only contain the ATP and MG in chain T and in chain U.   None of the ATP, ADP, or MG residues in chains V, X, Y, Z will be included.
> 
> I tested this by opening the 3 structures and (to speed up testing removed all chains except the ATP synthase, namely T,U,V and X,Y,Z) and it did agree with the above predictions.  See images below of input models and output morph.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On the left are the input models, you can see the ADP or ATP in all chains, and on the right is the morph, you can see ATP only in two chains.
> <inputs.png><output.png>
> 
>> On Aug 10, 2021, at 2:36 PM, Volodymyr Dvornyk via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> 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
>> 
>> 
>> ________________________________
>> 
>> DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While “Alfaisal University” has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.
>> 
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users