[Chimera-users] [EXTERNAL] Re: RMSF calculations

[Reza Khayat]

Hi Elaine,

Thanks for letting me know. I can use the rmsd command you mention. 

Best wishes,
Reza


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

________________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, May 12, 2022 6:46 PM
To: Reza Khayat
Cc: Chimera-users BB
Subject: Re: [Chimera-users] [EXTERNAL] Re:  RMSF calculations

Hi Reza,
Sorry, this approach in Chimera or ChimeraX only works with protein or nucleic acid chains, where the sequence alignment can be displayed in a separate window.

Both Chimera and ChimeraX have an "rmsd" command to calculate RMSD between any two sets of atoms (any types of molecules) in their current positions, without moving them to fit.  However, it only works pairwise, not among multiple structures, so you could only get the RMSD between two structures, not among more than two.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 12, 2022, at 2:15 PM, Reza Khayat via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Elaine and Eric,
>
> I was unaware that ChimeraX did this. I now have a script for ChimeraX; however, I have the problem of wanting to calculate the RMSF for non-standard residues (glycans). The sequence chain command does not extract the glycan sequence. Is it possible to calculate the RMSF of glycans with ChimeraX? Thanks.
>
> Best wishes,
> reza
>
> Reza Khayat, PhD
> Associate Professor
> City College of New York
> Department of Chemistry and Biochemistry
> New York, NY 10031
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> Sent: Thursday, May 12, 2022 12:50 PM
> To: Reza Khayat
> Cc: chimera-users at cgl.ucsf.edu
> Subject: [EXTERNAL] Re: [Chimera-users] RMSF calculations
>
> Hi Reza,
> As Elaine said, this may be simpler in ChimeraX.  Nonetheless, if you have a fasta file (or equivalent) with your sequence in it, all members of the ensemble should automatically associate with the sequence when you open it.  Nonetheless, the remaining steps (showing RMSD header, saving attributes file) do not have command equivalents and would require resorting to some moderately difficult Python code.  I don’t know if you’d prefer to do that or switch this to ChimeraX where it’s more directly supported.  I can provide guidance on the former if you really want to stick with Chimera for some reason.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On May 12, 2022, at 7:40 AM, Reza Khayat via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Hi,
>>
>> I'm trying to write a script to perform the procedure described here:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_pipermail_chimera-2Dusers_2017-2DMarch_013247.html&d=DwIFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=zTeDVN-xcJ2915dJUgkaBSXJizP41cWzlvx6RUBJHbA&s=8EOzsJ_BZwk9__IpjjHfJUxcKe-hbSwk6sCVysYFJCE&e=
>>
>> Can someone help with the command line syntax for associating a structure with a defined sequence? Thanks.
>>
>> Best wishes,
>> Reza
>>
>> Reza Khayat, PhD
>> Associate Professor
>> City College of New York
>> Department of Chemistry and Biochemistry
>> New York, NY 10031
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwIFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=zTeDVN-xcJ2915dJUgkaBSXJizP41cWzlvx6RUBJHbA&s=xuz5Aq_E0eqqqa9ixaG1O0d4SDesbkDQ4V4jZ7rHRl0&e=
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwIFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=zTeDVN-xcJ2915dJUgkaBSXJizP41cWzlvx6RUBJHbA&s=xuz5Aq_E0eqqqa9ixaG1O0d4SDesbkDQ4V4jZ7rHRl0&e=