Try POSA and FATCAT from Godzik group for structural clusters/trees and
multiple/flexible structure alignments:
https://academic.oup.com/nar/article/48/W1/W60/5848494
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086100/
https://posa.godziklab.org/
https://fatcat.godziklab.org/
Best regards,
Coot's ssm superposition does give the C-alpha rmsd, though, most easily seen
if you run it from a terminal window? I guess it can't be miles different from
a least-squares fit ;-?
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
On 06/03/2023 07:35, Armando Albert wrote:
I want to align several structures we obtained from a fragment screening
campaign and cluster them according to RMSD.
To what end, may I ask?
I would use LSQKAB, parse the log files for the RMSD and create an input
file for R.
(One cannot just do
.ms/AAb9ysg>
From: Krissinel, Eugene (STFC,RAL,SC)
Sent: Wednesday, March 8, 2023 12:54:07 PM
To: ccp4bb ; Eleanor Dodson
Cc: Celis Garza, Daniel (STFC,RAL,SC)
Subject: Re: [ccp4bb] Structural alignment and classification
yes selecting models and chains in SSM &a
yes selecting models and chains in SSM & Gesamt is possible -- Eugene
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: 06 March 2023 14:55
To: ccp4bb
Subject: Re: [ccp4bb] Structural
ore I need specific questions.
Eugene
From: CCP4 bulletin board on behalf of Armando Albert
Sent: 06 March 2023 15:19
To: ccp4bb
Subject: Re: [ccp4bb] Structural alignment and classification
Thank you all.
What about the analysis? Does any program cluster the
Dear Armando,
I have recently published a program which classifies/clusters protein
structures on the internal torsion angles, RoPE
(https://rope.hginn.co.uk). It is a GUI, in the form of a web
application and a preferable Mac executable (faster & multi-threaded).
I'm still working on
M
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Structural alignment and classification
[This email originated from outside of OSU. Use caution with links and
attachments.]
Thank you all.
What about the analysis? Does any program cluster the structures according to
their structural similarity?
Arma
Thank you all.
What about the analysis? Does any program cluster the structures according to
their structural similarity?
Armando
> El 6 mar 2023, a las 15:58, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió:
>
> Hi Eleanor
>
> According to
>
>
Hi Eleanor
According to
https://www.ccp4.ac.uk/html/gesamt.html
"Gesamt aligns two or more structures…”
and
https://www.ccp4.ac.uk/html/superpose.html
"superpose aligns and superposes two or more protein structures…”
But the real expert is probably Eugene.
Harry
> On 6
Does Superpose or GESAMT align multiple structures?
And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L
2 etc?
Eleanor
On Mon, 6 Mar 2023 at 14:53, Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Or you could use Gesamt - also in CCP4.
>
> Harry
>
>
Or you could use Gesamt - also in CCP4.
Harry
> On 6 Mar 2023, at 13:15, Kay Diederichs
> wrote:
>
> Dear Armando,
>
> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign
> (https://zhanggroup.org/US-align/).
> In my tests, THESEUS sometimes crashed in different ways. USalign is
Dear Armando,
besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign
(https://zhanggroup.org/US-align/).
In my tests, THESEUS sometimes crashed in different ways. USalign is very
robust; SUPERPOSE is fast.
HTH,
Kay
On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert wrote:
>Dear all,
See the answer last week to my query about aligning nmr structures - use
Theseus .
I wonder if it could be used for this task too?
Eleanor
On Mon, 6 Mar 2023 at 07:35, Armando Albert wrote:
> Dear all,
> I want to align several structures we obtained from a fragment screening
> campaign and
Dear all,
I want to align several structures we obtained from a fragment screening
campaign and cluster them according to RMSD.
Is MNYFIT still running? What else can I run?
Thank you
Armando
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