Re: [ccp4bb] Structural alignment and classification

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, De

Re: [ccp4bb] Structural alignment and classification

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 -

Re: [ccp4bb] Structural alignment and classification

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

Re: [ccp4bb] Structural alignment and classification

droid<https://aka.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

Re: [ccp4bb] Structural alignment and classification

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 ali

Re: [ccp4bb] Structural alignment and classification

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

Re: [ccp4bb] Structural alignment and classification

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 setting

Re: [ccp4bb] Structural alignment and classification

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

Re: [ccp4bb] Structural alignment and classification

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 > > https://www.ccp

Re: [ccp4bb] Structural alignment and classification

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 Ma

Re: [ccp4bb] Structural alignment and classification

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 > > >

Re: [ccp4bb] Structural alignment and classification

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 ve

Re: [ccp4bb] Structural alignment and classification

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, >

Re: [ccp4bb] Structural alignment and classification

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 clu

[ccp4bb] Structural alignment and classification

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 To unsubscribe from the CCP4B

Re: [ccp4bb] Structural Alignment

UCSF chimera or chimeraX versions both could do the alignment of multiple structures that also pop up the sequence alignment with secondary structures highlighted in different colors through Match Maker. Up-to six structures I have aligned. Best regards Rajivgandhi Sundaram. On Wed, Apr 8, 2020

Re: [ccp4bb] Structural Alignment

Thank you all, I have done it with chimera. It does structural alignment and use it as a template. Then, you can add sequences one after the other and align to this template. You can save this alignment in clustalw format and load it to ESPrit3 and do a nice picture. Armando > El 8 abr 202

Re: [ccp4bb] Structural Alignment

Hi Armando, The PyMol version of this would involve the 'align' command: https://pymolwiki.org/index.php/Align Import your two structures into a PyMol session. In the command line of PyMol, run "align NameOfStructure1, NameOfStructure2, object=SomeNameYouMadeUp". Next, run "save SomeNameYouMadeUp

Re: [ccp4bb] Structural Alignment

I used STRAP back in the late 2000s to do structure-based sequence alignments of some TonB Dependent transporters: http://www.bioinformatics.org/strap/ Looks like it is still being updated. Cheers, Jim -- Jim Fairman C: 1-240

Re: [ccp4bb] Structural Alignment

Hi Armando, This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ More specifically, its matchmaker command will align two structures and print the corresponding sequence alignment: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmak

[ccp4bb] Structural Alignment

Dear all, I want to align two structures and then, I want to align several sequences to that structural alignment. How can I do this? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jisc