Re: [ccp4bb] Structural alignment and classification

[Debanu Das]

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,
Debanu

On Thu, Mar 9, 2023 at 3:57 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> 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 9 Mar 2023, 13:55, Paul Emsley < pems...@mrc-lmb.cam.ac.uk> wrote:
>
>
> 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
> this in Coot, because, for LSQ fitting, Coot only returns the
> transformation matrix, not any fitting statistics - in retrospect this is
> obviously an oversight.) Paul.
>  To
> unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Jon Cooper]

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 9 Mar 2023, 13:55, Paul Emsley wrote:

> 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 
> this in Coot, because, for LSQ fitting, Coot only returns the transformation 
> matrix, not any fitting statistics - in retrospect this is obviously an 
> oversight.) Paul. 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message 
> was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by 
> www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] Structural alignment and classification

[Paul Emsley]

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 this in Coot, because, for LSQ fitting, Coot only 
returns the transformation matrix, not any fitting statistics - in 
retrospect this is obviously an oversight.)



Paul.



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Re: [ccp4bb] Structural alignment and classification

[Daniel Celis Garza - STFC UKRI]

This sounds suspiciously like what the team from EBI that Eugene and I have 
been working with either have done, or want to do.

They already have a way to cluster structures, but GESAMT is overfitting for 
their needs. It might not for yours, but it would depend on exactly what you 
want to do.

Where I've come in is in creating a program that can match and superpose 
analogous chains from different structures and spit out progressively more 
complete structures as more and more chains get matched and added. This assumes 
there is high homology between structures, but it's not a requirement, though 
its usefulness would decline as you move further away from homology.

The analysis would then be to try to figure out at what point do we say that 
there has been a conformation change in the quaternary structure at the chain 
level. I have some ideas, on how to accomplish this, but I'm still working on 
parsing the output.

As far as having structures with wildly different homologies, I'd probably use 
GESAMT, and try to figure out what parameters to use for clustering. Perhaps 
the convex hull of the matched residues? Or even using SSM if there are 
secondary structures and classifying them based on that? This paper I found 
while researching the problem may give you some idea of how convex hulls could 
be used to classify protein families.

@article{wang2007supervised,
  title={Supervised classification of protein structures based on convex hull 
representation},
  author={Wang, Yong and Wu, Ling-Yun and Chen, Luonan and Zhang, Xiang-Sun},
  journal={International Journal of Bioinformatics Research and Applications},
  volume={3},
  number={2},
  pages={123--144},
  year={2007},
  publisher={Inderscience Publishers}
}

Sent from Outlook for Android<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 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 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<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Or you could use Gesamt - also in CCP4.

Harry

> On 6 Mar 2023, at 13:15, Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 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 very 
> robust; SUPERPOSE is fast.
>
> HTH,
> Kay
>
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert 
> mailto:xalb...@iqfr.csic.es>> wrote:
>
>> 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 CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Eugene Krissinel - STFC UKRI]

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 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<mailto:193323b1e616-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Or you could use Gesamt - also in CCP4.

Harry

> On 6 Mar 2023, at 13:15, Kay Diederichs 
> mailto:kay.diederi...@uni-konstanz.de>> 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 very 
> robust; SUPERPOSE is fast.
>
> HTH,
> Kay
>
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert 
> mailto:xalb...@iqfr.csic.es>> wrote:
>
>> 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 CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of 
>> www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list 
>> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions 
>> are available at https://www.jiscmail.ac.uk/policyandsecurity/
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Eugene Krissinel - STFC UKRI]

Having indeed written Gesamt some 10-12 years ago, I had to refresh my memory 
before answering.

Gesamt definitely aligns multiple structures, just give them all on command 
line.

It should do clustering in "sheaf" mode (which assumes that chains have same 
lengths and atoms are matched one-to-one). May be Daniel (in cc) can see how to 
implement clustering in his doings.

Gesamt can also identify conformations, i.e. similar substructures with 
relative displacement or rotation in compared structures.

Run gesamt without parameters to print all command-line options.

For saying more 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 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.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 Mar 2023, at 14:55, Eleanor Dodson  wrote:
>>
>> 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
>>
>>> 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 very 
>>> robust; SUPERPOSE is fast.
>>>
>>> HTH,
>>> Kay
>>>
>>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
>>> wrote:
>>>
>>>> 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 CCP4BB list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>>
>>>> This message was issued to members of 
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>>>> list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & 
>>>> conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>> 
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Re: [ccp4bb] Structural alignment and classification

[Helen Ginn]

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 up other binaries.


The scientific write-up of the tool is here, and also contains a written 
tutorial for how to use the program:

https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4608

Additional instructions (particularly for loading your own PDB files or 
metadata for analysis) can be found here:

https://rope.hginn.co.uk/index.php?page=dox

One serious advantage of using the internal torsion angles is that you 
can skip the structural alignment (I would recommend using a different 
program for this explicitly), and it describes the conformation of the 
protein in the same parameter space as it naturally tends to flex. It 
can also highlight the 'hinge' regions within your structure (i.e. the 
backbone angles that vary the most). If you definitely want to cluster 
on RMSD alone, do ask (it's been implemented for comparison purposes in 
the paper, but is not the default option).


I'd recommend it to anyone who is looking to classify/understand 
conformational changes across a range of related structures, regarding 
both large and subtle modes of motion.


Best wishes
Helen

Dr Helen Ginn
Group leader, DESY
Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR)
Luruper Chaussee 149
22607 Hamburg



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Re: [ccp4bb] Structural alignment and classification

[Karplus, Andy]

HI Armando,

The “Ensemblator” (available on Github at 
https://github.com/Karplus-Lab-OSU/ensemblator ) is a program we published back 
in 2017 that aligns structures and clusters them.

Furthermore, the main purpose of the program and what I think is most unique 
about it, is that given two sets (clusters) of structures you are interested 
in, the program carries out analyses that identify the most significant 
structural differences both based on global overlays and in terms of local 
conformational differences.

The paper describing the Ensemblator is: 
https://pubmed.ncbi.nlm.nih.gov/28762605/

HTH, Andy

[Black Lives Matter]

Dr. P. Andrew Karplus (he, him, his)
Distinguished Professor of Biochemistry and Biophysics
NIGMS GCE4All Research Center<http://gce4all.oregonstate.edu/> Director of 
Communications
2133 ALS Building
Oregon State University
Corvallis, OR 97331
ph. 541-737-3200
andy.karp...@oregonstate.edu<mailto:andy.karp...@oregonstate.edu>

“Revealing how life works for the benefit of all!”
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https://www.facebook.com/OSUBB



From: CCP4 bulletin board  on behalf of Armando Albert 

Date: Monday, March 6, 2023 at 7:21 AM
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?
Armando


> El 6 mar 2023, a las 15:58, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió:
>
> Hi Eleanor
>
> According to
>
>   
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fgesamt.html=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=3PguIbtTuxtk8mtBgna2tafOMHIbPQxF13GTjopfZOw%3D=0
>
> "Gesamt aligns two or more structures…”
>
> and
>
>   
> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fsuperpose.html=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AH2jgosqwV%2FAK6mYaEJN4fUSYJw%2BH9NY%2BfQh9edQpfA%3D=0
>
> "superpose aligns and superposes two or more protein structures…”
>
> But the real expert is probably Eugene.
>
> Harry
>
>> On 6 Mar 2023, at 14:55, Eleanor Dodson  wrote:
>>
>> 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
>>
>>> On 6 Mar 2023, at 13:15, Kay Diederichs  
>>> wrote:
>>>
>>> Dear Armando,
>>>
>>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign 
>>> (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzhanggroup.org%2FUS-align%2F=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ZMl04%2B8PZVkXxpQpsEBt2bxUngxVsiBRGUhCVIOy7AE%3D=0).
>>> 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,
>>>> 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 CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Armando Albert]

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.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 Mar 2023, at 14:55, Eleanor Dodson  wrote:
>> 
>> 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
>> 
>>> 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 very 
>>> robust; SUPERPOSE is fast.
>>> 
>>> HTH,
>>> Kay
>>> 
>>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
>>> wrote:
>>> 
 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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Re: [ccp4bb] Structural alignment and classification

[Harry Powell]

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 Mar 2023, at 14:55, Eleanor Dodson  wrote:
> 
> 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
> 
> > 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 very 
> > robust; SUPERPOSE is fast.
> > 
> > HTH,
> > Kay
> > 
> > On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
> > wrote:
> > 
> >> 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 CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Eleanor Dodson]

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
>
> > 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
> very robust; SUPERPOSE is fast.
> >
> > HTH,
> > Kay
> >
> > On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert 
> wrote:
> >
> >> 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 CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
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Re: [ccp4bb] Structural alignment and classification

[Harry Powell]

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 very 
> robust; SUPERPOSE is fast.
> 
> HTH,
> Kay
> 
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert  
> wrote:
> 
>> 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 CCP4BB list, click the following link:
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Re: [ccp4bb] Structural alignment and classification

[Kay Diederichs]

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, 
>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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Re: [ccp4bb] Structural alignment and classification

[Eleanor Dodson]

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 cluster them according to RMSD.
> Is MNYFIT still running? What else can I run?
> Thank you
> Armando
>
> 
>
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[ccp4bb] Structural alignment and classification

[Armando Albert]

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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Re: [ccp4bb] Structural Alignment

[Rajiv gandhi.s]

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, 11:09 PM Armando Albert  wrote:

> 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 2020, a las 19:22, Guillaume Gaullier 
> escribió:
>
> 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/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> 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:
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>
>
>
>
> --
>
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Re: [ccp4bb] Structural Alignment

[Armando Albert]

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 2020, a las 19:22, Guillaume Gaullier  
> escribió:
> 
> 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/matchmaker.html 
> 
> You can then save the sequence alignment to a file, and use it in your 
> favorite sequence alignment program along with the sequences for which you 
> don’t have a structure.
> 
> This is one option among many, as pretty much every structure visualization 
> program can superimpose two similar structures (but I don’t know how many of 
> them make it as easy to save the sequence alignment).
> 
> Hope this helps,
> 
> Guillaume
> 
> 
>> On 8 Apr 2020, at 19:04, Armando Albert > > wrote:
>> 
>> 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:
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>> 
> 




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Re: [ccp4bb] Structural Alignment

[Nicholas Gao]

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.aln,
SomeNameYouMadeUp".  This will product a 2D sequence alignment that you can
then take off to other sequence aligners to use as a reference in
subsequent sequence alignments.

-Nick

On Wed, Apr 8, 2020 at 1:22 PM Guillaume Gaullier 
wrote:

> 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/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> 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.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] Structural Alignment

[Jim Fairman]

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: 1-240-479-6575


On Wed, Apr 8, 2020 at 10:22 AM Guillaume Gaullier 
wrote:

> 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/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> 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.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] Structural Alignment

[Guillaume Gaullier]

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/matchmaker.html 

You can then save the sequence alignment to a file, and use it in your favorite 
sequence alignment program along with the sequences for which you don’t have a 
structure.

This is one option among many, as pretty much every structure visualization 
program can superimpose two similar structures (but I don’t know how many of 
them make it as easy to save the sequence alignment).

Hope this helps,

Guillaume


> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
> 
> 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:
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[ccp4bb] Structural Alignment

[Armando Albert]

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



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