[ccp4bb] modelling in coot

[smita yadav]

Dear Community,
  I had a problem in correcting cis and tran peptide of
structure in coot. how i can resolve it.

-- 
Regards,
Smita Yadav
Ph.D JRF
Regional Centre for biotechnology,
Haryana-121001.



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Jessica Besaw]

THE PROBLEM IS SOLVED!

Thank you all for you suggestions. I applied all the suggestion across all
datasets collected (not just the one shown above).

The error & solution: Incorrect space group assignment (new space group P
21 2 21) and ignoring tNCS.

This is the BEST Christmas gift a crystallographer could get.  Thank you
everyone!

Cheers!

Jessica












On Mon, 16 Dec 2019 at 16:16, Wim Burmeister  wrote:

> Hello,
> I would guess that the badly fitting molecule may be upside down (related
> my an 2-fold axis).
> I would use the first, partially refined structure for another round of
> molecular replacement in P212121 with molrep, using the model as well as a
> partial solution as as asearch model.
> The translational self peak in the native Patterson may be misleading. I
> came recently across a similar problem.
> Regards
> Wim
>
> --
> *De: *"Jessica Besaw" 
> *À: *"CCP4BB" 
> *Envoyé: *Lundi 16 Décembre 2019 20:29:38
> *Objet: *Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in
> asymmetric unit does not fit density
>
> There have been two potential space groups:
> P212121 - Rfree = 36%
> P21212 - Rfree = 45%
>
> Xtriage reports that twinning is unlikely.
>
> Cheers!
>
> Jessica
>
>
>
>
>
> On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch  wrote:
>
>> What’s your spacegroup ? RWork / RFree?
>> Twinning by any chance?
>>
>> Jürgen
>>
>> __
>> Jürgen Bosch, Ph.D.
>> Division of Pediatric Pulmonology and Allergy/Immunology
>> Case Western Reserve University
>> 2109 Adelbert Rd, BRB 835
>> Cleveland, OH 44106
>> Phone: 216.368.7565
>> Fax: 216.368.4223
>> https://www.linkedin.com/in/jubosch/
>>
>> CEO & Co-Founder at InterRayBio, LLC
>>
>> Johns Hopkins University
>> Bloomberg School of Public Health
>> Department of Biochemistry & Molecular Biology
>>
>> On Dec 16, 2019, at 1:50 PM, Jessica Besaw  wrote:
>>
>> I am crystallizing this membrane protein in a medium (bicelles) that
>> forms lamella like sheets that stack on top of each other.
>> The layer packing is shown below. Is this structure unreasonable?
>>
>> 
>>
>> On Mon, 16 Dec 2019 at 13:38, Reza Khayat  wrote:
>>
>>> Hi Jessica,
>>>
>>>
>>> The gap between the two proteins is a bit troubling. Perhaps it's the
>>> image, but why would a crystal form if there is no crystal contact between
>>> the two proteins?
>>>
>>>
>>> Reza
>>>
>>>
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>> --
>>> *From:* CCP4 bulletin board  on behalf of Ashish
>>> Kumar 
>>> *Sent:* Monday, December 16, 2019 1:24 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric
>>> unit does not fit density
>>>
>>> Hi Jessica,
>>>
>>> It may be possible because of wrong MR solution as well. How were your
>>> stats after MR.
>>> Also it is correct that it could be possible because of wrong space
>>> group.
>>> Try changing the Space group and repeat MR.
>>>
>>> Best Regards
>>> Ashish
>>>
>>> On 16 Dec 2019 22:56, "Jessica Besaw"  wrote:
>>>
>>> Dear community,
>>>
>>> I am having a lot of trouble solving a protein structure. I think my
>>> problem may caused by incorrectly placed proteins in molecular replacement.
>>> I have two proteins in my asymmetric unit. It appears that one protein fits
>>> perfectly, and the other one has many errors. (See snapshots below). I have
>>> tried deleting the parts of the protein (and even the whole protein) to try
>>> and rebuild it in COOT, but it was a bit too difficult for me to solve.
>>>
>>> I would appreciate any and all suggestions for potential strategies
>>> moving forward.
>>>
>>> Other information:
>>> (1) 2.4 Angstrom
>>> (2) 99% complete
>>> (3) "Translational NCS may be present at a level that may complicate
>>> refinement"
>>>
>>> Cheers!
>>>
>>> Jessica
>>>
>>> 
>>> 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>> 
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>> 
>>>
>>> --
>>>
>>> To 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Wim Burmeister]

Hello, 
I would guess that the badly fitting molecule may be upside down (related my an 
2-fold axis). 
I would use the first, partially refined structure for another round of 
molecular replacement in P212121 with molrep, using the model as well as a 
partial solution as as asearch model. 
The translational self peak in the native Patterson may be misleading. I came 
recently across a similar problem. 
Regards 
Wim 


De: "Jessica Besaw"  
À: "CCP4BB"  
Envoyé: Lundi 16 Décembre 2019 20:29:38 
Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric 
unit does not fit density 

There have been two potential space groups: 
P212121 - Rfree = 36% 
P21212 - Rfree = 45% 

Xtriage reports that twinning is unlikely. 

Cheers! 

Jessica 





On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch < [ mailto:jxb...@case.edu | 
jxb...@case.edu ] > wrote: 



What’s your spacegroup ? RWork / RFree? 
Twinning by any chance? 

Jürgen 

__ 
Jürgen Bosch, Ph.D. 
Division of Pediatric Pulmonology and Allergy/Immunology 
Case Western Reserve University 
2109 Adelbert Rd, BRB 835 
Cleveland, OH 44106 
Phone: 216.368.7565 
Fax: 216.368.4223 
[ https://www.linkedin.com/in/jubosch/ | https://www.linkedin.com/in/jubosch/ ] 

CEO & Co-Founder at InterRayBio, LLC 

Johns Hopkins University 
Bloomberg School of Public Health 
Department of Biochemistry & Molecular Biology 


BQ_BEGIN

On Dec 16, 2019, at 1:50 PM, Jessica Besaw < [ mailto:jbesaw1...@gmail.com | 
jbesaw1...@gmail.com ] > wrote: 

I am crystallizing this membrane protein in a medium (bicelles) that forms 
lamella like sheets that stack on top of each other. 
The layer packing is shown below. Is this structure unreasonable? 

 

On Mon, 16 Dec 2019 at 13:38, Reza Khayat < [ mailto:rkha...@ccny.cuny.edu | 
rkha...@ccny.cuny.edu ] > wrote: 

BQ_BEGIN



​​Hi Jessica, 





The gap between the two proteins is a bit troubling. Perhaps it's the image, 
but why would a crystal form if there is no crystal contact between the two 
proteins? 





Reza 



Reza Khayat, PhD 
Assistant Professor 
City College of New York 
Department of Chemistry 
New York, NY 10031 

From: CCP4 bulletin board < [ mailto:CCP4BB@JISCMAIL.AC.UK | 
CCP4BB@JISCMAIL.AC.UK ] > on behalf of Ashish Kumar < [ 
mailto:mail2ashish...@gmail.com | mail2ashish...@gmail.com ] > 
Sent: Monday, December 16, 2019 1:24 PM 
To: [ mailto:CCP4BB@JISCMAIL.AC.UK | CCP4BB@JISCMAIL.AC.UK ] 
Subject: [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does 
not fit density 
Hi Jessica, 

It may be possible because of wrong MR solution as well. How were your stats 
after MR. 
Also it is correct that it could be possible because of wrong space group. 
Try changing the Space group and repeat MR. 

Best Regards 
Ashish 

On 16 Dec 2019 22:56, "Jessica Besaw" < [ mailto:jbesaw1...@gmail.com | 
jbesaw1...@gmail.com ] > wrote: 

BQ_BEGIN

Dear community, 

I am having a lot of trouble solving a protein structure. I think my problem 
may caused by incorrectly placed proteins in molecular replacement. I have two 
proteins in my asymmetric unit. It appears that one protein fits perfectly, and 
the other one has many errors. (See snapshots below). I have tried deleting the 
parts of the protein (and even the whole protein) to try and rebuild it in 
COOT, but it was a bit too difficult for me to solve. 

I would appreciate any and all suggestions for potential strategies moving 
forward. 

Other information: 
(1) 2.4 Angstrom 
(2) 99% complete 
(3) "Translational NCS may be present at a level that may complicate 
refinement" 

Cheers! 

Jessica 

 
 










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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[adarsh kumar]

Hi Jessica

You may try the following (if you haven't already):

1. Try solving it using P222 space group.
2. Re-index using different axes.


*Regards*



*Adarsh Kumar*

*Florida State University College of Medicine*


*Tallahassee, FL - 32304*



On Mon, Dec 16, 2019 at 2:30 PM Jessica Besaw  wrote:

> There have been two potential space groups:
>
> P212121 - Rfree = 36%
> P21212 - Rfree = 45%
>
> Xtriage reports that twinning is unlikely.
>
> Cheers!
>
> Jessica
>
>
>
>
>
> On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch  wrote:
>
>> What’s your spacegroup ? RWork / RFree?
>>
>> Twinning by any chance?
>>
>> Jürgen
>>
>> __
>> Jürgen Bosch, Ph.D.
>> Division of Pediatric Pulmonology and Allergy/Immunology
>> Case Western Reserve University
>> 2109 Adelbert Rd, BRB 835
>> Cleveland, OH 44106
>> Phone: 216.368.7565
>> Fax: 216.368.4223
>> https://www.linkedin.com/in/jubosch/
>>
>> CEO & Co-Founder at InterRayBio, LLC
>>
>> Johns Hopkins University
>> Bloomberg School of Public Health
>> Department of Biochemistry & Molecular Biology
>>
>> On Dec 16, 2019, at 1:50 PM, Jessica Besaw  wrote:
>>
>> I am crystallizing this membrane protein in a medium (bicelles) that
>> forms lamella like sheets that stack on top of each other.
>>
>> The layer packing is shown below. Is this structure unreasonable?
>>
>> 
>>
>> On Mon, 16 Dec 2019 at 13:38, Reza Khayat  wrote:
>>
>>> ​​Hi Jessica,
>>>
>>>
>>> The gap between the two proteins is a bit troubling. Perhaps it's the
>>> image, but why would a crystal form if there is no crystal contact between
>>> the two proteins?
>>>
>>>
>>> Reza
>>>
>>>
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>> --
>>> *From:* CCP4 bulletin board  on behalf of Ashish
>>> Kumar 
>>> *Sent:* Monday, December 16, 2019 1:24 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric
>>> unit does not fit density
>>>
>>> Hi Jessica,
>>>
>>> It may be possible because of wrong MR solution as well. How were your
>>> stats after MR.
>>> Also it is correct that it could be possible because of wrong space
>>> group.
>>> Try changing the Space group and repeat MR.
>>>
>>> Best Regards
>>> Ashish
>>>
>>> On 16 Dec 2019 22:56, "Jessica Besaw"  wrote:
>>>
>>> Dear community,
>>>
>>> I am having a lot of trouble solving a protein structure. I think my
>>> problem may caused by incorrectly placed proteins in molecular replacement.
>>> I have two proteins in my asymmetric unit. It appears that one protein fits
>>> perfectly, and the other one has many errors. (See snapshots below). I have
>>> tried deleting the parts of the protein (and even the whole protein) to try
>>> and rebuild it in COOT, but it was a bit too difficult for me to solve.
>>>
>>> I would appreciate any and all suggestions for potential strategies
>>> moving forward.
>>>
>>> Other information:
>>> (1) 2.4 Angstrom
>>> (2) 99% complete
>>> (3) "Translational NCS may be present at a level that may complicate
>>> refinement"
>>>
>>> Cheers!
>>>
>>> Jessica
>>>
>>> 
>>> 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>> 
>>>
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>> 
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>>
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>
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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Jessica Besaw]

There have been two potential space groups:

P212121 - Rfree = 36%
P21212 - Rfree = 45%

Xtriage reports that twinning is unlikely.

Cheers!

Jessica





On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch  wrote:

> What’s your spacegroup ? RWork / RFree?
>
> Twinning by any chance?
>
> Jürgen
>
> __
> Jürgen Bosch, Ph.D.
> Division of Pediatric Pulmonology and Allergy/Immunology
> Case Western Reserve University
> 2109 Adelbert Rd, BRB 835
> Cleveland, OH 44106
> Phone: 216.368.7565
> Fax: 216.368.4223
> https://www.linkedin.com/in/jubosch/
>
> CEO & Co-Founder at InterRayBio, LLC
>
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
>
> On Dec 16, 2019, at 1:50 PM, Jessica Besaw  wrote:
>
> I am crystallizing this membrane protein in a medium (bicelles) that forms
> lamella like sheets that stack on top of each other.
>
> The layer packing is shown below. Is this structure unreasonable?
>
> 
>
> On Mon, 16 Dec 2019 at 13:38, Reza Khayat  wrote:
>
>> ​​Hi Jessica,
>>
>>
>> The gap between the two proteins is a bit troubling. Perhaps it's the
>> image, but why would a crystal form if there is no crystal contact between
>> the two proteins?
>>
>>
>> Reza
>>
>>
>> Reza Khayat, PhD
>> Assistant Professor
>> City College of New York
>> Department of Chemistry
>> New York, NY 10031
>> --
>> *From:* CCP4 bulletin board  on behalf of Ashish
>> Kumar 
>> *Sent:* Monday, December 16, 2019 1:24 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric
>> unit does not fit density
>>
>> Hi Jessica,
>>
>> It may be possible because of wrong MR solution as well. How were your
>> stats after MR.
>> Also it is correct that it could be possible because of wrong space group.
>> Try changing the Space group and repeat MR.
>>
>> Best Regards
>> Ashish
>>
>> On 16 Dec 2019 22:56, "Jessica Besaw"  wrote:
>>
>> Dear community,
>>
>> I am having a lot of trouble solving a protein structure. I think my
>> problem may caused by incorrectly placed proteins in molecular replacement.
>> I have two proteins in my asymmetric unit. It appears that one protein fits
>> perfectly, and the other one has many errors. (See snapshots below). I have
>> tried deleting the parts of the protein (and even the whole protein) to try
>> and rebuild it in COOT, but it was a bit too difficult for me to solve.
>>
>> I would appreciate any and all suggestions for potential strategies
>> moving forward.
>>
>> Other information:
>> (1) 2.4 Angstrom
>> (2) 99% complete
>> (3) "Translational NCS may be present at a level that may complicate
>> refinement"
>>
>> Cheers!
>>
>> Jessica
>>
>> 
>> 
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
> 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] Problem with structural alignment

[Folmer Fredslund]

Dear Ishan

Would it be possible for you to use a fitting of the atoms of the ligand?
I've done that with success before.

Hope this helps
Folmer


man. 16. dec. 2019 07.38 skrev Ishan Rathore :

> Hi,
>
> I am trying to compare multiple homologous structures of a protein, where
> I am analysing the active site residues and the bound substrate/peptide. I
> have used multiple methods for alignment in coot and pymol. Every
> method gives a slightly different orientation in the active site. Based on
> the analysis I am trying to propose a hypothesis for the catalytic
> mechanism of the protein. But, I am a bit wary of getting biased with the
> alignment if that supports my hypothesis.
>
> What are the parameters that have to be considered for a reliable
> alignment?
> What are the other Softwares available for alignment?
>
>
>
> Thanks and regards
> Ishan
>
> --
>
> 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] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Jürgen Bosch]

What’s your spacegroup ? RWork / RFree?

Twinning by any chance?

Jürgen 

__
Jürgen Bosch, Ph.D.
Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University
2109 Adelbert Rd, BRB 835
Cleveland, OH 44106
Phone: 216.368.7565
Fax: 216.368.4223
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

> On Dec 16, 2019, at 1:50 PM, Jessica Besaw  wrote:
> 
> I am crystallizing this membrane protein in a medium (bicelles) that forms 
> lamella like sheets that stack on top of each other. 
> 
> The layer packing is shown below. Is this structure unreasonable?
> 
> 
> 
> On Mon, 16 Dec 2019 at 13:38, Reza Khayat  > wrote:
> ​​Hi Jessica,
> 
> 
> 
> The gap between the two proteins is a bit troubling. Perhaps it's the image, 
> but why would a crystal form if there is no crystal contact between the two 
> proteins?
> 
> 
> 
> Reza
> 
> 
> 
> Reza Khayat, PhD
> Assistant Professor 
> City College of New York
> Department of Chemistry
> New York, NY 10031
> From: CCP4 bulletin board  > on behalf of Ashish Kumar 
> mailto:mail2ashish...@gmail.com>>
> Sent: Monday, December 16, 2019 1:24 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does 
> not fit density
>  
> Hi Jessica,
> 
> It may be possible because of wrong MR solution as well. How were your stats 
> after MR. 
> Also it is correct that it could be possible because of wrong space group.
> Try changing the Space group and repeat MR.
> 
> Best Regards
> Ashish
> 
> On 16 Dec 2019 22:56, "Jessica Besaw"  > wrote:
> Dear community, 
> 
> I am having a lot of trouble solving a protein structure. I think my problem 
> may caused by incorrectly placed proteins in molecular replacement. I have 
> two proteins in my asymmetric unit. It appears that one protein fits 
> perfectly, and the other one has many errors. (See snapshots below). I have 
> tried deleting the parts of the protein (and even the whole protein) to try 
> and rebuild it in COOT, but it was a bit too difficult for me to solve. 
> 
> I would appreciate any and all suggestions for potential strategies moving 
> forward. 
> 
> Other information: 
> (1) 2.4 Angstrom
> (2) 99% complete
> (3) "Translational NCS may be present at a level that may complicate 
> refinement"
> 
> Cheers!
> 
> Jessica 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density

[Ethan A Merritt]

On Monday, 16 December 2019 09:25:59 PST Jessica Besaw wrote:
> Dear community,
> 
> I am having a lot of trouble solving a protein structure. I think my
> problem may caused by incorrectly placed proteins in molecular replacement.
> I have two proteins in my asymmetric unit. It appears that one protein fits
> perfectly, and the other one has many errors. (See snapshots below). I have
> tried deleting the parts of the protein (and even the whole protein) to try
> and rebuild it in COOT, but it was a bit too difficult for me to solve.
> 
> I would appreciate any and all suggestions for potential strategies moving
> forward.
> 
> Other information:
> (1) 2.4 Angstrom
> (2) 99% complete
> (3) "Translational NCS may be present at a level that may complicate
> refinement"

Try turning off the translational NCS check.
We have had two structures where incorrect diagnosis of tNCS prevented
Phaser from finding the correct solution.  If you are not using Phaser, the
caveat still stands in principle.

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment

[Anastassis Perrakis]

Dear Herman et al,

On Dec 16, 2019, at 17:52, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

Dear Ishan,

A structural alignment should be independent of the software used.
However, the residues being selected for the alignment can make a big 
difference and different programs have different selection criteria.
There are two cases:

  1.  Different proteins. Here one needs to decide what the equivalent residues 
are. Usually this is based on a sequence alignment, but once a crude 
superposition has been obtained, the equivalent residue pairs can be optimized.

Theseus can do that well. https://theobald.brandeis.edu/theseus/


  1.  The same protein undergoing a conformation change (e.g. loop or domain 
movement). Here one has to decide what the rigid regions are and where the 
moving loop or linker is. By looking at the coarse superposition with coot or 
any other graphics program, one quickly sees what would be the best borders.

In this case I would be inclined to use the RAPIDO server.

http://webapps.embl-hamburg.de/rapido/

I like algorithms making these choice ;-) I am lazy!

Best regards,

Tassos



  1.

If it is really critical for your hypothesis, you will have to define manually 
the equivalent pairs.

Best,
Herman


Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Eleanor Dodson
Gesendet: Montag, 16. Dezember 2019 11:53
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Well CCP4mg does this very nicely and it is easy to check the results - all 
displayed on the screen so you can pinpoint outliers..
Eleanor

On Mon, 16 Dec 2019 at 06:38, Ishan Rathore 
mailto:ishanrathor...@gmail.com>> wrote:
Hi,

I am trying to compare multiple homologous structures of a protein, where I am 
analysing the active site residues and the bound substrate/peptide. I have used 
multiple methods for alignment in coot and pymol. Every method gives a slightly 
different orientation in the active site. Based on the analysis I am trying to 
propose a hypothesis for the catalytic mechanism of the protein. But, I am a 
bit wary of getting biased with the alignment if that supports my hypothesis.

What are the parameters that have to be considered for a reliable alignment?
What are the other Softwares available for alignment?



Thanks and regards
Ishan



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment

[Schreuder, Herman /DE]

Dear Ishan,

A structural alignment should be independent of the software used.
However, the residues being selected for the alignment can make a big 
difference and different programs have different selection criteria.
There are two cases:

  1.  Different proteins. Here one needs to decide what the equivalent residues 
are. Usually this is based on a sequence alignment, but once a crude 
superposition has been obtained, the equivalent residue pairs can be optimized.
  2.  The same protein undergoing a conformation change (e.g. loop or domain 
movement). Here one has to decide what the rigid regions are and where the 
moving loop or linker is. By looking at the coarse superposition with coot or 
any other graphics program, one quickly sees what would be the best borders.

If it is really critical for your hypothesis, you will have to define manually 
the equivalent pairs.

Best,
Herman



Von: CCP4 bulletin board  Im Auftrag von Eleanor Dodson
Gesendet: Montag, 16. Dezember 2019 11:53
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Problem with structural alignment


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Well CCP4mg does this very nicely and it is easy to check the results - all 
displayed on the screen so you can pinpoint outliers..
Eleanor

On Mon, 16 Dec 2019 at 06:38, Ishan Rathore 
mailto:ishanrathor...@gmail.com>> wrote:
Hi,

I am trying to compare multiple homologous structures of a protein, where I am 
analysing the active site residues and the bound substrate/peptide. I have used 
multiple methods for alignment in coot and pymol. Every method gives a slightly 
different orientation in the active site. Based on the analysis I am trying to 
propose a hypothesis for the catalytic mechanism of the protein. But, I am a 
bit wary of getting biased with the alignment if that supports my hypothesis.

What are the parameters that have to be considered for a reliable alignment?
What are the other Softwares available for alignment?



Thanks and regards
Ishan



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[ccp4bb] EMBL and Intruct-ERIC membership

[Claudia Alen Amaro]

We are delighted to announce that 
EMBL
 has become the latest member of 
Instruct-ERIC.
 European Molecular Laboratory (EMBL) is a pioneering research institution and 
Europe's flagship laboratory for the life science. Funded by public research 
funds from its member countries, the EMBL is involved in molecular biology 
research, training and services.



EMBL and Instruct have a long history of collaboration, and so this partnership 
reinforces a close relationship that we hope will greatly benefit the 
structural biology community across Europe and beyond.



As members of Instruct-ERIC, EMBL scientists are now eligible to apply for 
funded visits to Instruct-ERIC 
Centres,
 training 
calls,
 
internships
 and R 
grants.



We welcome our EMBL colleagues to Instruct and invite you to find out more at 
our 
website.
 To apply for research visits, submit your proposal 
here
 to submit proposal



As the integration continues, we will keep you up-to-date with changes to our 
technology 
catalogue.



Best wishes

Instruct-ERIC Team


Dr Claudia Alen Amaro
Senior Project Manager
Instruct-ERIC
Oxford House
Parkway Court
John Smith Drive
Oxford
OX4 2JY, UK
Tel:+44 1865987629
email: clau...@instruct-eric.eu
Follow us on twitter @instructhub



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Re: [ccp4bb] Problem with structural alignment

[Eleanor Dodson]

Well CCP4mg does this very nicely and it is easy to check the results - all
displayed on the screen so you can pinpoint outliers..
Eleanor

On Mon, 16 Dec 2019 at 06:38, Ishan Rathore 
wrote:

> Hi,
>
> I am trying to compare multiple homologous structures of a protein, where
> I am analysing the active site residues and the bound substrate/peptide. I
> have used multiple methods for alignment in coot and pymol. Every
> method gives a slightly different orientation in the active site. Based on
> the analysis I am trying to propose a hypothesis for the catalytic
> mechanism of the protein. But, I am a bit wary of getting biased with the
> alignment if that supports my hypothesis.
>
> What are the parameters that have to be considered for a reliable
> alignment?
> What are the other Softwares available for alignment?
>
>
>
> Thanks and regards
> Ishan
>
> --
>
> 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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[ccp4bb] Deadline extended: First CCP4 Study Weekend illustration competition

[Jon Agirre]

Dear colleagues,

thanks to those of you who have sent entries for this CCP4 Study Weekend
competition. As a number of people have requested it, we have decided to
extend the deadline until Monday 23 December (one week from now).

Looking forward to receiving your entries – see below for the guidelines.

Best wishes,
Jon, Alan, Robbie and Karen

On Mon, 4 Nov 2019 at 11:37, Jon Agirre  wrote:

> Dear colleagues,
>
> We are pleased to announce the opening of the first CCP4 Study Weekend
> illustration competition, made possible by CCP4’s long standing
> collaboration with IUCr Journals.
>
> Getting your science out to the public requires more than good research.
> You need to make it memorable! And what better way to do it than with
> excellent figures? We invite you to make a figure that tells a structural
> biology story in a creative and informative way. The submitted figures will
> be showcased during the Study Weekend at several locations at the
> conference venue.
>
> *Prize*
> The creator of the winning illustration gets to design the cover
> illustration of the Study Weekend’s proceedings to be published early 2021.
> Apart from this commission there may be another (sur)prize.
>
> *Format*
> Illustrations, along with a short description of content and methods used,
> are to be sent to jon.agi...@york.ac.uk before December 15th 2019.
>
> Images must have a resolution of 1920x1080 (16:9) in order to fit the
> format of the screens and main room projector. Any combination of graphics
> and (if any) post-processing software may be used, as long as details are
> given with the submission. The format of the illustration should be PNG.
>
> *Judges*
> As you may know, Dr Jeroen Claus (founder of Phospho Biomedical Animation)
> will give the closing talk at the 2020 edition of the CCP4 Study Weekend.
> He, along with Louise Jones (managing editor of Acta Crystallographica
> sections D & F) will judge the submitted figures based on their graphical
> quality as well as their ability to convey a complex structural message
> clearly.
>
> *Decision*
> The winner will be announced on January 8th at the dinner - before the
> céilidh.
>
> Up to date information and registration:
> http://www.cvent.com/d/fyq0g9/4K?cpc=FCNF5V7H4B4
>
> Looking forward to receiving your images!
>
> Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre
> --
> Dr Jon Agirre
> Royal Society University Research Fellow
> York Structural Biology Laboratory / Department of Chemistry
> University of York, Heslington, YO10 5DD, York, UK
> http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
> Office: /B/K/065 Phone: +44 (0) 1904 32 8252
> Twitter: @glycojones
>


-- 
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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[ccp4bb] PhD studentships at University of Leicester, UK

[Panne, Daniel (Prof.)]

Dear all,
Could you please forward the following opportunities to suitable candidates?

Applications are invited for BBSRC funded PhD studentships positions in the 
laboratory of Prof Daniel Panne. The group studies higher–order signalling 
complexes that are important in gene/chromatin regulation and assembly (e.g. 
see Nature 2018, 562(7728):538-544). The group is part of a new Institute for 
Structural and Chemical Biology at the University of Leicester which has 
excellent access to state-of-the-art structural biology technologies.

Further particulars, including details on how to apply can be accessed online.

Deadline 6 January: 
http://www.findaphd.com?pj=116664
Deadline 12 January: 
https://warwick.ac.uk/fac/cross_fac/mibtp/pgstudy/phd_opportunities/structural_biology/gene_transcription


Thanks and all the best,
Daniel








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