Re: [ccp4bb] Easy/Silly question

2022-07-01 Thread Krieger, James M 
Oh, yes. Sorry.

From: Robbie Joosten 
Sent: Friday, July 1, 2022 10:02 AM
To: Krieger, James M ; CCP4BB@JISCMAIL.AC.UK 

Subject: RE: [ccp4bb] Easy/Silly question

BMA is mannose, not maltose

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Krieger,
> James M
> Sent: Friday, July 1, 2022 09:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Easy/Silly question
>
> How about BMA for beta-D-maltose?
>
>
>On 1 Jul 2022, at 05:55, Nigel Moriarty  wrote:
>
>
>
>
>Yes, MAL was obsoleted about 2 years ago.
>
>Cheers
>
>
>Nigel
>
>
>---
>Nigel W. Moriarty
>Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>Lawrence Berkeley National Laboratory
>Berkeley, CA 94720-8235
>Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>Fax   : 510-486-5909  Web  : CCI.LBL.gov
> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.l%2Fdata=05%7C01%7CKRIEGERJ%40PITT.EDU%7Cd8813ad1de8c47af33be08da5b3804a0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637922593564804787%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=9546E6%2Fs5dCrDM18mHlaat1dwaQu6HUr%2FDgge4m4nEM%3Dreserved=0
> bl.gov%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171
> a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C6
> 37922481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7
> C=PlWqacZfxRwjFqAdkMmtlz92YFpBwhFRBxa13p4wFx4%3D
> d=0>
>ORCID : orcid.org/-0001-8857-9464
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Forc
> id.org%2F-0001-8857-
> 9464=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171a470
> 8da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C63792
> 2481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL
> CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
> data=cOI56DuPY4K95dxf0HIIfAZ7mgoLvLLCxD7M%2BXjqa4g%3D=
> 0>
>
>
>
>On Thu, Jun 30, 2022 at 9:26 PM Diana Tomchick
>  <mailto:diana.tomch...@utsouthwestern.edu> > wrote:
>
>
>It's GLC
>
>otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-
> glucose.
>
>See PDB ID 1ANF
>
>also
>
>
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FMaltosedata=05%7C01%7CKRIEGERJ%40PITT.EDU%7Cd8813ad1de8c47af33be08da5b3804a0%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637922593564961025%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7Csdata=dqzT33PxgoSZOQQKu0FLJEt1%2FxM3X74qY%2FyBcliepgY%3Dreserved=0
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
>
>
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose - Wikipedia
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as 
> maltobiose or
> malt sugar, is a disaccharide formed from two units of glucose joined with an
> α(1→4) bond.In the isomer isomaltose, the two glucose molecules are joined
> with an α(1→6) bond.Maltose is the two-unit member of the amylose
> homologous series, the key structural motif of starch.When alpha-amylase
> breaks ...
> en.wikipedia.org
> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fen.
> wikipedia.org%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec
> 94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526

Re: [ccp4bb] Easy/Silly question

2022-07-01 Thread Casper Wilkens 
Hello,

You can build it from the two monomers in Coot.

All the best,
Casper

From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 1. juli 2022 06:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Easy/Silly question



On 01/07/2022 04:50, Joel Tyndall wrote:
Hi folks,

I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. 
Does any one have the code for the ligand? Surely its been used before.




In Coot:

File -> Search Monomer Library -> "maltose" -> Search

-> MAL





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Re: [ccp4bb] Easy/Silly question

2022-07-01 Thread Robbie Joosten 
BMA is mannose, not maltose

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Krieger,
> James M
> Sent: Friday, July 1, 2022 09:59
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Easy/Silly question
> 
> How about BMA for beta-D-maltose?
> 
> 
>   On 1 Jul 2022, at 05:55, Nigel Moriarty  wrote:
> 
> 
> 
>   
>   Yes, MAL was obsoleted about 2 years ago.
> 
>   Cheers
> 
> 
>   Nigel
> 
> 
>   ---
>   Nigel W. Moriarty
>   Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>   Lawrence Berkeley National Laboratory
>   Berkeley, CA 94720-8235
>   Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>   Fax   : 510-486-5909  Web  : CCI.LBL.gov
> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcci.l
> bl.gov%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171
> a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C6
> 37922481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7
> C=PlWqacZfxRwjFqAdkMmtlz92YFpBwhFRBxa13p4wFx4%3D
> d=0>
>   ORCID : orcid.org/-0001-8857-9464
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Forc
> id.org%2F-0001-8857-
> 9464=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec94d171a470
> 8da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C63792
> 2481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL
> CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
> data=cOI56DuPY4K95dxf0HIIfAZ7mgoLvLLCxD7M%2BXjqa4g%3D=
> 0>
> 
> 
> 
>   On Thu, Jun 30, 2022 at 9:26 PM Diana Tomchick
>  <mailto:diana.tomch...@utsouthwestern.edu> > wrote:
> 
> 
>   It's GLC
> 
>   otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-
> glucose.
> 
>   See PDB ID 1ANF
> 
>   also
> 
>   https://en.wikipedia.org/wiki/Maltose
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> 
> 
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose - Wikipedia
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.
> wikipedia.org%2Fwiki%2FMaltose=05%7C01%7Ckriegerj%40PITT.EDU
> %7Cc0630e52bec94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526
> 112fd0d%7C1%7C0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0
> %3D%7C3000%7C%7C%7C=6w8tDRVJN2wdTOoumoljHoDa3VDudJIRg
> H7QtK8MXpw%3D=0>
> Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as 
> maltobiose or
> malt sugar, is a disaccharide formed from two units of glucose joined with an
> α(1→4) bond.In the isomer isomaltose, the two glucose molecules are joined
> with an α(1→6) bond.Maltose is the two-unit member of the amylose
> homologous series, the key structural motif of starch.When alpha-amylase
> breaks ...
> en.wikipedia.org
> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fen.
> wikipedia.org%2F=05%7C01%7Ckriegerj%40PITT.EDU%7Cc0630e52bec
> 94d171a4708da5b1dc6b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C
> 0%7C637922481423292553%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w
> LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C
> %7C%7C=q6tgL29oHtiVRlDicK39FdGgKI3JcDyUXHxxfLLBfAA%3D
> rved=0>
>   Diana
> 
> 
>   **
>   Diana R. Tomchick
>   Professor
>   Departments of Biophysics and Biochemistry
>   UT Southwestern Medical Center
>   5323 Harry Hines Blvd.
>   Rm. ND10.214A
>   Dallas, TX 75390-8816
>   diana.tomch...@utsouthwestern.edu
>   (214) 645-6383 (phone)
>   (214) 645-6353 (fax)
> 
> 
>   From: CCP4 bulletin board  <mailto:CCP4B

Re: [ccp4bb] Easy/Silly question

2022-07-01 Thread Krieger, James M 
How about BMA for beta-D-maltose?

On 1 Jul 2022, at 05:55, Nigel Moriarty  wrote:


Yes, MAL was obsoleted about 2 years ago.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov
ORCID : 
orcid.org/-0001-8857-9464


On Thu, Jun 30, 2022 at 9:26 PM Diana Tomchick 
mailto:diana.tomch...@utsouthwestern.edu>> 
wrote:
It's GLC

otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-glucose.

See PDB ID 1ANF

also

https://en.wikipedia.org/wiki/Maltose
[https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Maltose2.svg/1200px-Maltose2.svg.png]
Maltose - 
Wikipedia
Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as maltobiose 
or malt sugar, is a disaccharide formed from two units of glucose joined with 
an α(1→4) bond.In the isomer isomaltose, the two glucose molecules are joined 
with an α(1→6) bond.Maltose is the two-unit member of the amylose homologous 
series, the key structural motif of starch.When alpha-amylase breaks ...
en.wikipedia.org
Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>>
Sent: Thursday, June 30, 2022 10:50 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Easy/Silly question


EXTERNAL MAIL

Hi folks,



I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. 
Does any one have the code for the ligand? Surely its been used before.



Thanks in advance



J



Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo

PO Box 56 9054

Dunedin | Ōtepoti

New Zealand | Aotearoa

Ph: 64 3 479 7293
Skype: jtyndall

Website | 
pharmacy.otago.ac.nz







To

Re: [ccp4bb] Easy/Silly question

2022-06-30 Thread Nigel Moriarty 
Yes, MAL was obsoleted about 2 years ago.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Jun 30, 2022 at 9:26 PM Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:

> It's GLC
>
> otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-glucose.
>
> See PDB ID 1ANF
>
> also
>
> https://en.wikipedia.org/wiki/Maltose
> 
> Maltose - Wikipedia 
> Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as
> maltobiose or malt sugar, is a disaccharide formed from two units of
> glucose joined with an α(1→4) bond.In the isomer isomaltose, the two
> glucose molecules are joined with an α(1→6) bond.Maltose is the two-unit
> member of the amylose homologous series, the key structural motif of
> starch.When alpha-amylase breaks ...
> en.wikipedia.org
> Diana
>
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> --
> *From:* CCP4 bulletin board  on behalf of Joel
> Tyndall 
> *Sent:* Thursday, June 30, 2022 10:50 PM
> *To:* CCP4BB@JISCMAIL.AC.UK 
> *Subject:* [ccp4bb] Easy/Silly question
>
>
> EXTERNAL MAIL
>
> Hi folks,
>
>
>
> I frustratingly cant find “maltose” as a ligand in the pdb or ccp4
> database. Does any one have the code for the ligand? Surely its been used
> before.
>
>
>
> Thanks in advance
>
>
>
> J
>
>
>
> Joel Tyndall | BSc(Hons) PhD
>
> Associate Professor in Medicinal Chemistry
> School of Pharmacy | He Rau Kawakawa
> University of Otago | Te Whare Wānanga o Otāgo
>
> PO Box 56 9054
>
> Dunedin | Ōtepoti
>
> New Zealand | Aotearoa
>
> Ph: 64 3 479 7293
> Skype: jtyndall
>
> Website | pharmacy.otago.ac.nz
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> CAUTION: This email originated from outside UTSW. Please be cautious of
> links or attachments, and validate the sender's email address before
> replying.
>
>
> --
>
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>
> Medical Center
>
> The future of medicine, today.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] Easy/Silly question

2022-06-30 Thread Diana Tomchick 
It's GLC

otherwise known as 4-ortho-alpha-D-Glucopyranosyl-D-glucose.

See PDB ID 1ANF

also

https://en.wikipedia.org/wiki/Maltose
[https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Maltose2.svg/1200px-Maltose2.svg.png]
Maltose - Wikipedia
Maltose (/ ˈ m ɔː l t oʊ s / or / ˈ m ɔː l t oʊ z /), also known as maltobiose 
or malt sugar, is a disaccharide formed from two units of glucose joined with 
an α(1→4) bond.In the isomer isomaltose, the two glucose molecules are joined 
with an α(1→6) bond.Maltose is the two-unit member of the amylose homologous 
series, the key structural motif of starch.When alpha-amylase breaks ...
en.wikipedia.org
Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Joel Tyndall 

Sent: Thursday, June 30, 2022 10:50 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Easy/Silly question


EXTERNAL MAIL

Hi folks,



I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 database. 
Does any one have the code for the ligand? Surely its been used before.



Thanks in advance



J



Joel Tyndall | BSc(Hons) PhD

Associate Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo

PO Box 56 9054

Dunedin | Ōtepoti

New Zealand | Aotearoa

Ph: 64 3 479 7293
Skype: jtyndall

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Re: [ccp4bb] Easy/Silly question

2022-06-30 Thread Paul Emsley 


On 01/07/2022 04:50, Joel Tyndall wrote:


Hi folks,

I frustratingly cant find “maltose” as a ligand in the pdb or ccp4 
database. Does any one have the code for the ligand? Surely its been 
used before.




In Coot:

File -> Search Monomer Library -> "maltose" -> Search

-> MAL




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