Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
Dear Jiang, to draw a line or a dotted line is a question of graphics and definitions of the specific software and has nothing to do with the specific nature of a chemical bond. "link" defines in your case only an additional chemical bond that is not defined for the common polypeptide chain. best, Winfried Hinrichs -- Dr. rer. nat. Winfried Hinrichs Professor and Chair of Biochemistry, Emeritus University of Greifswald Institute for Biochemistry Felix-Hausdorff-Str. 4 D-17487 Greifswald, Germany E-mail winfried.hinri...@uni-greifswald.de http://orcid.org/-0002-0435-4565 -- Am Donnerstag, den 24-06-2021 um 13:40 schrieb jiang: Hello guys, I am a little bit confused. Since the polysaccharide is attached to asparagine via covalent bond. I am not sure what “link” means anyway. Does it mean some other chemical bonds? Or not chemical bond at all. As you can see from the book link below, the nitrogen atom from the N-glycosylation site has covalent bond with only one hydrogen atom. The bond is referred to as glycosidic bond. https://www.ncbi.nlm.nih.gov/books/NBK22521/ Thank you, Best, Jiang Sent from my iPhone On Jun 24, 2021, at 12:35 AM, Folmer Fredslund wrote: Dear Jiang As Paul Emsley was already kind to point out: Coot draws solid lines for bonds between neighbouring monomers in a polymer. The bond between NAG and ASN is not such a bond - it is a link. Links are drawn as dashed lines in Coot. So, a dashed line is simply how such a bond is represented in Coot. It's not a bug in the software. I'm not quite sure why you want the bond to be represented with a solid line instead of a dashed line. It makes no difference whatsoever on the validity of the model. Best wishes Folmer Fredslund ons. 23. jun. 2021 01.23 skrev Jiang Xu : Hello David, I used the "Make Link" under the "Modeling..." tab to create the bond. It worked, but the bond displayed is still a dashed line, not a solid line as shown below. I still don't know how to use phenix to add a solid bond between the two atoms. So, is it a bug in the software or I didn't do it correctly? Thank you, Best, Jiang On Tue, Jun 22, 2021 at 3:48 PM Jiang Xu wrote: Hello David, I tried to rebuild the polysaccharide chain using the N-link add NAG, NAG, BMA method, saved the model and ran phenix.refine without checking the "automatically add hydrogens to the model". I also double checked to make sure that the "Link carbohydrates to protein and other carbohydrates" within the "Automatic Linking Options" was checked. The "Carbohydrate bond cutoff" is the set to the default value of 1.99, which I didn't change. However, after running phenix.refine, the bond disappeared again. As shown below, on the left is the input model, on the right is the refined output. You can see that the bond is gone and the distance between C1 of NAG and the Nitrogen atom of the amine group is 1.42 A. So Could anything else cause the problem? Thank you, Best, Jiang On Mon, Jun 21, 2021 at 11:11 PM David Briggs wrote: Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link). If the second H is added, this breaks the refinement of the Asn-NAG bond. My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box. I hope this fixes your problem. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs [1] - From: CCP4 bulletin board on behalf of Jiang Xu Sent: Tuesday, June 22, 2021 6:47:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine External Sender: Use caution. Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosa
Re: [ccp4bb] missing covalent bond between asparagine and N-
Hi Jiang,I can understand why you are confused. I think I faced such case once. But Paul & Folmer's description is correct, that's the way coot works. Here is the way I solved it.In coot, after linking save the pdb without hydrogen.(Optional, if Phenix says it needs cif file - do readyset)Refine that pdb in Phenix without hydrogen.Then check it in coot & pymol. Even coot shows dotted lines, pymol will show a solid bond😀!Hope it helps! Best,Reza Md Rezaul Karim, Ph.D. Postdoctoral Research Fellow Department of Drug Discovery H. Lee Moffitt Cancer Center and Research Institute Tampa, FL 33612 Email: reza.ka...@moffitt.org, rez...@usf.edu Phone: (813) 745 4673 ext. 5462 https://orcid.org/-0002-0424-127X On Thu, Jun 24, 2021 at 7:40 AM, jiang wrote: Hello guys, I am a little bit confused. Since the polysaccharide is attached to asparagine via covalent bond. I am not sure what “link” means anyway. Does it mean some other chemical bonds? Or not chemical bond at all. As you can see from the book link below, the nitrogen atom from the N-glycosylation site has covalent bond with only one hydrogen atom. The bond is referred to as glycosidic bond. https://www.ncbi.nlm.nih.gov/books/NBK22521/ Thank you,Best,Jiang Sent from my iPhone On Jun 24, 2021, at 12:35 AM, Folmer Fredslund wrote: Dear Jiang As Paul Emsley was already kind to point out: Coot draws solid lines for bonds between neighbouring monomers in a polymer. The bond between NAG and ASN is not such a bond - it is a link. Links are drawn as dashed lines in Coot. So, a dashed line is simply how such a bond is represented in Coot. It's not a bug in the software. I'm not quite sure why you want the bond to be represented with a solid line instead of a dashed line. It makes no difference whatsoever on the validity of the model. Best wishesFolmer Fredslund ons. 23. jun. 2021 01.23 skrev Jiang Xu : Hello David, I used the "Make Link" under the "Modeling..." tab to create the bond. It worked, but the bond displayed is still a dashed line, not a solid line as shown below. I still don't know how to use phenix to add a solid bond between the two atoms. So, is it a bug in the software or I didn't do it correctly? Thank you,Best,Jiang On Tue, Jun 22, 2021 at 3:48 PM Jiang Xu wrote: Hello David, I tried to rebuild the polysaccharide chain using the N-link add NAG, NAG, BMA method, saved the model and ran phenix.refine without checking the "automatically add hydrogens to the model". I also double checked to make sure that the "Link carbohydrates to protein and other carbohydrates" within the "Automatic Linking Options" was checked. The "Carbohydrate bond cutoff" is the set to the default value of 1.99, which I didn't change. However, after running phenix.refine, the bond disappeared again. As shown below, on the left is the input model, on the right is the refined output. You can see that the bond is gone and the distance between C1 of NAG and the Nitrogen atom of the amine group is 1.42 A. So Could anything else cause the problem? Thank you,Best,Jiang On Mon, Jun 21, 2021 at 11:11 PM David Briggs wrote: Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link). If the second H is added, this breaks the refinement of the Asn-NAG bond. My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box. I hope this fixes your problem. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs From: CCP4 bulletin board on behalf of Jiang Xu Sent: Tuesday, June 22, 2021 6:47:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine External Sender: Use caution. Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of
Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
Hello guys, I am a little bit confused. Since the polysaccharide is attached to asparagine via covalent bond. I am not sure what “link” means anyway. Does it mean some other chemical bonds? Or not chemical bond at all. As you can see from the book link below, the nitrogen atom from the N-glycosylation site has covalent bond with only one hydrogen atom. The bond is referred to as glycosidic bond. https://www.ncbi.nlm.nih.gov/books/NBK22521/ Thank you, Best, Jiang Sent from my iPhone > On Jun 24, 2021, at 12:35 AM, Folmer Fredslund wrote: > > Dear Jiang > > As Paul Emsley was already kind to point out: > > Coot draws solid lines for bonds between neighbouring monomers in a polymer. > The bond between NAG and ASN is not such a bond - it is a link. > Links are drawn as dashed lines in Coot. > > > So, a dashed line is simply how such a bond is represented in Coot. It's not > a bug in the software. > > I'm not quite sure why you want the bond to be represented with a solid line > instead of a dashed line. > It makes no difference whatsoever on the validity of the model. > > Best wishes > Folmer Fredslund > > > > > > > ons. 23. jun. 2021 01.23 skrev Jiang Xu : >> Hello David, >> I used the "Make Link" under the "Modeling..." tab to create the bond. >> It worked, but the bond displayed is still a dashed line, not a solid line >> as shown below. I still don't know how to use phenix to add a solid bond >> between the two atoms. So, is it a bug in the software or I didn't do it >> correctly? >> >> >> Thank you, >> Best, >> Jiang >> >>> On Tue, Jun 22, 2021 at 3:48 PM Jiang Xu wrote: >>> Hello David, >>> I tried to rebuild the polysaccharide chain using the N-link add NAG, >>> NAG, BMA method, saved the model and ran phenix.refine without checking the >>> "automatically add hydrogens to the model". I also double checked to make >>> sure that the "Link carbohydrates to protein and other carbohydrates" >>> within the "Automatic Linking Options" was checked. The "Carbohydrate bond >>> cutoff" is the set to the default value of 1.99, which I didn't change. >>> However, after running phenix.refine, the bond disappeared again. As shown >>> below, on the left is the input model, on the right is the refined output. >>> You can see that the bond is gone and the distance between C1 of NAG and >>> the Nitrogen atom of the amine group is 1.42 A. So Could anything else >>> cause the problem? >>> >>> >>> >>> Thank you, >>> Best, >>> Jiang >>> >>>> On Mon, Jun 21, 2021 at 11:11 PM David Briggs >>>> wrote: >>>> Hi Jiang Xu, >>>> >>>> (Phenixbb added as I suspect this is Phenix not coot that has caused your >>>> issue) >>>> >>>> Did you check the "add hydrogens" button in Phenix.refine? Sometimes this >>>> can erroneously add a second H to the ND of glycosylated Asn residues. (I >>>> assume this is because bond distances in the input PDB file fall outside >>>> Phenix's definitions of an Asn-NAG link). >>>> >>>> If the second H is added, this breaks the refinement of the Asn-NAG bond. >>>> >>>> My work around is to run "Ready Set" to add hydrogens as a separate job, >>>> and then manually inspect and correct the Asn residues as necessary before >>>> running Phenix.refine and _not_ checking the "add hydrogens" box. >>>> >>>> I hope this fixes your problem. >>>> >>>> Good luck, >>>> >>>> Dave >>>> >>>> -- >>>> Dr David C. Briggs >>>> Senior Laboratory Research Scientist >>>> Signalling and Structural Biology Lab >>>> The Francis Crick Institute >>>> London, UK >>>> == >>>> about.me/david_briggs >>>> >>>> From: CCP4 bulletin board on behalf of Jiang Xu >>>> >>>> Sent: Tuesday, June 22, 2021 6:47:36 AM >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> Subject: [ccp4bb] missing covalent bond between asparagine and >>>> N-acetylglucosamine using coot carbohydrate module and phenix.refine >>>> >>>> >>>> External Sender: Use caution. >>>> >>>> Hello guys, >>>>I have
Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
On 22/06/2021 06:47, Jiang Xu wrote: I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. Coot draws solid lines for bonds between neighbouring monomers in a polymer. The bond between NAG and ASN is not such a bond - it is a link. Links are drawn as dashed lines in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. If there is no link for a ASN, then there should be two hydrogen atoms add to the ND2. I find it fascinating that these programs work so well together that it didn't even occur to you to examine the conduit through which structral information is passed. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
Hi Jiang Xu, (Phenixbb added as I suspect this is Phenix not coot that has caused your issue) Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link). If the second H is added, this breaks the refinement of the Asn-NAG bond. My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box. I hope this fixes your problem. Good luck, Dave -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs From: CCP4 bulletin board on behalf of Jiang Xu Sent: Tuesday, June 22, 2021 6:47:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine External Sender: Use caution. Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? [image.png] Thank you, Best, Jiang Xu Lin Chen's Research Group University of Southern California To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7C%7C48beee7b9a244fc683ba08d93542c46d%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C637599383149545061%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=QP5gUcvAYN43BkYOgqf9ynTIgA0mEmEGxXRmfsQi86s%3D&reserved=0> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? [image: image.png] Thank you, Best, Jiang Xu Lin Chen's Research Group University of Southern California To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 https://www.jiscmail.ac.uk/policyandsecurity/
