problem with showing broken peptide after residues with alternative conformation
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
[cid:0D42E809-5937-4AC1-83FB-07A00C355333] Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
Dear Wangshu Jiang, I’m not sure exactly what’s going on with 3LR2, but you can add the missing bonds, for example with commands (also attached as a command file for your convenience):
bond :42.a@c :43.a@n bond :47.a@c :48.a@n bond :51.a@c :52.a@n bond :125.a@c :126.a@n bond :47.b@c :48.b@n bond :48.b@c :49.b@n
I think I got all of the breaks. Hey, seems like this a good protein for Halloween (spider silk)! :-)
Sorry for the hassle. Our newer program ChimeraX doesn’t have this problem with 3LR2, but it handles alternate locations differently. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 3:18 PM, Wangshu Jiang wangshu.jiang@icm.uu.se wrote:
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
<BrokenPeptide.png>
Dear Elaine,
Thank you so much for your help! The commands work like a charm:-) I am happy that you did not regard my question as a Halloween prank. Very grateful to have support from you guys so fast!
I will have a look at your new program ChimeraX. May I ask if I install ChimeraX on my mac, does it mean it will replace my previous Chimera or can they exist at the same time?
Thanks again and hope you have a lovely day!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
On 31 Oct 2017, at 23:58, Elaine Meng <meng@cgl.ucsf.edumailto:meng@cgl.ucsf.edu> wrote:
Dear Wangshu Jiang, I’m not sure exactly what’s going on with 3LR2, but you can add the missing bonds, for example with commands (also attached as a command file for your convenience):
bond :42.a@c :43.a@n bond :47.a@c :48.a@n bond :51.a@c :52.a@n bond :125.a@c :126.a@n bond :47.b@c :48.b@n bond :48.b@c :49.b@n
I think I got all of the breaks. Hey, seems like this a good protein for Halloween (spider silk)! :-)
Sorry for the hassle. Our newer program ChimeraX doesn’t have this problem with 3LR2, but it handles alternate locations differently. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 3:18 PM, Wangshu Jiang <wangshu.jiang@icm.uu.semailto:wangshu.jiang@icm.uu.se> wrote:
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
<BrokenPeptide.png>
<bondit.cmd>
Dear Wangshu Jiang, There is no problem having both on your computer - they are different programs with different names, so will not replace each other. Have a lovely day too!
ChimeraX download, user guide, … http://www.rbvi.ucsf.edu/chimerax/index.html
Elaine
On Nov 1, 2017, at 2:36 AM, Wangshu Jiang wangshu.jiang@icm.uu.se wrote:
Dear Elaine,
Thank you so much for your help! The commands work like a charm:-) I am happy that you did not regard my question as a Halloween prank. Very grateful to have support from you guys so fast!
I will have a look at your new program ChimeraX. May I ask if I install ChimeraX on my mac, does it mean it will replace my previous Chimera or can they exist at the same time?
Thanks again and hope you have a lovely day!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
On 31 Oct 2017, at 23:58, Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Wangshu Jiang, I’m not sure exactly what’s going on with 3LR2, but you can add the missing bonds, for example with commands (also attached as a command file for your convenience):
bond :42.a@c :43.a@n bond :47.a@c :48.a@n bond :51.a@c :52.a@n bond :125.a@c :126.a@n bond :47.b@c :48.b@n bond :48.b@c :49.b@n
I think I got all of the breaks. Hey, seems like this a good protein for Halloween (spider silk)! :-)
Sorry for the hassle. Our newer program ChimeraX doesn’t have this problem with 3LR2, but it handles alternate locations differently. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 31, 2017, at 3:18 PM, Wangshu Jiang wangshu.jiang@icm.uu.se wrote:
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
<BrokenPeptide.png>
<bondit.cmd>
Hi Wangshu, This certainly seems to be a bug. This structure is shown correctly in ChimeraX, so depending on your needs you could use that. Also, it is shown correctly in Chimera if you use the mmCIF version. You can do that by using File->Fetch By ID and choosing “PDB (mmCIF)” as the database and then typing in 3lr2. Lastly, you can manually fix the PDB version by adding the missing peptide bonds by entering the following commands:
bond :42.a@c :43.a@n bond :47.a@c :48.a@n bond :51.a@c :52.a@n bond :125.a@c :126.a@n bond :47.b@c :48.b@n bond :48.b@c :49.b@n
Thanks for reporting the problem. I will work on a fix.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 31, 2017, at 3:18 PM, Wangshu Jiang wangshu.jiang@icm.uu.se wrote:
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
<BrokenPeptide.png> Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric,
Thank you very much for such efficient reply and taking my report! The commands work magic and I will have a look at ChimeraX, seem cool and exciting:-)
I am so glad that I actually reach out and ask for support, the problem looks very simple but has hunted me for months.
Thanks again and have a nice day!
Best Regards,
Wangshu
On 01 Nov 2017, at 00:05, Eric Pettersen <pett@cgl.ucsf.edumailto:pett@cgl.ucsf.edu> wrote:
Hi Wangshu, This certainly seems to be a bug. This structure is shown correctly in ChimeraX, so depending on your needs you could use that. Also, it is shown correctly in Chimera if you use the mmCIF version. You can do that by using File->Fetch By ID and choosing “PDB (mmCIF)” as the database and then typing in 3lr2. Lastly, you can manually fix the PDB version by adding the missing peptide bonds by entering the following commands:
bond :42.a@c :43.a@n bond :47.a@c :48.a@n bond :51.a@c :52.a@n bond :125.a@c :126.a@n bond :47.b@c :48.b@n bond :48.b@c :49.b@n
Thanks for reporting the problem. I will work on a fix.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 31, 2017, at 3:18 PM, Wangshu Jiang <wangshu.jiang@icm.uu.semailto:wangshu.jiang@icm.uu.se> wrote:
Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'.
Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon!
Best Regards, Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
<BrokenPeptide.png> Wangshu Jiang
PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Wangshu Jiang