Peptide Builder in 1.4x
Hi All, I was very excited to download the 1.4 version of Chimera with it many improved features yesterday. However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x) Thought you would like to know. I appreciate your excellent software. Thanks, Jim Nettles
Hi Jim, I just tried this and it is working fine for me in the 1.4 release. Here are the steps that I tried: (1) start Build Structure (2) in Add Atoms tab, choose "peptide sequence" and enter sequence AAAAKVLKDD (for example) (3) click Add, which raises secondary dialog for setting backbone angles (4) the secondary dialog initially has all angles set for alpha-helix; you can choose a different secondary structure, e.g. "antiparallel beta strand" (but this won't have an effect until the following steps) (5) choose the rows to which you want to apply those angles using the mouse; I used click-drag to choose all the rows (6) click the "Set" button right below the list of residues to fill in those rows with the desired angles. I just noticed this button is blank in the mac aqua version... maybe that led to confusion? Clicking it still works, though. It should look like [Set] selected rows to phi[phi-value] psi[psi-value] where the [Set] part is a button. (7) click Apply or OK (which also dismisses the dialog) to create the peptide with the phi/psi angles that are listed in the table Step 4 is for your convenience if you know what secondary structure you want. You can also edit the angle values in the "Set" line arbitrarily. Let us know if this series of steps is not working for you. You can use "Help... Report a Bug" in the Chimera menu to report bugs, which would automatically include information about exactly which build you are using and what kind of computer you are using. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 10, 2010, at 1:26 PM, nettles wrote:
Hi All,
I was very excited to download the 1.4 version of Chimera with it many improved features yesterday.
However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x)
Thought you would like to know.
I appreciate your excellent software.
Thanks,
Jim Nettles_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
That was it. I couldn't tell that I needed to explicitly set the angles for this version. Makes sense now. Thanks for the quick response. Jim On Feb 10, 2010, at 4:50 PM, Elaine Meng wrote:
Hi Jim, I just tried this and it is working fine for me in the 1.4 release. Here are the steps that I tried:
(1) start Build Structure (2) in Add Atoms tab, choose "peptide sequence" and enter sequence AAAAKVLKDD (for example) (3) click Add, which raises secondary dialog for setting backbone angles (4) the secondary dialog initially has all angles set for alpha- helix; you can choose a different secondary structure, e.g. "antiparallel beta strand" (but this won't have an effect until the following steps) (5) choose the rows to which you want to apply those angles using the mouse; I used click-drag to choose all the rows (6) click the "Set" button right below the list of residues to fill in those rows with the desired angles. I just noticed this button is blank in the mac aqua version... maybe that led to confusion? Clicking it still works, though. It should look like
[Set] selected rows to phi[phi-value] psi[psi-value]
where the [Set] part is a button.
(7) click Apply or OK (which also dismisses the dialog) to create the peptide with the phi/psi angles that are listed in the table
Step 4 is for your convenience if you know what secondary structure you want. You can also edit the angle values in the "Set" line arbitrarily.
Let us know if this series of steps is not working for you. You can use "Help... Report a Bug" in the Chimera menu to report bugs, which would automatically include information about exactly which build you are using and what kind of computer you are using.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 10, 2010, at 1:26 PM, nettles wrote:
Hi All,
I was very excited to download the 1.4 version of Chimera with it many improved features yesterday.
However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x)
Thought you would like to know.
I appreciate your excellent software.
Thanks,
Jim Nettles_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
In tomorrow's daily build, the 'Set' button will show it's text in the mac aqua version. --Eric On Feb 10, 2010, at 2:11 PM, James Nettles wrote:
That was it. I couldn't tell that I needed to explicitly set the angles for this version. Makes sense now.
Thanks for the quick response.
Jim
On Feb 10, 2010, at 4:50 PM, Elaine Meng wrote:
Hi Jim, I just tried this and it is working fine for me in the 1.4 release. Here are the steps that I tried:
(1) start Build Structure (2) in Add Atoms tab, choose "peptide sequence" and enter sequence AAAAKVLKDD (for example) (3) click Add, which raises secondary dialog for setting backbone angles (4) the secondary dialog initially has all angles set for alpha- helix; you can choose a different secondary structure, e.g. "antiparallel beta strand" (but this won't have an effect until the following steps) (5) choose the rows to which you want to apply those angles using the mouse; I used click-drag to choose all the rows (6) click the "Set" button right below the list of residues to fill in those rows with the desired angles. I just noticed this button is blank in the mac aqua version... maybe that led to confusion? Clicking it still works, though. It should look like
[Set] selected rows to phi[phi-value] psi[psi-value]
where the [Set] part is a button.
(7) click Apply or OK (which also dismisses the dialog) to create the peptide with the phi/psi angles that are listed in the table
Step 4 is for your convenience if you know what secondary structure you want. You can also edit the angle values in the "Set" line arbitrarily.
Let us know if this series of steps is not working for you. You can use "Help... Report a Bug" in the Chimera menu to report bugs, which would automatically include information about exactly which build you are using and what kind of computer you are using.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 10, 2010, at 1:26 PM, nettles wrote:
Hi All,
I was very excited to download the 1.4 version of Chimera with it many improved features yesterday.
However, I was surprised today when I tried to build an anti parallel beta sheet and it came out looking like an alpha helix. After experimenting around i realized all option give alpha helix. This is true for 1.4 (build 26788) and 1.4.1 (build 29977)and . The old version 1 build 2540 works fine. (It worked with a newer version I had too, but silly me overwrote that with the 1.4.x)
Thought you would like to know.
I appreciate your excellent software.
Thanks,
Jim Nettles_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Phew, that's a relief! You're welcome. It was changed to allow creating peptides with different phi/psi values at different positions. Best, Elaine On Feb 10, 2010, at 2:11 PM, James Nettles wrote:
That was it. I couldn't tell that I needed to explicitly set the angles for this version. Makes sense now.
Thanks for the quick response.
Jim
O
I can definitely see the utility in the new method. Thanks again, Jim On Feb 10, 2010, at 5:21 PM, Elaine Meng wrote:
Phew, that's a relief! You're welcome.
It was changed to allow creating peptides with different phi/psi values at different positions.
Best, Elaine
On Feb 10, 2010, at 2:11 PM, James Nettles wrote:
That was it. I couldn't tell that I needed to explicitly set the angles for this version. Makes sense now.
Thanks for the quick response.
Jim
O
________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) VA Medical Center - Medical Research 151H / 5A-146 1670 Clairmont Road, Decatur, GA 30033, USA Email: jnettle@emory.edu VAMC: 1+404-321-6111 Ext: Office 7279 Lab 2272 ________________________________________________________
participants (4)
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Elaine Meng -
Eric Pettersen -
James Nettles -
nettles