Dear all,
I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions.
Andy Hinck
Andrew P. Hinck, Ph.D. Professor, Department of Biochemistry, MC 7760 University of Texas Health Science Center at San Antonio San Antonio, TX 78229-3900 office: 210-567-8780 mobile: 210-725-4438 fax: 210-567-8778 email: hinck@uthscsa.edu websites: http://hincklab.uthscsa.edu http://nmr.uthscsa.edu
Dear Andy, Yes, there is a much easier way: use the Rotamers tool (under Tools... Structure Editing). You can specify residue type and rotamer library, and that will give you a "bouquet" of rotamers at that position. You can calculate H-bonds and clashes for the rotamers (or even how well they fit into a density map!) to help you choose the best one, and then have it replace the original sidechain. This tool could be used to generate different rotamers for the same amino acid type or to mutate to a different amino acid type. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.h...
The "Structure Analysis and Comparison" tutorial includes use of Rotamers: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html>
There is also a command-line implementation, "swapaa": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html
Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 30, 2009, at 2:57 PM, Andrew P. Hinck wrote:
Dear all,
I was hoping to make some single amino acid substitutions in the context of a protein binding interface. I've only briefly poked around, but so far the only way I see to do this is to delete existing atoms/bonds one by one, and then rebuild (the alternate amino acid) atom-by-atom/bond-by-bond. Is there an easier way (like, telling the program to substitute an Asp for a Lys, or something akin to this)? Thanks in advance for any suggestions.
Andy Hinck
Dear All,
I try to put stickers and balls in my EM density to trace secondary structures of protein. During this process, I put a number to label each of the secondary structures. However, these labels are all lost after I save this session and restore the session. Any suggestion to solve this problem would be greatly appreciated. Thanks.
Hi Xing,
If you placed markers with the Volume Tracer dialog and use Features / Marker Note in that dialog to label the markers they will be saved in session files. I see that if you use Actions / Label / other... to label the markers then that is not saved in Chimera 1.3, and it is saved but not restored in Chimera 1.4, because the empty Marker Note overrides the label.
I'll try to fix this for the upcoming Chimera 1.4 release, so that labels set with Actions / Label are treated the same as marker notes. For now, use the Volume Tracer dialog Features / Marker Note and it will be saved and restored from sessions.
Thanks for reporting the problem.
Tom
-------- Original Message -------- Subject: [Chimera-users] Cannot save the labels in Volume trace From: Xing Zhang To: 'Chimera BB' chimera-users@cgl.ucsf.edu Date: 8/31/09 10:10 AM
Dear All,
I try to put stickers and balls in my EM density to trace secondary structures of protein. During this process, I put a number to label each of the secondary structures. However, these labels are all lost after I save this session and restore the session. Any suggestion to solve this problem would be greatly appreciated. Thanks.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Xing,
Yes, now I see that if you select a link and use menu Actions / Label / other... and type a text label such as a number for your helices then that label is not saved in sessions. This is a bug, that labels on links or bonds are not saved in sessions. Eric Pettersen says he will fix it this week (probably today).
The marker notes only apply to the markers, not the links. I will fix the code so that marker labels created with Actions / Label / other... are saved. Currently having an empty marker note overrides such labels. I expect to fix this later in the week. Will let you know when it is fixed.
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] Cannot save the labels in Volume trace From: Xing Zhang To: 'Thomas Goddard' Date: 9/1/09 10:09 AM
Thanks, Tom,
I just found my mistake. I actually want to label the*_ linker_**_s_* (not markers) between two makers to represent the sequence of each secondary structure. So how can I do that in Chimera which could be saved and restored? Thank you very much.
-------- Original Message -------- Subject: Re: [Chimera-users] Cannot save the labels in Volume trace From: Thomas Goddard To: Xing Zhang Date: 8/31/09 5:53 PM
Hi Xing,
If you placed markers with the Volume Tracer dialog and use Features / Marker Note in that dialog to label the markers they will be saved in session files. I see that if you use Actions / Label / other... to label the markers then that is not saved in Chimera 1.3, and it is saved but not restored in Chimera 1.4, because the empty Marker Note overrides the label.
I'll try to fix this for the upcoming Chimera 1.4 release, so that labels set with Actions / Label are treated the same as marker notes. For now, use the Volume Tracer dialog Features / Marker Note and it will be saved and restored from sessions.
Thanks for reporting the problem.
Tom
-------- Original Message -------- Subject: [Chimera-users] Cannot save the labels in Volume trace From: Xing Zhang To: 'Chimera BB' chimera-users@cgl.ucsf.edu Date: 8/31/09 10:10 AM
Dear All,
I try to put stickers and balls in my EM density to trace secondary structures of protein. During this process, I put a number to label each of the secondary structures. However, these labels are all lost after I save this session and restore the session. Any suggestion to solve this problem would be greatly appreciated. Thanks.
participants (4)
-
Andrew P. Hinck -
Elaine Meng -
Thomas Goddard -
Xing Zhang