To whom may concern, This is Yanhe Zhao from UT Southwestern Medical Center. I have to question when use Chimera as below, hopefully someone could do me a favor to answer it. 1, my crystal structure have four copies in one Asymmetrical structural unit. When I try to combine two of them by selection and combine command, always combine all of them. I pretty sure that I only select two of them; 2, I got one PDB from SASDB, how can I show it as a density map like CryoEM? When I open, it's shown as lines-like map so as to which couldn't be used for docking. I really appreciate it if someone could do me this favor. Thanks a lot. Best, Yanhe
Hi Yanhe, (1) Combine is for merging multiple models (usually multiple input files) into one model. If all four of your copies are already in one model (one input file) it makes no difference. Maybe you meant you just wanted to remove the other copies when saving a file. If you already have all the atoms you want to keep selected, just use menu: File… Save PDB, and in the resulting dialog, turn on the option “Save selected atoms only” (2) PDB is not a map format; it contains coordinates of points, usually atoms. I see in SASDB that some entries have PDB files that are fully modeled proteins, and others are just a set of balls that fit the shape of the envelope. Since you said “lines-like” the one you have is probably just a set of balls. Chimera doesn’t know they aren’t really a protein, so it is trying to show a ribbon. Try commands to turn off ribbon and show all points as spheres: ~ribbon display repr sphere Then it should look like a bunch of balls that show the shape of the SAS data. Either way (full protein or set of balls) you can use the “molmap” command to simulate a density map from the points, for example: molmap #0 8 … meaning to create a map from the “atoms” (the balls are fake atoms) in model #0 using resolution 8. I don’t know what resolution value is best, but in the Volume Viewer dialog that automatically appears when you create the map, you can change from “surface” to “mesh” display and judge for yourself. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2018, at 7:37 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
To whom may concern, This is Yanhe Zhao from UT Southwestern Medical Center. I have to question when use Chimera as below, hopefully someone could do me a favor to answer it. 1, my crystal structure have four copies in one Asymmetrical structural unit. When I try to combine two of them by selection and combine command, always combine all of them. I pretty sure that I only select two of them; 2, I got one PDB from SASDB, how can I show it as a density map like CryoEM? When I open, it's shown as lines-like map so as to which couldn't be used for docking. I really appreciate it if someone could do me this favor. Thanks a lot.
Best, Yanhe
Awesome, thanks! I will try. Elaine Meng <meng@cgl.ucsf.edu> 于 2018年7月2日周一 11:41写道：
Hi Yanhe, (1) Combine is for merging multiple models (usually multiple input files) into one model. If all four of your copies are already in one model (one input file) it makes no difference. Maybe you meant you just wanted to remove the other copies when saving a file. If you already have all the atoms you want to keep selected, just use menu: File… Save PDB, and in the resulting dialog, turn on the option “Save selected atoms only”
(2) PDB is not a map format; it contains coordinates of points, usually atoms. I see in SASDB that some entries have PDB files that are fully modeled proteins, and others are just a set of balls that fit the shape of the envelope. Since you said “lines-like” the one you have is probably just a set of balls. Chimera doesn’t know they aren’t really a protein, so it is trying to show a ribbon. Try commands to turn off ribbon and show all points as spheres:
~ribbon display repr sphere
Then it should look like a bunch of balls that show the shape of the SAS data. Either way (full protein or set of balls) you can use the “molmap” command to simulate a density map from the points, for example:
molmap #0 8
… meaning to create a map from the “atoms” (the balls are fake atoms) in model #0 using resolution 8. I don’t know what resolution value is best, but in the Volume Viewer dialog that automatically appears when you create the map, you can change from “surface” to “mesh” display and judge for yourself.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 30, 2018, at 7:37 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
To whom may concern, This is Yanhe Zhao from UT Southwestern Medical Center. I have to question when use Chimera as below, hopefully someone could do me a favor to answer it. 1, my crystal structure have four copies in one Asymmetrical structural unit. When I try to combine two of them by selection and combine command, always combine all of them. I pretty sure that I only select two of them; 2, I got one PDB from SASDB, how can I show it as a density map like CryoEM? When I open, it's shown as lines-like map so as to which couldn't be used for docking. I really appreciate it if someone could do me this favor. Thanks a lot.
Best, Yanhe
participants (2)
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Elaine Meng -
Yanhe Zhao