Dropdown list of models in groups
Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser
Hi Yasser, This doesn’t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn’t a way for the user to group models manually (at least yet) or add notes to a model or group. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com> wrote:
Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser
Correction: someone just reminded me that in ChimeraX, users CAN group models by using the “rename” command to specify new hierarchical model ID numbers. I keep forgetting that this command can change ID numbers, not just model names. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html>
On Aug 22, 2018, at 10:41 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yasser, This doesn’t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn’t a way for the user to group models manually (at least yet) or add notes to a model or group. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2018-08-22 at 10.39.53 AM.png>
On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com> wrote:
Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser
Hello Elaine, Thank you for your answer. I will try ChimeraX and the rename command. In any case, I think many users would appreciate the addition of this functionality to Chimera. I am a big fan of Chimera, and have been using it since 10 years. I have some suggestions for new functionalities. Is this users mailing list proper platform for suggestions? Best regards Yasser On 22.08.2018 20:14, Elaine Meng wrote:
Correction: someone just reminded me that in ChimeraX, users CAN group models by using the “rename” command to specify new hierarchical model ID numbers. I keep forgetting that this command can change ID numbers, not just model names. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html>
On Aug 22, 2018, at 10:41 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yasser, This doesn’t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn’t a way for the user to group models manually (at least yet) or add notes to a model or group. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2018-08-22 at 10.39.53 AM.png>
On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com> wrote:
Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser
Hello Yasser, Yes, you can make suggestions for Chimera to this list, and we appreciate your thoughts. However, most effort in our group is now on developing ChimeraX, so it may be more likely for your suggestions to be implemented in ChimeraX than in Chimera. In addition to improvements and completely new features, ChimeraX already has a lot of the same features for working with maps: the “volume” and “vop” commands are almost exactly same, “fitmap” (fitting), “molmap” (map from atoms), “vseries” (play volume time series), etc. However, missing currently are segmentation, volume eraser, and many GUI tools (although the same thing may be available in a command). Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 23, 2018, at 12:35 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com> wrote:
Hello Elaine,
Thank you for your answer.
I will try ChimeraX and the rename command. In any case, I think many users would appreciate the addition of this functionality to Chimera.
I am a big fan of Chimera, and have been using it since 10 years. I have some suggestions for new functionalities. Is this users mailing list proper platform for suggestions?
Best regards
Yasser
Hi Yasser, If you want to try ChimeraX you can make the grouping of models and submodels however you like using the ChimeraX “rename” command to change the model id numbers. For instance to put models #1-10 under a single group #11.1-10 rename #1-10 id #11 You should also be able to rename to id #1 but I got an error doing that which I will fix today. Tom
On Aug 22, 2018, at 10:41 AM, Elaine Meng wrote:
Hi Yasser, This doesn’t solve your problem for a user-defined group, but in ChimeraX, the Models list has disclosure triangles to expand and collapse groups. Opening an NMR ensemble of atomic models (e.g. 1plx) or showing multiple isosurfaces for the same density map automatically makes a group, as in the attached image. However, there isn’t a way for the user to group models manually (at least yet) or add notes to a model or group. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2018-08-22 at 10.39.53 AM.png>
On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com <mailto:yasser.almeida@gmail.com>> wrote:
Hello, I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models. Best Yasser
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Hi Yasser, Grouping was something that was shoehorned into the Model Panel well after it was originally designed and implemented, and so it doesn’t work quite as naturally as it could otherwise. Others have pointed out that ChimeraX has a more natural grouping mechanism in its Model Panel, though it lack other capabilities (such as adding notes). I guess I don’t understand what you’re saying about “losing notes”. Groups don’t have notes themselves — any note you add to a group gets added to all the models in the group instead. If you then ungroup and regroup those models, it will show the same note that you added (unless you then add/edit notes in the individual models). You are correct that you lose which particular models were composing the group though. —Eric
On Aug 22, 2018, at 2:16 AM, Yasser Almeida Hernández <yasser.almeida@gmail.com> wrote:
Hello,
I am working with groups of models, and I wonder if there is a way to make a group, with a defined name, and then inspect each models independently without lose the group. Currently, if I make a group, and then ungroup, I lose the definition, notes ans any other action on it. If there is no possibility, I would suggest the developers to consider the option to make groups with dropdown list of models.
Best
Yasser
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participants (4)
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Elaine Meng -
Eric Pettersen -
Tom Goddard -
Yasser Almeida Hernández