Multiple Volume Viewer Windows and saving PDB file
Hi,
I am just wondering if there is any way that I can have two or more volume viewer windows open at the same time. I am comparing two density maps and to be able to change the threshold and color for both maps, without having to go back and forth in the same window, would be much easier and useful.
Also, I recently fitted a pdb crystal structure into a density map but was not able to save it with relation to the density map (the feature which was available in previous releases). However, if I have multiple pdb files open then I can save the pdb file of my interest with respect to the map. Is there anyway to save a fitted pdb file with respect to a density map without opening other pdb files?
Thank you,
Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400
Hi Batsal,
It isn't possible to have more than one volume viewer dialog. I agree this would be very helpful and I've added it to my list of projects. There is a problem that some Chimera tools like volume eraser or volume path tracer act on the volume shown in the unique volume viewer dialog. Also I'll have to think about the user interface details of creating, hiding, and removing extra volume viewer dialogs.
For now one small aid to working with multiple volume data sets is to use the volume dialog Features / Data Set List menu entry. This shows a list of the volume data sets and you can click on list entries to switch between them rather than using the more cumbersome menu of data sets. If this is frequently useful you can use Features / Save Default Dialog Settings so the data set list is shown by default.
There is a bug in Chimera version 1.2304 when using menu entry File / Save PDB.... If you have one PDB model and a map open it does not offer you a choice of saving the PDB coordinates relative to the map. This is fixed in Chimera snapshot version 1.2309. You can work around the problem in 1.2304 by opening two PDB models. Then Chimera will give you the choice to save coordinates relative to the map. The second PDB model can be anything (another copy of the first model) and does not need to be saved. That's inconvenient and I recommend using Chimera 1.2309 instead.
Tom
Dear Chimera Folks,
I am familiar with adding experimental features to Chimera installations on linux and pc. I'd like to do the same for the working installation of Chimera on my new intel dual-core iMac, but I cannot find the share folder that I should put them into.
I'm using UCSF Chimera beta version 1 build 2309 (2006/11/08), platform: darwin, windowing system:X11. After I installed the software following instructions I moved the icon that was on the desktop to the applications folder, as suggested. When I use the finder search I cannot find any folders named chimera or chimera.app. Yet they must be there somewhere! But where?
thanks in advance for your help...
Cathy
Hi Cathy,
In the Finder, right click on the Chimera icon, and choose "Show Package Contents," and navigate from there.
Applications in Mac OS X are actually folders called foo.app, you can accomplish the same thing in the command line by changing to the / Applications/Chimera.app/ directory
Ciao, Jeramia
On Nov 28, 2006, at 5:52 PM, Catherine Lawson wrote:
Dear Chimera Folks,
I am familiar with adding experimental features to Chimera installations on linux and pc. I'd like to do the same for the working installation of Chimera on my new intel dual-core iMac, but I cannot find the share folder that I should put them into.
I'm using UCSF Chimera beta version 1 build 2309 (2006/11/08), platform: darwin, windowing system:X11. After I installed the software following instructions I moved the icon that was on the desktop to the applications folder, as suggested. When I use the finder search I cannot find any folders named chimera or chimera.app. Yet they must be there somewhere! But where?
thanks in advance for your help...
Cathy
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participants (4)
-
Batsal Devkota -
Catherine Lawson -
Jeramia Ory -
Thomas Goddard