Hi Tom, There is a “dumpHeaders” option of the volume command to send info to the Reply Log, e.g. vol #1 dump true <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> I believe that group/ungroup models is only in the Model Panel. Undoubtedly it could be done with python, but someone else would have to help with that. (Best to send questions to the list since the “group knowledge” exceeds mine!) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 4, 2019, at 5:36 AM, Tom Marlovits <thomas.marlovits@cssb-hamburg.de> wrote:
Elaine, one more question … is there a command file to also group models? Thx Tom
Hi Elaine, is there an easy solution to read out the header metadata of an .mrc file in chimera and report it to a text file? Thx Tom
Number of columns, rows, sections ..... 80 80 80 Map mode .............................. 2 (32-bit real) Start cols, rows, sects, grid x,y,z ... 0 0 0 80 80 80 Pixel spacing (Angstroms).............. 0.6370 0.6370 0.6370 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... -25.48 -25.48 -25.48 Minimum density ....................... -0.80182E-01 Maximum density ....................... 0.11564 Mean density .......................... 0.19742E-03 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens .
On Jan 4, 2019, at 10:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
I believe that group/ungroup models is only in the Model Panel. Undoubtedly it could be done with python, but someone else would have to help with that.
Indeed you need to use Python. In Python, assuming you had the models you wanted to group in a variable named “models”, it would be: from ModelPanel import groupCmd groupCmd(models, name=“group name”) You can obtain a list of all open models from Chimera’s “openModels” variable, e.g.: from chimera import openModels allModels = openModels.list() Every model has a ‘name’ attribute, and ‘id’ attribute containing the main model ID number and ‘subid’ containing the sub-ID number, if any. Therefore you could get a list of all models whose name starts with ‘exp1_’ with: from chimera import openModels models = [m.name.startswith(“exp1_”) for m in openModels.list()] This whole process may be easy or quite difficult, depending on your pre-existing familiarity with working with Chimera’s Python. —Eric Eric Pettersen UCSF Computer Graphics Lab
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