Chimera-users May 2012

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chimera-users@cgl.ucsf.edu

34 participants
42 discussions

changing map dimensions
by Elaine Meng 01 May '12

01 May '12

On Apr 30, 2012, at 6:56 PM, Yuhong Li wrote: > Hi Elaine, > Thanks for your help, now I've understood what those numbers mean. But I was wondering if you could tell me how I can change those gird points, such as change 88 66 94 to 94 94 94 or any cubic numbers ? > Best Wishes, > Yuhong Lee > Hi Yuhong, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of directly to me. Those numbers are the size of your input data file, so I'm not sure what you mean. You can't just change the numbers arbitrarily. It is possible to make a new data set by cutting off part of the original data set. One way to do that is to use the "volume" command to save a new map file, using the "saveSubregion" option to include only part of the original map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> However, it sounds like you want to make a new data set that is bigger than your original map. There is a "vop cover" command that will make a bigger map, but it assumes periodicity of the input map. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> If instead you wanted values of zero at the additional grid points, however, I don't know how to do that -- maybe the others have ideas. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Just want atom distances
by Patricia LiWang 30 Apr '12

30 Apr '12

Hello users group, I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table. I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking" So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane". Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program. Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance? Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"? Thanks! Patti ---------------------------------------------------------------------------

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