September 2008 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

3 3

using EMAN/AIRS/SSEHunter
by Peter Hildebrand 10 Dec '08

10 Dec '08

Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: <function command at 0x89f67d4> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter

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Re: [Chimera-users] 1HLA- how to make ribbon image?
by Elaine Meng 30 Sep '08

30 Sep '08

Hi David, To summarize for the chimera-users list: 1HLA is an alpha-carbon-only structure, which cannot be shown as a ribbon in Chimera. However, there are many other structures of this protein, several at higher resolution and including all backbone atoms, allowing them to be displayed as ribbons. This Uniprot page has a long list of structures (about 80% of the way down is a "3d structure databases" section): http://www.uniprot.org/uniprot/P01892 The best resolution looks like 1.4 Angstroms, structures 1i4f and 1oga. Both match up with the CA-trace in 1hla quite well. Since they include all backbone atoms, they can be displayed as ribbons. I suggest using 1i4f. 1oga is just as good but has two copies. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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1HLA- how to make ribbon image?
by Edelshtein, David 30 Sep '08

30 Sep '08

Hello, I am an ITL researcher, I use chimera for making a ribbon image of 1HLA molecule, and I need to mark specific residues, (by the number/position). So far, I am unsuccessful in converting wire style to the ribbon style. Please let me know if you can help, advice or direct me to required info. David, Edelshtein SRA II UCSF ITL

2 1

COLOURING A SUBUNIT
by Tom Goddard 30 Sep '08

30 Sep '08

skmolugu(a)miners.utep.edu wrote: > Hi, > thank you very much for your reply, > I have another question, is there a way to colour a symmetric map which has 4 subunits in to four different colours? > thank you for your time, > regards, > sudheer. > Hi Sudheer, If you have 4 monomer PDB models fit into the map, color them differently (e.g. command "rainbow chain"), then use the Color Zone tool to color the map to match the monomers. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorz… The Chimera volume guide may help with future questions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html Tom

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Re: [Chimera-users] SEPARATING A SUBUNIT
by skmolugu＠miners.utep.edu 29 Sep '08

29 Sep '08

Hi, I have a CryoEM density map with 14 subunits with seven fold symmetry. Is there a way in chimera to separate only one subunit from the entire map. thanks, sudheer

2 1

Calculating RMSD for ligand
by 吴超 27 Sep '08

27 Sep '08

Hi, dear folks, I want to evaluate the docking performance by calculating the RMSD of heavy atoms between ligand crystal conformation and docked conformation. I use the following command: rmsd #0:1.het & ~element.H #1:1.het & ~element.H But Chimera seems to forget the correct order and give a pairwise alignment not the way I want . I wonder if there is a way that I can get the correct selection order so as to calculate RMSD. Best -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206

2 1

calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

2 1

calculating symmetry for a dimer structure
by Katryna Cisek 26 Sep '08

26 Sep '08

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna

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Chimera-users September 2008