[Chimera-users] suggested improvements

Tom Goddard goddard at sonic.net
Wed Jul 2 12:14:36 PDT 2014


Hi Matt,

  Ok, I added abbreviations for icosahedral symmetry orientations (222,2n3,n25,...) to menu entries in Icosahedron Surface dialog. Also I added a dumpHeader option to the volume command, for instance

	volume #0 dumpHeader true

and below is an example of the output for EMDB 1303.  I don’t know what kind of validation of map files you have in mind — the CCP4 format used by EMDB has very little redundancy.

	Tom


File header for emd_1303.map
alpha = 90.0
amax = 349.51
amean = 8.21659
amin = -73.2553
beta = 90.0
gamma = 90.0
ispg = 1
labels = ['::::EMDATABANK.org::::EMD-1303::::                                              ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ', '                                                                                ']
lskflg = 0
machst = 538984772
map = MAP 
mapc = 1
mapr = 2
maps = 3
mode = 2
mx = 155
my = 155
mz = 155
nc = 155
ncstart = -78
nlabl = 1
nr = 155
nrstart = -78
ns = 155
nsstart = -78
nsymbt = 0
rms = 31.0903
skwmat = [ 0.  0.  0.  0.  0.  0.  0.  0.  0.]
skwtrn = [ 0.  0.  0.]
symop = 
type = ccp4
user = [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
xlen = 437.1
ylen = 437.1
zlen = 437.1



	Tom


On Jul 1, 2014, at 8:01 PM, Dougherty, Matthew T <matthewd at bcm.edu> wrote:

>> Is your first suggestion to add the abbreviations 222,2n5,2n3,… to the menu entries in the Icosahedron Surface dialog?  
> 
> yes
> 
> What I am finding with EM viruses approaching atomic resolution, is one researcher will produce the EM reconstruction, another segments the ASU, and another does the PDB.  For me to test it I want to generate the entire PDB capsid using the sym command, so I use the icosahedron surface to match the symmetry on EM density, then apply the symmetry to the ASU.  Having the abbreviations in the menu entries would reduce confusion/accidents.
> 
> 
>  I agree having the ability to dump an MRC map header would be handy.  I can probably dump that to the Chimera reply log automatically if the MRC map load fails.  I have to think about how to show it in the reply log if the map opens correctly.  I don’t want to dump it to the reply log every time since it would just be useless info in almost all cases.  Not sure we have a Chimera command that I could sneak this into as an option, maybe the “volume” command.
> 
> 
> It would also provide a gold standard tool to determine EMDB compliance. A button on the volume dialog would be good, an abort during reading spitting out the header would be a useful diagnostic. 
> 
> 
> Matthew
> 
> 
> On Jun 30, 2014, at 3:54 PM, Dougherty, Matthew T wrote:
> 
>> 1) first suggestion
>> 
>> on the sym command the following is defined
>> 
>> icosahedral symmetry I[,orientation] around center
>> 
>>   Example: i,n25
>> 
>> where orientation can be:
>> 
>>   222 (default) - with two-fold symmetry axes along the X, Y, and Z axes
>>   2n5 - with two-fold symmetry along X and 5-fold along Z
>>   n25 - with two-fold symmetry along Y and 5-fold along Z
>>   2n3 - with two-fold symmetry along X and 3-fold along Z
>>   222r - same as 222 except rotated 90° about Z
>>   2n5r - same as 2n5 except rotated 180° about Y
>>   n25r - same as n25 except rotated 180° about X
>>   2n3r - same as 2n3 except rotated 180° about Y
>> 
>> 
>> 
>> In the chimera tool->higher order structure -> the icosahedral structure
>> it defines similar orientations, assume in the same order.
>> 
>> It would be helpful on the selections to include the sym syntax as part of the icosahedral structure text
>> ie {222} xyz 2 fold
>>  {2n5} x 2 fold z 5 fold
>> 
>> 
>> 
>> 
>> 2) second suggestion
>> When reading an MRC file I occasionally see situations that make me question whether the file is EMDB complaint.
>> 
>> It would be good to have the means to dump the MRC header, even if chimera refuses to read the file in its entirety.
>> 
>> 
>> 
>> 
>> Matthew Dougherty
>> National Center for Macromolecular Imaging
>> Baylor College of Medicine
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>> 
> 




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