From: shukunluo <shu...@gm...> - 2011-09-11 08:51:24
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Dear Pymol users, I want to compare the crystal packing and contacts of two different space groups of the same protein using pymol. Here's what I did: (1)loaded two structures; (2) aligned two structures; (3) generated symmetry-related objects of two structures. However, the symmetry-related molecules didn't move with the source structure. I tried in coot to superimposed two structures then save the moved molecules, but the space group changed to the target structures. I also tried the matrix_copy command with failure. Does anyone know how to do this? Thanks in advance. Best, Shukun |
From: Nat E. <nat...@gm...> - 2011-09-11 13:50:17
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I've never found a clean way to do this - what I do is to save a PDB file with the original model and the relevant symmetry mates, which I then use for the alignments. There may be a way to do is with object groups, however. (FYI, you'll probably also need to rename the chain IDs for the symmetry mates so you can still use a unique atom selection for the original chain(s).) -Nat On Sunday, September 11, 2011, shukunluo <shu...@gm...> wrote: > Dear Pymol users, > > I want to compare the crystal packing and contacts of two different space groups of the same protein using pymol. Here's what I did: (1)loaded two structures; (2) aligned two structures; (3) generated symmetry-related objects of two structures. However, the symmetry-related molecules didn't move with the source structure. I tried in coot to superimposed two structures then save the moved molecules, but the space group changed to the target structures. I also tried the matrix_copy command with failure. > > Does anyone know how to do this? Thanks in advance. > > Best, > Shukun |
From: Thomas H. <sp...@us...> - 2011-09-12 07:48:01
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Hi Shukun, why and how did the matrix_copy command fail? If you swap step (2) and (3) everything should be fine. Try this: fetch 2xwu 2x19, async=0 as ribbon symexp mates, 2x19, 2x19, 6.0, segi=1 align /2x19//B, /2xwu//B matrix_copy 2x19, mates* By the way, the segi=1 argument of the symexp command gives every symmetry mate a uniqe segment identifier, so if you would save them all to the same PDB file there is no need to rename chain IDs. Cheers, Thomas shukunluo wrote, On 09/11/11 10:51: > Dear Pymol users, > > I want to compare the crystal packing and contacts of two different > space groups of the same protein using pymol. Here's what I did: > (1)loaded two structures; (2) aligned two structures; (3) generated > symmetry-related objects of two structures. However, the > symmetry-related molecules didn't move with the source structure. I > tried in coot to superimposed two structures then save the moved > molecules, but the space group changed to the target structures. I also > tried the matrix_copy command with failure. > > Does anyone know how to do this? Thanks in advance. > > Best, > Shukun -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Thomas H. <sp...@us...> - 2011-09-13 07:55:02
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Hi Shukun, > Thanks for your nice replies. I followed Tom's script, and the problem > solved. Also, I found there was no difference whether the > "segi=1"argument was appended or not. I've checked at the PymolWiki site > and haven't found any "matrix_copy" arguments like 'segi'. "matrix_copy" does not have a segi argument, but "symexp" has. I've updated the PyMOLWiki page: http://pymolwiki.org/index.php/Symexp > By the way, the old version of Pymol(0.99) may be the cause of failure > last time I used the "Matrix_copy" command? I upgraded pymol to the > version of 1.4.1, . yes, the matrix_copy command was introduced after 0.99! Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |