[Chimera-users] PDB model merging

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 27 08:54:39 PDT 2012

Hi Nikolay,
I can't tell from the description what is wrong -- we would need to see input and output files and exactly what version of Chimera you are using.  However, you are doing some unnecessary steps.   Here is what I tried, which does not change secondary structure:

open 3i47
sym #0
... Model Panel, choose #0,1.1,1.2, copy/combine to create model 2
menu File... Save PDB
 in that dialog,
 (a) choose only model #2 in the "Save models" area
 (b) check "Save relative to model" #0 (do not check other options)

...then close session and reopen saved PDB in Chimera, which shows the same secondary structure for all subunits.
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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On Mar 26, 2012, at 7:04 PM, Nikolay Igorovich Rodionov wrote:

> Yes, I have verified PDB2PQR does not remove secondary structure method. To confirm, I rendered my PDB file in Chimera and built a new biological assembly PDB file by
> 	1.Open subunit file
> 	2.Activate model #0
> 	3.sym #0 --> builds biological assembly file
> 	4.Open model panel and select new models
> 	5.Create and Combine function
> 	6.Deactivate and hide all but the new combination model
> 	7.Select Write PDB and created new file
> Please see the attached image. It compares renderings of the biological assembly PDB I created and the original subunit file from RCSB. Both are displayed using secondary structure representation. The helices and sheets are clearly visible on the subunit but are absent on the biological assembly file which is composed of identical copies of the subunit. 
> Can you think anything I am doing wrong?
> Thank you,
> Nikolay Rodionov

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