[Chimera-users] PDB model merging

Nikolay Igorovich Rodionov nirodion at syr.edu
Mon Mar 26 19:04:31 PDT 2012

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

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, March 26, 2012 12:12 PM
To: Nikolay Igorovich Rodionov
Cc: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] PDB model merging

Hi Nikolay,
PDB files written from Chimera *do* preserve helix and strand assignments, so if you read them back into Chimera the secondary structures will be the same.  I just doublechecked that this is true even after combining models.

Also, since Chimera 1.5 (Dec 2010), you can read PQR format into Chimera.

Have you checked to make sure that the PDB2PQR step does not remove the secondary structure records?

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 25, 2012, at 3:11 PM, Nikolay Igorovich Rodionov wrote:

> Hi Eric,
> I am only concerned with preserving records that are involved in various renderings of each subunit. I am taking the combination pdb file and assigning partial charges to the residues using pdb2pqr and then rendering  the resulting pqr file in VMD because Chimera does not support pqr files. 
> The main issue I have experienced is that I am unable to render several representations such as secondary structures because the combined pdb file is missing these records. Is this possibly due to an error on my part? Do you know a way to remedy the situation?
> Thank You,
> Nikolay
> On Mar 23, 2012, at 8:13 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:
>> On Mar 23, 2012, at 3:30 PM, Nikolay Igorovich Rodionov wrote:
>>> Hi all,
>>> I'm working on a project that requires me to merge models created through PDB BIOMT records. I have been using the copy&combine feature in the model panel to merge all of my models, and then writing a new PDB of only the combined model. I've noticed that this method deletes a large amount of information about the structure, including secondary structure records. Is there a way to merge models without losing such data?
>>> If it is relevant, I am merging 90+ models.
>> Hi Nikolay,
>> So, why do you want to preserve the various header records in the merged models?  Chimera will write out appropriate HELIX and SHEET records for your merged structure if you save it in PDB format.
>> I guess I'm pretty unclear as to how to "merge" many of the various record types when combining models.  Such as:  AUTHOR, COMPND, CRYST1, EXPDTA, HEADER, ORIGX, various REMARK records, TITLE, and so on.
>> --Eric
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu

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