[Chimera-users] Reading and saving large files in chimera
conrad at cgl.ucsf.edu
Tue Mar 27 12:46:35 PDT 2018
Elaine is indisposed for a few days, so I'm looking into this problem.
Unfortunately, from what I can tell, it is a problem with the PDB format
itself.The official standard
only allows for three-character residue names in columns 18-20 and
one-character chain identifiers in column 22. It looks like Phenix,
seeing that column 21 is unused, is allowing two-character chain
identifiers in columns 21-22. Chimera (and ChimeraX), on the other
hand, seeing that column 21 is unused, is allowing four-character
residue names. So the string "ASPA1" is interpreted by Phenix as
residue "ASP" in chain "A1", but by Chimera as residue "ASPA" in chain
"1". (Doubly unfortunate, the one-character chain identifier limit is
built into the Chimera data structures so we cannot simply change the
PDB parser to support two-character chains.)
As Elaine suggested earlier, your best bet is probably using mmCIF
format instead of PDB. mmCIF is not column-based and is explicitly
designed to handle very large structures. Phenix version 1.8.2 and
later support mmCIF as does ChimeraX. I would not recommend Chimera for
large mmCIF files as it requires excessive memory resources and is very
slow to boot. (ChimeraX can open 5ire_BIOMT_expanded.pdb in under a
minute and renders a beautiful [tooting our own horn :-)] image with
On 3/26/2018 10:08 PM, #TOFAYEL AHMED# wrote:
> Hi Elaine,
> Thanks for getting back to me so promptly. Please find below the google
> drive link for the files. I am describing what I have in the folder: I
> have downloaded the model 5IRE from PDB website (filename:5ire.pdb) and
> applied phenix to operate on the transformation matrix (BIOMT record in
> REMARK 350) to generate the icosahedral complete
> virus (filename:5ire_BIOMT_expanded.pdb). Now, phenix has used two
> letter IDs for the chains and these chain IDs get changed when I open
> 5ire_BIOMT_expanded.pdb in Chimera1.12. I have then resaved the file
> again using Chimera1.12 and this file is named as chimera-saved.pdb.
> This is just an example case and it closely matches my problem. In real
> scenario, I need to use fit in map option in chimera and move the
> coordinates, so there is no way I can avoid "opening my model in chimera
> and resave them in new position".
> Kindly suggest after going through the files !
> Best regards,
> *From:* Elaine Meng <meng at cgl.ucsf.edu>
> *Sent:* Tuesday, March 27, 2018 1:04:22 AM
> *To:* #TOFAYEL AHMED#
> *Cc:* UCSF Chimera Mailing List
> *Subject:* Re: [Chimera-users] Reading and saving large files in chimera
> Hi Tofayel,
> Not being a phenix user, I may need more specifics, like:
> - are you getting a single PDB file of the whole capsid from applying
> the biomt in phenix, and opening that single PDB file in Chimera?
> - does that file have more than one chain with the same ID, or chain IDs
> with multiple characters?
> - is the chain ID different as soon as you read the structure in to
> Chimera, or is it only different when you write to an output file?
> - are you saving as Chimera session or writing a single PDB file?
> I know the capsid in your example has many chains, so I can only guess
> that in the file from phenix, there are either duplicate chain IDs or
> chain IDs with more characters than Chimera or PDB format allow.
> One idea is to try using ChimeraX instead. It can write mmCIF format.
> However, with my limited understanding of what is happening (sorry), I
> don’t know if that would solve your problem.
> Best regards,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# <TOFAYEL001 at e.ntu.edu.sg> wrote:
>> Hi Chimera developers and users,
>> I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the
> idea. If I take model bearing PDB id 5IRE and apply
> "phenix.pdb.biomt_reconstruction" I can generate the complete virus
> icosahedral structure from the asymmetric unit. But when I open this
> complete virus structure in Chimera and save it back again the chain IDs
> get changed. Is there any work around to maintain the original chain IDs
> and therefore maintain the secondary structure definitions in the file
> header, after opening and thereafter saving using Chimera?
>> Best regards,
>> NTU Singapore
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