[Chimera-users] Downloading HIV PDB 3j3q?

[Elaine Meng]

Hi Maja,
Please try the "PDB-format like files” download from RCSB PDB first, before some more complicated procedure in ChimeraX that I’m not sure will work anyway because of the atom serial-numbering issue.

However, in ChimeraX, you could select multiple chains with commands like:

select /A-F,Q,Y-Z

…fully described here
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>

Elaine

> On Apr 4, 2019, at 5:37 AM, Divjak Maja <Maja.Divjak at petermac.org> wrote:
> 
> Hi Elaine,
> 
> Thanks for your reply.
> Unfortunately,  mMaya  (the import plugin) hasn't updated its pdb file parser since dot, and is strung to the old PDB format, which doesn't have the expressive capacity for these larger structures. Hopefully that will change sometime soon, to adopt the newer ones and hopefully be more permissive, etc. So, in the meantime, all we can do is open them in an app that can (such as ChimeraX), and export subsets of chains, then reassemble them back in mMaya. I did try exactly the command sequence you outlined below prior to your suggesting it, but I couldn't work out how to select multiple chains simultaneously to do this, so I was just doing one at a time. Is there a simple way to do this please, or what is the command?  Of course, as you say, the numbering could become all messed up and will not work anyway. 
> 
> Thanks so much for your help, as always and best wishes,
> 
> Maja
> 
> -----Original Message-----
> From: Elaine Meng <meng at cgl.ucsf.edu> 
> Sent: Thursday, 4 April 2019 3:23 AM
> To: Divjak Maja <Maja.Divjak at petermac.org>
> Cc: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Downloading HIV PDB 3j3q?
> 
> Hi Maya,
> The problem is that there are too many atoms to save as a single PDB file no matter what visualization program you use — the large atom serial numbers simply do not fit in the columns allotted to them in PDB format, and there also might be too many chains.
> 
> As I mentioned before, if you’re just trying to get coordinates, see the “Download Files” options available directly from the RCSB PDB for this entry: 
> <https://www.rcsb.org/structure/3j3q>
> 
> The "PDB format” options are grayed out, but other options are “PDB format-like files” (not sure what this means but sounds promising) and “EM Map” (is that what you meant by emd?).
> 
> In ChimeraX you could *probably* do it by selecting subsets and writing only the atoms that are selected (save command, format pdb, selectedOnly true, possibly also serialNumbering h36), but it’s not worth all the hassle of trying to figure out how many atoms you can write at once and how to divide the structure up if you can just download the files from the RCSB PDB.  I say “probably” because I’m not sure if ChimeraX would actually renumber the atoms of the smaller subset, or try to use their original serial numbers which wouldn’t fit in the format.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
> 
> Best,
> Elaine   
> 
>> On Apr 3, 2019, at 1:29 AM, Divjak Maja <Maja.Divjak at petermac.org> wrote:
>> 
>> Thanks Elaine,
>> 
>> I tried ChimerX at your suggestion and it is able to upload the molecule. The difficulty now is saving it as a PDB. I found it only seems to save some of the subunits in PDB format that I was able to import into Maya. It does save the whole structure as obj, but this file format is not compatible with the import plugin mMaya. I was wondering if there is a way of selecting a number of chains simultaneously and then saving those in a PDB and repeating until the whole capsid is saved out and then reconstruct in Maya? There are a very large number of chains and I seem only able to select one at a time from the drop down menu. Alternatively, can you save as emd files from ChimeraX?
>> 
>> Thanks so much and best wishes,
>> 
>> Maja
>> 
>> 
>> From: Elaine Meng <meng at cgl.ucsf.edu>
>> Sent: Tuesday, 2 April 2019 3:16 AM
>> To: Divjak Maja <Maja.Divjak at petermac.org>; UCSF Chimera Mailing List 
>> <chimera-users at cgl.ucsf.edu>
>> Subject: Fwd: Downloading HIV PDB 3j3q?
>> 
>> 
>> From: Divjak Maja <Maja.Divjak at petermac.org>
>> Subject: Downloading HIV PDB 3j3q?
>> Date: April 1, 2019 at 5:23:39 AM PDT
>> To: Elaine Meng <meng at cgl.ucsf.edu>
>> 
>> Hi Elaine,
>> 
>> It's me again! Hope you had a nice weekend...
>> 
>> I'm having some trouble downloading the HIV capsid file, PDB 3j3q. When I try to import it to Chimera it begins downloading, but the molecule never quite appears, even though it ends up in the entry list. The screen stays blue like it has yet to be uploaded. If I try to upload it from the list, again, nothing appears. I realise the molecule is very large, but I think I'm missing something important here?
>> 
>> Thanks so much for your help, as always,
>> 
>> Maja
>> 
>> Dr Maja Divjak
>> BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator 
>> Office of Cancer Research
>> 
>> 
>> Hi Maja,
>> (forwarding to the address that should be used for for Chimera 
>> questions)
>> 
>> It is probably just too big for the memory on your computer to open this structure in Chimera.
>> 
>> Depending on what you’re trying to do with this capsid, maybe you could try using ChimeraX instead of Chimera.  It handles large structures much more efficiently, but it does not have the same set of features as Chimera.
>> <http://www.rbvi.ucsf.edu/chimerax/index.html>
>> 
>> If you are just trying to get the atomic coordinates of the entire capsid, they are already in the file(s) you could download directly from the RCSB PDB without using any visualization program. 
>> <https://www.rcsb.org/structure/3j3q>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry University of California, San 
>> Francisco
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