VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Mon May 02 2016 - 12:25:44 CDT

Surendra, do you have pdb/psf or just pdb? If just the pdb then the distance between atoms might matter. Can you post the structure files somewhere so that we can have a look at them?

> On May 2, 2016, at 10:57, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I looked at this visually the other night but did not manage
> to find an obvious explanation. Unless I missed something that
> someone else happens to catch, I may have to dig into the code to
> figure out why the other two protein chains are not being recognized
> as protein. While I didn't see anything when looking, I'm guessing that
> the problem has to do with an unusual bond topology somewhere or
> unexpected atom types in the residues at the start/end of the affected chains.
> My time is extremely limited for the next three weeks, so
> I can't promise anything until later this month. Someone else might
> be able to catch this in the mean time if they have a close look.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Apr 30, 2016 at 09:52:26AM +0530, surendra jain wrote:
>> Hi John,
>>
>> many thanks for your message. I get the following message from VMD
>>
>> Info) Atoms: 11656
>> Info) Bonds: 12005
>> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
>> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
>> Info) Residues: 1503
>> Info) Waters: 0
>> Info) Segments: 4
>> Info) Fragments: 4 Protein: 2 Nucleic: 0
>>
>> I have 4 protein chains, but it can identify only 2 of those. I am
>> attaching the full protein structure.
>>
>> Kindly check what is the problem.
>>
>> Best Regards,
>> Surendra
>>
>> On 4/30/16, John Stone <johns_at_ks.uiuc.edu> wrote:
>>> Hi,
>>> When you load the structure, VMD will print out how many protein
>>> fragments it finds. If VMD is unable to identify your chains as
>>> protein fragments, e.g. due to unrecognized atom or residue names,
>>> then the various cartoon representations will not work because
>>> they specifically target protein fragments. The nomenclature VMD
>>> is expecting for the proteins is derived from protein data bank
>>> atom and residue naming conventions, so if Modeler did something
>>> else, that would explain the issue. If you read the mailing list
>>> archive and/or tutorials you will find that you can rename atoms quite
>>> easily, and then cause VMD to reanalyze the structure, and to save out
>>> new structure files if necessary.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Sat, Apr 30, 2016 at 08:04:47AM +0530, surendra jain wrote:
>>>> Hi,
>>>> There were some residues missing in the protein that I use for my
>>>> study. I did a homology modeling and added the missing residues using
>>>> Modeler. I can view my final protein structure using lines and bonds
>>>> in VMD. But I cannot view the full protein in cartoon, trace or tube
>>>> format ( only 2 chains out of 4 chains are visible).
>>>>
>>>> Any help will be appreciated.
>>>>
>>>> Best Regards,
>>>> Surendra
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/