VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Aug 06 2008 - 14:28:00 CDT

Thanks again. Indeed, I had previously built a psf and crd using CHARMM
for this molecule, but loading this files also results in vmd
recognizing them as a fragment other than protein. A workaround was to
save a new pdb of only the backbone atoms. After loading this new file
into vmd I get the info

Fragments: 1 Protein: 1 Nucleic: 0

Best regards
Cesar

John Stone escribió:
> Cesar,
> In your case for 1Q71, the easiest solution is to use the
> Extensions->Modeling->Automatic PSF Builder tool
> (just click the "I'm feeling lucky" button at the bottom)
> to build a complete structure. This cures the problem for me
> with both VMD 1.8.6, and also with the the current test builds
> of VMD 1.8.7. I'll have to investigate what it is that's upsetting
> the structure analyzer in VMD, but given that you can use the
> autopsf plugin to build a complete structure that displays correctly,
> you've got a short-term solution to use in the mean time. I suspect
> this may be an atom naming issue of some sort.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Aug 06, 2008 at 02:01:49PM -0300, Cesar Luis Avila wrote:
>
>> Dear John,
>> Thanks for your fast and detailed reply. As you suggested, vmd is not
>> recognizing the fragment as a protein while loading
>> Fragments: 1 Protein:0 Nucleic:0
>> How may I indicate vmd that this fragment is a protein? The structure
>> that is giving me problems is 1Q71 from PDB.
>> Best Regards
>> Cesar
>>
>> John Stone escribió:
>>
>>> Cesar,
>>> There's more involved in rendering secondary structure representations
>>> than just the classification performed by STRIDE. Beyond that, the
>>> structure must be recognized by VMD as either a "protein" or
>>> "nucleic acid" according to the structure analysis VMD does when
>>> the file is first loaded. You can determine what's going on with
>>> that by looking at the output VMD prints when the file is loaded,
>>> of particular interest is this line (a typical example):
>>> Fragments: 1 Protein: 1 Nucleic: 0
>>>
>>> If you see a line that looks like this on the other hand, it
>>> would indicate that VMD doesn't recognize the fragment as either
>>> protein or nucleic acid, so it would not be drawable in any of
>>> the ribbons or cartoon representations:
>>> Fragments: 1 Protein: 0 Nucleic: 0
>>>
>>> Going further, in order to draw ribbons or cartoon representations,
>>> VMD needs to be able to identify certain atoms within each residue
>>> in order to compute the backbone spline and orientation vectors.
>>> If VMD doesn't recognize or can't find the necessary atoms, it
>>> may bail out and issue a warning that it can't draw the structure
>>> for this reason.
>>>
>>> Last, VMD uses the secondary structure codes provided by STRIDE to
>>> determine which cross-section shape to use when rendering the
>>> backbone spline. VMD will still be able to render a ribbon
>>> even if STRIDE aborts or is otherwise unable to assign secondary
>>> structure codes.
>>>
>>> Since you're having trouble with both the ribbon and cartoon
>>> representations, I suspect the cause of your problem is one of the
>>> items I listed above, independent of what STRIDE says.
>>>
>>> If you send me the structure that's giving you trouble, I'd be
>>> happy to take a look at it.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Wed, Aug 06, 2008 at 01:17:58PM -0300, Cesar Luis Avila wrote:
>>>
>>>
>>>> Hi all,
>>>> I have a short peptide of 21 aminoacids for which I am trying to get a
>>>> New cartoon representation. Even though STRIDE seems to work without
>>>> problems, as seen from running the command on Tk console
>>>>
>>>> [atomselect top "name CA"] get structure
>>>> C C C C C C E E E E E T T T E E E E E C C
>>>>
>>>> Nevertheless when I try to use any of the drawing methods Ribbons,
>>>> NewRibbons, Cartoon or NewCartoon, I don't see anything rendered (empty
>>>> screen). Which might be the problem? I am using vmd 1.8.6 on linux with
>>>> Nvidia drivers.
>>>>
>>>> In line with the above question, is it possible to use this drawing
>>>> representations with custom secondary structure information other than
>>>> STRIDE? (perhaps derived from other tools).
>>>>
>>>> Thanks
>>>> Cesar Avila
>>>>
>>>>
>>>
>>>
>
>