VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 04 2005 - 18:47:45 CDT

Residues are defined in the pdb and are not adjusted by VMD based on
position of the atoms, afaik (but can be changed in the tkcon window).

Before and after doing the rotation, hit 0 (for query) and then click
that atom. In the vmd console, you should see the same information
regarding atom name, residue name and number, etc. Perhaps with this
information, you can determine why it is being excluded?

Your other option, I think, would be to create a psf file before doing
the rotation so the bonds are explicitly defined. Then the atom would
move like it was supposed to.

On Oct 4, 2005, at 6:32 PM, Samuel Flores wrote:

> Hi John,
>
> I selected by residue number. I think the atom was too far away and
> VMD
> didn't recognize it as part of that residue, therefore didn't include
> it in
> the selection set. The question is, how to counter this problem? I
> can't
> select all, and then deselect the unwanted residues, because then the
> extra
> atoms would end up in ALL selections, not just the intended one.
>
> Sam
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tuesday, October 04, 2005 3:27 PM
> To: Samuel Flores
> Cc: 'mashaojie163'; 'vmd'
> Subject: Re: vmd-l: VMD removing slightly misplaced atoms
>
>
> Sam,
> VMD won't remove any atoms... If you're missing the atom it's
> because
> the atom wasn't part of the atom selection you saved with "$sel
> writepdb" or
> however you chose to do it. If you saved an atom selection that was
> specified like this:
> set sel [atomselect top "all"]
> $sel writepdb my.pdb
>
> Then you should not be missing any atoms.
> If you had some selection other than "all", then you may have made a
> mistake and excluded the atom of interest unintentionally.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 04, 2005 at 03:03:46PM -0400, Samuel Flores wrote:
>> Hi guys,
>>
>> I have a CE atom in a methionine residue that is a little distant
>> from its
>> corresponding sulfur. When I open the molecule using VMD, make some
>> minor
>> rotations and then save the protein, the saved protein is missing this
> atom.
>> Presumably it was too far away to be recognized as part of the MET
>> residue
>> (in fact no bond is displayed in the viewer) and was truncated. I'd
> rather
>> not have this truncated (I'll do an energy minimization later,
>> hopefully
> fix
>> the problem that way). Can anyone tell me how to instruct VMD to not
> remove
>> atoms?
>>
>> Many thanks
>>
>> Sam
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
>> Behalf
> Of
>> mashaojie163
>> Sent: Monday, October 03, 2005 9:16 PM
>> To: vmd; John Stone
>> Subject: Re: vmd-l: How can I compile win32-vmd
>>
>> Thank you
>> Maybe you just provide the current windows vmd for me. I have
>> compiled plugins successfully by use of cygwin and was compiling vmd
>> by
> use
>> of MSVC and now meeting some errors. Please send me the new vmd in
>> windows
> .
>> I will compile it when I have spare time.
>> Best Regards
>>
>> Ma shaojie
>>
>>
>> ----- Original Message -----
>> From: "John Stone" <johns_at_ks.uiuc.edu>
>> To: "mashaojie163" <mashao_jie_at_163.com>
>> Cc: "vmd" <vmd-l_at_ks.uiuc.edu>
>> Sent: Tuesday, October 04, 2005 12:15 AM
>> Subject: Re: vmd-l: How can I compile win32-vmd
>>
>>
>>>
>>> Hi,
>>> If you need a current build of VMD on Windows, I can provide one
>>> for
>> you.
>>> If you really want to build from source, you should be warned that
>>> the
>> build
>>> requires you to use MSVC and if you plan to build the plugins from
> source,
>>
>>> you'll also need cygwin to get the 'make' and other utilities we're
> using
>>> there. Let me know what you're trying to do and I can help you solve
>> this.
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Sun, Oct 02, 2005 at 01:18:11PM +0800, mashaojie163 wrote:
>>>>
>>>>
>>>>
>>>> Dear Sir:
>>>> I get the source code by vmd-cvs and by use of make command to
>> compile linux vmd. But can you tell me how I should compile window
>> vmd. I
> do
>> not know make command in windows
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>