From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Oct 10 2007 - 10:09:52 CDT
Hi Marcus,
for building proteins residue by residue, you could give the protein
builder of the molefacture plugin a shot. It's in the vmd extensions
menu under modeling. You may want to grab a vmd1.8.7 alpha release from
biocore to give this a try, as the plugin is developing fairly rapidly.
Peter
Marcus Rölz wrote:
> Hi Peter,
>
> thx for your input. I am considering to build a collagen strand residue by residue - so a copy of pdb files is not really handy for me. Any other ideas how to create or copy residues?
>
> Marcus
>
>
>> Hi Marcus,
>> the best way to do this is going to be to make new pdb files (initially
>> identical to the one you start with) for the copy, and then use VMD's
>> matrix operations to translate/rotate them (see the matrix routines
>> section in the VMD user's guide for how to do this). You can then use
>> psfgen to get them all into a usable coordinate/topology pair.
>> Best,
>> Peter
>>
>> Marcus Rölz wrote:
>>
>>> Hello out there ;)
>>>
>>> I'd like to lengthen a collagen-strand (Triple-Helix).
>>> To do this i'd like to create new atoms, copy existing atoms, and do
>>>
>> translations and rotations on atom selections via matrix operations.
>>
>>> I'm not sure which program to use for this purpose. Is VMD + psfgen
>>>
>> capable of doing this? I'd like to select some atoms copy them and relocate
>> them.
>>
>>> Can pdb-files be imported in sciLab? Or is there any other tool around?
>>>
>>>
>>> Thx,
>>>
>>> Marcus Rölz
>>>
>>>
>>>
>>>
>
>
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