[Biopython] writing a PDB----PLEASEEEE HELP
martin djokovic
martin.djokovic at gmail.com
Wed Oct 27 13:02:10 UTC 2010
Mitch, and everyone else.
Thanks sooooo much for all your help guys. I really appreciate this.
Martin
On Wed, Oct 27, 2010 at 6:44 AM, Mitchell Stanton-Cook <
m.stantoncook at gmail.com> wrote:
> Hi,
>
> I was playing around with writing additional residues to PDB files using
> biopython last week.
>
> I've included a simple snippet that gives you the basic idea of adding
> residues/atoms...
>
> Mitch
>
>
> for model in struct:
> for chain in model:
> for i in range(0, len(t_l)):
> # create new residue
> new_res = Residue(t_l[i], 'TSR', '')
> for j in range(0, 4):
> #populate the residue with atoms
> cur_c = dat[i+fill+j]
> new_at = Atom(n_l[j], cur_c, 0, 1, ' ', n_l[j],
> \
> int(str(90)+str(i)+str(j)),
> element='X')
> new_res.add(new_at)
> fill = fill +3
> chain.add(new_res)
> # Add the residue to the chain
> io=PDBIO()
> io.set_structure(s1)
> io.save(outname+'.pdb')
>
>
>
> On 27/10/10 04:25, Eric Talevich wrote:
>
>> Hi Martin,
>>
>> It sounds like VMD displays just one model at a time, unless you make a
>> movie out of it. You could get around that by writing the two structures
>> as
>> two different chains within the same model.
>>
>> But if the goal is just to view two structures superimposed, you'd be
>> better
>> off scripting your molecular viewer of choice to do it for you.
>>
>> In PyMOL, to view 1ABC and 2XYZ (made up), write this to a file called
>> 1ABC_vs_2XYZ.pml:
>>
>> # This is a generated PyMOL script
>> load /path/to/1ABC.pdb, 1ABC
>> load /path/to/2XYZ.pdb, 2XYZ
>> align 1ABC, 2XYZ
>>
>> # Optional viewing tweaks
>> hide all
>> show cartoon, 1ABC
>> show cartoon, 2XYZ
>> reset
>>
>>
>> Then launch the viewer from the command line:
>> pymol 1ABC_vs_2XYZ.pml
>>
>> If the two structures don't have the same peptide sequence, you'll have
>> better results with the "fit" function instead of "align":
>> http://www.pymolwiki.org/index.php/Fit
>>
>> I know VMD has something similar, but I don't have an example offhand.
>>
>> Best,
>> Eric
>>
>>
>> On Tue, Oct 26, 2010 at 1:05 PM, martin djokovic
>> <martin.djokovic at gmail.com>wrote:
>>
>>
>>
>>> Hello David and everyone else,
>>>
>>> Yes David at the moment I am actually doing that-formatting the PDB into
>>> 2
>>> models then superimposing them.
>>> Merging the structures when they are in 2 differant PDB files is not
>>> working.
>>> I tried the following:
>>> from Bio.PDB.Model import Model
>>> model1=Model(2ndModel)
>>> structure1.add(model1)
>>> Its not working-I think I might have to better understand the object
>>> "structure"
>>> Is there a better way to merge two structures? Else I will write the 2
>>> pdb
>>> files as models into a single PDB then superimpose.
>>>
>>> Another question-maybe some of you use VMD-if I open 1JOY in VMD I can
>>> only
>>> see one of the models, I need to scroll using the scroll bar to see the
>>> others-I cannot see them all at once.
>>> So for running the warwick code and seeing its eefect I use RASMOL, is
>>> there
>>> a way to look at all the models in the same time without scrolling in
>>> VMD?
>>> I
>>> prefer VMD to RASMOL so just wondering about that.
>>>
>>> Thanks everyone foe all the help.
>>>
>>>
>>> On Mon, Oct 25, 2010 at 11:49 AM, Lapointe, David<
>>> David.Lapointe at umassmed.edu> wrote:
>>>
>>>
>>>
>>>> Hi Martin,
>>>>
>>>> If you look at the PDB structure files based on NMR determinations,
>>>>
>>>>
>>> you'll
>>>
>>>
>>>> see that they contain different models. Perhaps you can format the file
>>>>
>>>>
>>> that
>>>
>>>
>>>> way. For example look at 2GDT.pdb
>>>>
>>>> David
>>>>
>>>> -----Original Message-----
>>>> From: biopython-bounces at lists.open-bio.org [mailto:
>>>> biopython-bounces at lists.open-bio.org] On Behalf Of Peter Cock
>>>> Sent: Monday, October 25, 2010 11:33 AM
>>>> To: martin djokovic
>>>> Cc: biopython at lists.open-bio.org
>>>> Subject: Re: [Biopython] writing a PDB----PLEASEEEE HELP
>>>>
>>>> On Mon, Oct 25, 2010 at 4:26 PM, martin djokovic
>>>> <martin.djokovic at gmail.com> wrote:
>>>>
>>>>
>>>>> Hi Peter,
>>>>> I want a new PDB with structures A and B superimposed so that I can see
>>>>>
>>>>>
>>>> them
>>>>
>>>>
>>>>> both at the same in the same file
>>>>>
>>>>> So at the end of the simulation/run I would have A and B (original)
>>>>>
>>>>>
>>>> and
>>>
>>>
>>>> the
>>>>
>>>>
>>>>> 'ans.pdb' with A as it was but B rotated and translated to be
>>>>>
>>>>>
>>>> superimposed
>>>>
>>>>
>>>>> on A in the same PDB
>>>>> I want to try this first simple superimposition but actually I want to
>>>>> connect A and B together to make a longer strand
>>>>> The last residue of A and first residue of B are the same so I can use
>>>>>
>>>>>
>>>> those
>>>>
>>>>
>>>>> coordinates to rotate/translate B then connect to A
>>>>> I can do that manually using SWISS PDB but I want to do it for many
>>>>> structures and its time consuing.
>>>>>
>>>>>
>>>> Won't that mean there would be a duplicate residue? i.e. The last
>>>> residue
>>>> of A and first residue of B are the same thing, but would be in the file
>>>> twice.
>>>>
>>>> Anyway - that basic idea is you must create a Bio.PDB structure object
>>>> with both A and B in it (perhaps as two chains in the same model), then
>>>> write that to the PDB file. The details depend on how you want to do
>>>> the combination - there is more than one way to represent A and B
>>>> in the same PDB file (quite separate from how to do it in Biopython).
>>>>
>>>> Peter
>>>>
>>>> P.S. You could trying writing out two separate PDB files and try simply
>>>> concatenating them... it might do what you want.
>>>>
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