Re: [PyMOL] disulbond break

[Edward A. B. <Be...@up...>]

That would seem to violate rule #1 of macromolecular depiction:
Never change the coordinates!
But then I can't imagine why one would want to not draw a disulfide bond
in a real protein structure, so maybe this is some kind of exercise
where it is not important to adhere to the experimental results,
like generating a peptide that spells out your name with its
sequence.
If it is a real protein and you want to present your result
as that protein's structure, i would prefer breaking the
bond every time, perhaps with a script.

eab



On 05/14/2014 11:23 AM, Thomas Holder wrote:
> Hi Neshatul,
>
> as Takanori already pointed out, PyMOL will bond those atoms based on distance when loading the PDB file. So after unbonding and before writing the structure out as a PDB file, you should change the coordinates of the cysteine sulfur atoms. A neat way to accomplish this is to use PyMOL's sculpting feature, which involves a VDW terms and thus will move the sulfur atoms away from each other, because they clash after unbonding.
>
> Example:
>
> fetch 4ins, async=0
> as cartoon
> show sticks, resn CYS
> unbond name SG, name SG
> protect not name SG
> sculpt_activate *
> sculpt_iterate *, 1, 1000
>
> Cheers,
>    Thomas
>
> On 14 May 2014, at 07:25, T. Nakane <tn...@ca...> wrote:
>> Hi,
>>
>> This is because PyMOL does not read SSBOND records
>> in PDB files. Actually, PyMOL determines if a bond
>> is present based on atomic distances and CONECT records.
>> http://www.pymolwiki.org/index.php/Connect_mode
>>
>> PyMOL does not write SSBOND records when saving a
>> PDB file.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2014-05-14 12:07, neshat haq wrote:
>>> Hello every one,
>>> I am not able save the pdb file, after I broke the disulfide bond.
>>> what I did was
>>> 1-loaded the pdb file
>>> 2-selected 3-button editing mode
>>> 3-selected the two atoms bonded by disulfide bond
>>> 4-unbond pk1,pk2
>>> Now it shows the bond break, but when I was saving the file without
>>> disulfide bond, it was not working.----------all the time file was
>>> saved with disulfide bond.
>>> How can it be solved......................anyone suggest something.
>>>
>>> --
>>> Best regards
>>> Neshatul Haque
>>> PhD, Dpt of Biotechnology
>>> university of hyderabad
>