Re: [PyMOL] how to write out a pdb file including all residues 10 A around a ligand or residue?

[zjxu <zj...@ma...>]

Dear jie,
Glad to be help but sorry not to know Xu Zhijie. And the answer is 
outlined below:

jy wrote:
> Hi Zhijian!
>
> Thanks a lot for the quick reply! How nice to get on-the-fly help from 
> a country-mate! Do you by chance know Xu Zhijie?
>
> I have 3 more questions, hope you dont mind -
>
> 1. as the example 1ATP, the i.d of ATP is 1, so I used (1atp within 10 
> of i. 1), worked great! since the protein sequence starts at 14.  I am 
> wondering what if the protein sequence starts at Glycine 1,  how would 
> you distinguish Gly 1 and ATP 1? is there a way to do it without go to 
> the file to rename the i.d?
As I have ever seen, the ID for every residue is unique in a PDB chain.  
If the ID for ATP is 1, then Gly ID in the same chain should not be 1 
and vice versa. If there are multiple chains, you can using something 
like: create ligand_10A_3, byres(1ATP within 10 of (i. 355 and c. e))
If the ATP and Gly both to be 355 in the same chain (impossible in my 
mind), then you can using the following command: create ligand_10A_4, 
byres(1ATP within 10 of (i. 355  and c. e  and r. ATP))

>
> 2. and how do get rid of some of the residues within that 10A, for 
> example, if I dont want to include those coming from chain I or a 
> certain residue?
If you do not want something, just use "NOT": create ligand_10A_5, 
byres((1ATP and not c. I) within 10 of (i. 355 and c. E))

>
> 3. do you know how to show electron density map only for selected 
> residues, in Coot or pymol or other easy-to-use program :-) ?
sorry, did not deal with this task before, maybe the list can help.

>
>
> Sorry for these many questions, and thank you very much for your time!!
>
> Kindly,
>
> Jie
>
> zjxu wrote:
>> Dear jie yang, 
>> you can use some routine like this:
>> In your pymol:
>> fetch 1ATP
>> create ligand_10A, byres(1ATP within 10 of i. 355)
>> then you can save the object 'ligand_10A' as a pdb file from the menu: 
>> file - save molecule
>> i. 355 is the ligand residue ID
>>
>> Or if you do not want the ligand to be included:
>> create ligand_10A_2, byres(i. 355 around 10)
>>
>> cheers,
>> Zhijian Xu
>>
>> jy wrote:
>>   
>>> Hi all,
>>>
>>> How can I select all the residues that are within a certain distance, 
>>> say 10A, around a certain residue or ligand? and once I select that, how 
>>> can I write out that pdb file?
>>>
>>> Thank you very much!
>>>
>>> jie yang
>>>
>>>
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>>
>> .
>>
>>   
>