[Pmv] How to select some sugar atoms

Jean Richelle jean.richelle at ulb.ac.be
Wed Apr 26 07:57:35 PDT 2006


Hi Sargis,

What you suggested for selecting 'O4*' works but, as far as I  
understand  it is not because '*' is replaced by '.*' , but because  
it is a regular expression, and as a consequence 'O4.*' stands not  
only for 'O4*', but also O4M or O4xyz ! (if such a name would exist)
I finally found the right way to do it : 'O4[*]'.

Concerning your second point, effectivelly PMV rewrites the PDB names  
according to the IUPAC rule ; thank you for pointing it out.

Regards,

Jean

Le 21 avr. 06 à 18:43, Sargis Dallakyan a écrit :

> Hi Jean,
>
> I just checked the code for MolKit/StringSelector.py and it turns out
> that it replaced '*'with '.*', so to select all 'O4*', you need to  
> type
> 'O4.*'
>
> Regarding hydrogens, pdbparser moves the first letter to the end,  
> if its
> '1','2' or '3', so to select '1H2' you need to type 'H21' and
> correspondingly '1H2*' goes to 'H2.*1'
>
> Hope this helps,
> Sargis
>
> Jean Richelle wrote:
>> Hi,
>> I wanted to select ribose atoms of a DNA structure, and it appeared
>> that the "Select From String" will have a problem with the * in, e.g.
>> O4*. I tried quotes (simple or double) and backslash without
>> success.  I finally decided to rename O4* as O4', and similarly for
>> all the other * atoms, and then I could select them.  Is there a more
>> correct way to do it ?
>>
>> I faced another problem when I tried to select some Hydrogen atoms.
>> It seams that it is only possible to select names composed of 3
>> letters, and so impossible with, e.g. 1H2' .  Do I miss something ?
>>
>> Best regards,
>>
>> Jean
>>
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>
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