[Pmv] How to select some sugar atoms
jean.richelle at ulb.ac.be
Wed Apr 26 07:57:35 PDT 2006
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.
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
> 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,
> Jean Richelle wrote:
>> 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,
>> Pmv mailing list
>> Pmv at scripps.edu
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