Property Selectors

2010-04-19T16:21:26Z

Zpete: Removed a couple extraneous tags

==Property Selectors==
PyMOL reads data files written in PDB, MOL/SDF, Macromodel, ChemPy Model, and Tinker XYZ formats. Some of the data fields in these formats allow PyMOL to assign properties to atoms. You can group and select atoms according to these properties using property selectors and identifiers: the selectors correspond to the fields in the data files, and the identifiers correspond to the target words to match, or the target numbers to compare.

===General===
The items in a list of identifiers are separated by plus signs (+) only. Do not add spaces within a list of identifiers. The selector '''resi''' takes (+)-separated lists of identifiers, as in
<source lang="python">
PyMOL> select nterm, resi 1+2+3
</source>
or, alternatively, it may take a range given with a dash
<source lang="python">
PyMOL> select nterm, resi 1-3
</source>
However, you will get an error message if you try to combine a list and a range in an identifier to a '''resi''' as in
<source lang="python">
PyMOL> select mistake, resi 1-3+6 <--This is WRONG
</source>
The identifier for a blank field in an input file is and empty pair of quotes
<source lang="python">
PyMOL> select unstruct, ss "" # A named selection is created
# to contain all atoms that are not assigned
# a secondary structure.
</source>

===Property Selector Table===
Most property selectors select matches to their identifiers
<TABLE BORDER="1">
<TR><TH>Matching Property Selector</TH>
<TH ALIGN="CENTER"> Short Form Selector</TH>
<TH> Identifier and Example</TH>
</TR>
<TR><TD ALIGN="CENTER"> symbol</TD><TD ALIGN="CENTER"> e.</TD><TD>

chemical-symbol-list
 list of 1- or 2-letter chemical symbols from the periodic table
 
<pre>PyMOL> select polar, symbol o+n</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">name</TD><TD ALIGN="CENTER"> n.</TD><TD>
atom-name-list

 list of up to 4-letter codes for atoms in proteins or nucleic acids
 
<pre>PyMOL> select carbons, name ca+cb+cg+cd</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">resn</TD><TD ALIGN="CENTER"> r.</TD><TD>
residue-name-list
 list of 3-letter codes for amino acids

 
<pre>PyMOL> select aas, resn asp+glu+asn+gln </pre>
or list of up to 2-letter codes for nucleic acids
 
<pre>PyMOL> select bases, resn a+g</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">resi</TD><TD ALIGN="CENTER"> i.</TD><TD>

residue-identifier-list
 list of up to 4-digit residue numbers
 
<pre>PyMOL> select mults10, resi 1+10+100+1000</pre>
 residue-identifier-range
 
<pre>PyMOL> select nterm, resi 1-10</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">alt</TD><TD ALIGN="CENTER"> alt</TD><TD>
alternate-conformation-identifier-list
 list of single letters
<pre>PyMOL> select altconf, alt a+""</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">chain</TD><TD ALIGN="CENTER"> c.</TD><TD>

chain-identifier-list
 list of single letters or sometimes numbers
 
<pre>PyMOL> select firstch, chain a</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> segi</TD><TD ALIGN="CENTER"> s.</TD><TD>
segment-identifier-list

 list of up to 4 letter identifiers
<pre>PyMOL> select ligand, segi lig </pre>
</TD></TR>
<TR><TD ALIGN="CENTER">flag</TD><TD ALIGN="CENTER"> f.</TD><TD>
flag-number
 a single integer from 0 to 31
 

<pre>PyMOL> select f1, flag 0</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">  numeric_type  </TD><TD ALIGN="CENTER"> nt.</TD><TD>
 type-number
 a single integer
 
<pre>PyMOL> select type1, nt. 5</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">text_type</TD><TD ALIGN="CENTER"> tt.</TD><TD>
type-string
 a list of up to 4 letter codes
<pre>PyMOL> select subset, text_type HA+HC</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">id</TD><TD ALIGN="CENTER"> id</TD><TD>

external-index-number
 a single integer
 
<pre>PyMOL> select idno, id 23</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">index</TD><TD ALIGN="CENTER"> idx.</TD><TD>
internal-index-number

 a single integer
 
<pre>PyMOL> select intid, index 11</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> ss</TD><TD ALIGN="CENTER"> ss</TD><TD>
secondary-structure-type
 list of single letters

 
<pre>PyMOL> select allstrs, ss h+s+l+""</pre>
</TD></TR>
</TABLE>

===Numeric Selector Table===
Other ''property selectors'' select by comparison to numeric identifiers

<TABLE BORDER="1">
<TR><TH>Numeric Selector</TH>
<TH ALIGN="CENTER"> Short Form</TH>
<TH>Argument and Example</TH></TR>
<TR><TD ALIGN="CENTER">b</TD><TD ALIGN="CENTER"> b</TD><TD>
comparison-operator b-factor-value
 a real number
<pre>PyMOL> select fuzzy, b > 10</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">q</TD><TD ALIGN="CENTER"> q</TD><TD>
comparison-operator occupancy-value
 a real number
<pre>PyMOL> select lowcharges, q <0.50</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">  formal_charge  </TD><TD ALIGN="CENTER"> fc.</TD><TD>

 comparison-operator formal charge-value
 an integer
<pre>PyMOL> select doubles, fc. = -1</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">  partial_charge  </TD><TD ALIGN="CENTER"> pc.</TD><TD>
 comparison-operator partial charge-value

 a real number
<pre>PyMOL> select hicharges, pc. > 1</pre>
</TD></TR>
</TABLE>

==User Notes==

===Select by PDB Assigned Atom Number===
To select atoms by their PDB ATOM number, use the '''id''' selector:
<source lang="python">
select Nt, id 1-30
</source>
makes a new selection called Nt and puts in it the first 30 atoms (assuming your PDB starts numbering at 1).

===Alternate Locations===
====Select All Alternate Locations====
*To select '''all''' residues with alternate locations (alt, alt loc), simply do:
<source lang="python">
select aa, not alt ""
</source>
Try it on 1CBN.

====Select All Alternate Locations Except the A-Locations====
* To select and remove all atoms with alternate locations (ALT, alt loc) that aren't the '''A''' record try the following. This removes all alt locations that are not the original '''A''' location. For example given the following pdb record,
<source lang="python" line="1">
ATOM 949 N ARG A 124 6.039 8.484 9.313 1.00 9.82 N
ATOM 950 CA ARG A 124 5.839 7.071 8.980 1.00 10.05 C
ATOM 951 C ARG A 124 6.009 6.809 7.493 1.00 9.18 C
ATOM 952 O ARG A 124 5.803 7.715 6.648 1.00 9.06 O
ATOM 953 CB ARG A 124 4.437 6.660 9.425 1.00 10.61 C
ATOM 954 CG AARG A 124 4.381 6.539 10.955 0.50 12.54 C
ATOM 955 CG BARG A 124 4.170 6.743 10.930 0.50 14.58 C
ATOM 956 CD AARG A 124 2.996 6.418 11.561 0.50 11.86 C
ATOM 957 CD BARG A 124 2.700 7.091 11.242 0.50 17.41 C
ATOM 958 NE AARG A 124 2.110 7.506 11.144 0.50 13.01 N
ATOM 959 NE BARG A 124 2.229 6.746 12.588 0.50 19.94 N
ATOM 960 CZ AARG A 124 0.912 7.729 11.654 0.50 12.21 C
ATOM 961 CZ BARG A 124 2.123 5.510 13.067 0.50 21.42 C
ATOM 962 NH1AARG A 124 0.433 6.958 12.627 0.50 12.93 N
ATOM 963 NH1BARG A 124 2.470 4.470 12.319 0.50 24.35 N
ATOM 964 NH2AARG A 124 0.185 8.735 11.188 0.50 11.89 N
ATOM 965 NH2BARG A 124 1.658 5.310 14.313 0.50 18.28 N
</source>
the command below will remove the (not A so) B-locations (lines 7, 9, 11, 13, 15, 17).
<source lang="python">
# select & remove all non A altlocs
remove not (alt ''+A)
# reset the PDB information
alter all, alt=''
</source>

See also, [[removeAlt]] for a script to do this for you.

[[Category:Selector Quick Reference]]
[[Category:Selecting|Selector Quick Reference]]

PyMOL Wiki - User contributions [en]

Property Selectors