Alter - Revision history

Bell: 1 revision

2016-01-03T07:02:36Z

1 revision

Speleo3: redirect iterate

2015-12-23T21:01:24Z

redirect iterate

Bell: 4 revisions

2015-10-19T01:04:39Z

4 revisions

OsvaldoMartin: /* PYMOL API */

2015-09-15T14:52:59Z

PYMOL API

OsvaldoMartin: /* PYMOL API */

2015-09-15T14:25:31Z

PYMOL API

OsvaldoMartin: add PyMOl API syntax

2015-09-15T14:09:51Z

add PyMOl API syntax

OsvaldoMartin at 20:34, 28 August 2015

2015-08-28T20:34:38Z

Pyadmin: 18 revisions

2014-03-28T01:06:17Z

18 revisions

New page

'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===

====Change chain label and residue index====
<source lang="python">
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
</source>

====Change van der Waals radius of a given atom====
<source lang="python">
alter (name P), vdw=1.90
</source>
Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
<source lang="python">
rebuild
</source>

====Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file====
<source lang="python">
# The first residue in the structure file for 1cll is 4. To change this to 0, maybe to match scripts
# outputted from other programs, just remove the offset of 4 from each atom
alter 1cll, resi=str(int(resi)-4)
# refresh (turn on seq_view to see what this command does).
sort
</source>

====Change the b values of all atoms to the distance of the atoms to a reference point====
<source lang="python">
# reference point
x0,y0,z0=[1,2,3]
# calculate distance values between the reference point and all the atoms
alldist = []
iterate_state 1, yourstruc, alldist.append(((x-x0)**2.0+(y-y0)**2.0+(z-z0)**2.0)**0.5)
# assign distance values to b-factors
di = iter(alldist)
alter yourstruc, b=di.next()
# visualize the distances
spectrum b, rainbow, yourstruc
</source>

===SEE ALSO===
[[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]]

[[Category:Commands|Alter]]

Hongbo zhu: /* EXAMPLES */

2011-07-29T09:59:25Z

EXAMPLES

New page

'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are:
name, resn, resi, chain, alt, elem, q, b, segi,
type (ATOM,HETATM), partial_charge, formal_charge,
text_type, numeric_type, ID, vdw

All strings must be explicitly quoted. This operation typically takes several seconds per thousand atoms altered.

'''WARNING''': You should always issue a '''sort''' command on an object
after modifying any property which might affect canonical atom
ordering (names, chains, etc.). Failure to do so will confound
subsequent "create" and "byres" operations.

===USAGE===
alter (selection),expression

===EXAMPLES===

* Change chain label and residue index
<source lang="python">
alter (chain A),chain='B'
alter (all),resi=str(int(resi)+100)
sort
</source>

* Change van der Waals radius of a given atom
<source lang="python">
alter (name P), vdw=1.90
</source>
Note that is if dots, spheres, mesh or surface representation is used. You have to refresh the view with
<source lang="python">
rebuild
</source>

* Renumber the amino acids in a protein, so that it starts from 0 instead of its offset as defined in the structure file.
<source lang="python">
# The first residue in the structure file for 1cll is 4. To change this to 0, maybe to match scripts
# outputted from other programs, just remove the offset of 4 from each atom
alter 1cll, resi=str(int(resi)-4)
# refresh (turn on seq_view to see what this command does).
sort
</source>

* Change the b values of all atoms to the distance of the atoms to a reference point
<source lang="python">
# reference point
x0,y0,z0=[1,2,3]
# calculate distance values between the reference point and all the atoms
alldist = []
iterate_state 1, yourstruc, alldist.append(((x-x0)**2.0+(y-y0)**2.0+(z-z0)**2.0)**0.5)
# assign distance values to b-factors
di = iter(alldist)
alter yourstruc, b=di.next()
# visualize the distances
spectrum b, rainbow, yourstruc
</source>

===SEE ALSO===
[[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]]

[[Category:Commands|Alter]]

Vinnyrose at 13:37, 20 June 2009

2009-06-20T13:37:30Z

← Older revision		Revision as of 21:01, 23 December 2015
Line 1:		Line 1:
		+	#REDIRECT [[iterate]]
		+
	'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are:		'''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom. The symbols defined in the name space, which are are explained in [[Iterate]] are:
	name, resn, resi, chain, alt, elem, q, b, segi,		name, resn, resi, chain, alt, elem, q, b, segi,

@@ Line 69: / Line 69: @@
 </source>
-As explained before, all strings must be explicitly quoted.
+As explained before, all strings must be explicitly quoted. For example to change all HETATM records to ATOM you should do:
 <source lang="python">

← Older revision		Revision as of 14:25, 15 September 2015
Line 69:		Line 69:
	</source>		</source>

		+	As explained before, all strings must be explicitly quoted.
		+
		+	For example to change all HETATM records to ATOM you should do
		+
		+	<source lang="python">
		+	cmd.alter('all', 'type="ATOM"')
		+	</source>

	===SEE ALSO===		===SEE ALSO===

← Older revision		Revision as of 13:37, 20 June 2009
Line 45:		Line 45:
	[[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]]		[[Alter_State]], [[iterate]], [[Iterate_State]], [[sort]]

−	[[Category:Commands\|~~alter~~]]	+	[[Category:Commands\|Alter]]

← Older revision	Revision as of 07:02, 3 January 2016
(No difference)

← Older revision	Revision as of 01:04, 19 October 2015
(No difference)

@@ Line 62: / Line 62: @@
 recolor
 </source>
 ===SEE ALSO===

@@ Line 1: / Line 1: @@
 '''alter''' changes one or more atomic properties over a selection using the python evaluator with a separate name space for each atom.  The symbols defined in the name space, which are are explained in [[Iterate]] are:
   name, resn, resi, chain, alt, elem, q, b, segi,
@@ Line 54: / Line 53: @@
 # visualize the distances
 spectrum b, rainbow, yourstruc
 </source>