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...the used method, so you can for example adjust outlier cutoff or create an alignment object. ...structures on CA atoms using the [[super]] method. It will also create an alignment object.

Image:1xbb_proteins.png|Ligand-based alignment of 1XBB and 1OPJ Image:heme18.png|Alignment of 1V07 and 1HBI using heme

** '''objects''' Structure objects # structure align all proteins in PyMOL to the protein named "PROT". Effectively a

[[Image:after_alignment.png|400px|thumb|right|Two proteins after structure alignment]] '''align''' performs a sequence alignment followed by a structural superposition, and then carries out zero or more c

## ''[[:Category:Structure_Alignment|Structure Alignment]]''' ## Structure Alignment Editor

...elections. The typical use case is for two conformations of a multi-domain structure, which is first aligned on domain 1 (e.g. chain A), and then '''angle_betwe * '''method''' = str: alignment command like "align", "super" or "cealign" {default: align}

transformation takes place. It is changed during structure alignment

secondary structure elements with a matching moved after alignment.

...types of functionalities. Sequence similarity searches, multiple sequence-structure alignments and evolutionary/phylogeny analyses can all be performed in the PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL.

# We look at the structure for 2 seconds, zoom in to each ligand === Animating an Alignment ===

...ence-independent''' (unlike [[align]]) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by el

I wrote a structure alignment program that needs to update the coordinates of the 2nd protein by translat

...n PyMOL plugin. The CE algorithm is a fast and accurate protein structure alignment algorithm, pioneered by Drs. Shindyalov and Bourne (See .... The first image below shows the results from PyMol's `align` command: an alignment of '''221 atoms''' (not residues) to an RMSD of '''15.7 Angstroms'''. The

#automatical alignment # select alpha carbon of selected residues in reference structure

...hydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water * Color by [[DSSP]] or [[Stride]] secondary structure assignment

===Manually Assigning Secondary Structure=== PyMOL can deduce bonds from the PDB structure file, even if the '''CONECT''' records are missing. In fact, PyMOL guesses

::: Would this then feed back to the structural alignment? [[User:Jedgold|Jedgold]] * Add display of secondary structure into the sequence viewer.

'''WHAT THIS DOESN'T DO''': This program does NOT provide a pairwise alignment of two structures from scratch. You have to tell it what the equivalent it # Load the alignment script: '''run Kabsch.py''' (The command '''optAlign''' is now defined in

...he secondary structure assignments in the header. Otherwise, the secondary structure assignment made by pymol may be inaccurate. # If you dont have secondary structure assignments