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<img src="icos_label.jpg" alt="drawing" align="right" width="300"/>

# PointSuite v.0.7


![labelled icosahedron](icos_label.jpg) PointSuite is a set of programs to process macromolecular assemblies described by point and helical symmetry operations, with the goals of uniform annotation, archiving, and viewing.  In order to handle coordinates deposited in any orthogonal Cartesian frame, the relationships between the deposition, standard point and crystal frames are captured as frame transformations.  For example, the transformation required to move icosahedral virus structures from deposited position to the standard frame shown at left is calculated and recorded.  All point symmetries are fully handled; helical entries are handled only for non-crystal cases. <br> <br>Written/compiled by C. Lawson, with thanks to V.J. Reddy (TSRI) for sharing PDB2VIPER code (findframe);  Tom Goddard (UCSF) for Chimera scripts (runchimera.csh); Huanwang Yang (RCSB PDB) for importmats and cif-handling subroutines. <br> <br>Please look at this open access article that describes how Pointsuite was used to remediate virus structures in the PDB: Lawson CL, Dutta SD, Westbrook JD, Henrick K, Berman HM (2008)   [Representation of viruses in the remediated PDB archive](http://journals.iucr.org/d/issues/2008/08/00/mv5020/index.html), Acta Cryst D, 874-882.
[PointSuite](https://github.com/rcsb/PointSuite) is a set of programs to process macromolecular assemblies described by point and helical symmetry operations, with the goals of uniform annotation, archiving, and viewing.  In order to handle coordinates deposited in any orthogonal Cartesian frame, the relationships between the deposition, standard point and crystal frames are captured as frame transformations.  For example, the transformation required to move icosahedral virus structures from deposited position to the standard frame shown at left is calculated and recorded.  All point symmetries are fully handled; helical entries are handled only for non-crystal cases. Written/compiled by C. Lawson, with thanks to V.J. Reddy (TSRI) for sharing PDB2VIPER code (findframe);  Tom Goddard (UCSF) for Chimera scripts (runchimera.csh); Huanwang Yang (RCSB PDB) for importmats and cif-handling subroutines. Please look at this open access article that describes how Pointsuite was used to remediate virus structures in the PDB: Lawson CL, Dutta SD, Westbrook JD, Henrick K, Berman HM (2008)   [Representation of viruses in the remediated PDB archive](http://journals.iucr.org/d/issues/2008/08/00/mv5020/index.html), Acta Cryst D, 874-882.

[Virus Processing Tutorial](virusproc-tutorial.md)

INSTALL/COMPILE/CONFIGURE:
View instructions at the [PointSuite GitHub Repository](https://github.com/rcsb/PointSuite)
To INSTALL/COMPILE/CONFIGURE, view the instructions in the [PointSuite GitHub Repository](https://github.com/rcsb/PointSuite)

To make full use of the package, the graphics program [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/) should be installed and in your path.

TEST:
**cd demo****rundemo.csh 1RUG**  (runs the 1RUG demo)
**rundemo.csh all**   (runs all of the demos)
DEMO TESTING:
```
cd demo
```
to run the demo for 1RUG:
```
rundemo.csh 1RUG
```
to run all of the demos:
```
rundemo.csh all
```


browse the demos to view functionality
  1RUG: Generate archival cif for icosahedral virus crystal structure.
Expand All @@ -22,69 +29,31 @@ browse the demos to view functionality
  1M4X:  Generate matrix representations for complex virus particle sub-assemblies.
  IMPORT:  Generate BIOMT, CIF from typical author-uploaded example input files using importmats.
Additional icosahedral virus examples: 2XD8 (EM), 2W0C, 2VF9, 3N7X (X-ray). 
See [Virus processing tutorial](virusproc-tutorial.html) for more info.



RELEASE INFO:
version 0.5.8 (12 June 2007) initial stable release

version 0.6 (20 June 2011) minor updates:
\*importmats (from H. Yang)  handles additional matrix type (xncsrel) from CNS ncs.def.
\*update of scripts automating image generation to work with v.1.4 Chimera and higher
\*when run without arguments, runpt.csh autoscript now prints brief documentation
\*new virus processing tutorial
\*additional documentation now provided for utilities: importmats, autoscripts, multiplymats
\*RCSBvirusimages.csh script to generate set of virus images for web display.

version 0.7 (15 January 2013):
\*improved cif parsing subroutines added by H. Yang (cifparse.c).
\*file input reading improvements in importmats, findframe, makeassembly
\*findframe single input file with matrices and coordinates can now be either PDB or CIF; optional 2nd file in BIOMT format (overrides 1st file matrices)
\*new program cif2pdb creates simple pdb file (matrices, cryst1 record, coordinates) from cif (H. Yang).
\*simplified scripts, PDB-dependency removed for runpt.csh
\*RCSBvirusimages.csh script handles split entry cases (modifications by Ezra Peisach)



- - -

PROGRAM DOCUMENTATION:

* [FINDFRAME](#mozTocId650023)
* [Description](#mozTocId237557)
* [Use](#mozTocId981060)
* [Algorithm](#mozTocId45430)
* [Output](#mozTocId229292)
* [POINTMATS](#mozTocId629505)
* [Description](#mozTocId506963)
* [Use](#mozTocId615010)
* [Output](#mozTocId315225)
* [MAKEASSEMBLY](#mozTocId352913)
* [Description](#mozTocId671271)
* [Use](#mozTocId789206)
* [Algorithm](#mozTocId100314)
* [Output](#mozTocId615797)

* [FINDFRAME](#program-findframe)
* [POINTMATS](#program-pointmats)
* [MAKEASSEMBLY](#program-makeassembly)
* [Utilities](#utilities)
* [importmats](#importmats)
* [autoscripts](#autoscripts)

* [autoscripts](#autoscripts)
* [frac2orth](#frac2orth)
* [movecoords](#movecoords)
* [multiplymats](#multplymats)


- - -

## PROGRAM FINDFRAME
## <a name="program-findframe"></a>PROGRAM FINDFRAME

### Description


The program FINDFRAME calculates the transformation matrix that moves the asymmetric unit of a particle with point symmetry in an arbitrary (skew) frame into a defined position within a standard point frame.  The standard icosahedral frame is defined as having the 5-fold axis of the first pentamer centered on the vector (x=0,y=1, z=phi), where phi is the golden ratio (sqrt(5)+1)/2.  This convention is also employed by the VIPER database and the is proposed convention of Belnap et. al. for cryoEM maps.

FINDFRAME is an extension of the [PDB2VIPER](http://viperdb.scripps.edu/pdb2viper.php) program from the VIPERdb (Shepherd, et al. (2006) Nucleic Acids Res, 34, D386-389) that incorporates the qikfit least-squares fitting routine from [Bioplib](http://www.bioinf.org.uk/software/profit/index.html) (A.C.R. Martin, personal communication). Algorithm steps have been added to increase the precision of the calculated transformation matrix and to improve uniformity of coordinate placement relative to the standard icosahedron symmetry axes (see description below).  



### Use
Expand Down Expand Up @@ -112,19 +81,15 @@ modifications to PDB2VIPER (from V.J. Reddy) are in italics
7. _The position of the reference atom unit vector relative to the 5-3 and 5-2 planes is evaluated.  If the reference atom is closer to the 5-3 plane, the icosahedral a.u. is classified as "3-fold centric" and the closest 3-fold is selected for alignment in the next step.  If the reference atom is closer to the 5-2 plane (typically true for T=3 viruses), the icosahedral a.u. is classified as "2-fold centric" and the 3-fold to the right of the 2-fold is selected for alignment._
8. The  input structure's 5-fold and 3-fold are aligned onto the standard icosahedral frame 5-fold (0, 1, phi) and 3-fold (phi/3, 0, (2\*phi+1)/3) axes in two steps.  First, the rotation that superimposes the normal to the 5-3 plane of the deposited structure onto the normal to the 5-3 plane of the standard icosahedron 5-fold is found and applied.  Second, the rotation around the aligned normals that superimposes the pair of 5-fold axes is found and applied.  The initial estimate for the findframe matrix is based on these two rotation matrices and the translation vector determined in step 2.
9. _Fitting/refinement: The input-supplied transformations are applied to the reference atom, and the resulting 60-atom constellation is transformed to the icosahedral frame by the initial findframe matrix.  A reference set is generated by applying icosahedral symmetry operations to the 1st  transformed atom.  The 60-atom constellation is fitted to the icosahedral reference set, yielding a correction matrix.  The final findframe matrix is generated by applying the correction matrix to the initial estimate.  This step is particularly helpful for cases where the input file-supplied matrices have either low precision or small random errors, as these errors tend to be averaged out._



### Output

General info about the calculation is provided in the standard output.  On successful execution a cif file with symmetry and frame transformation info is  also output called \*findframe.cif\*. 




- - -

## PROGRAM POINTMATS
## <a name="program-pointmats"></a>PROGRAM POINTMATS

### Description

Expand All @@ -148,7 +113,7 @@ General info about the calculation is provided in the standard output; the matri

- - -

## PROGRAM MAKEASSEMBLY
## <a name="program-makeassembly"></a>PROGRAM MAKEASSEMBLY

### Description

Expand Down Expand Up @@ -260,5 +225,4 @@ Writing 1680 matrices to \*mult.biomt\*

- - -

last modified 14 Jan 2013
[C. Lawson](http://chem.rutgers.edu/%7Elawson)
last modified 21 Aug 2024 C. Lawson

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