My software notes

February 24, 2012

add protons (hydrogens) to structure

Filed under: pymol/ molmol,servers,softwares and scripts — kpwu @ 6:08 pm
Tags: , ,

A list of online servers or programs as I know which can add hydrogens on the structures (most likely determined by X-ray crystallography).

  1. WHATIF server (
    –> check “Hydrogen (bonds)” in the left frame
  2. Molprobity server (
    –> after uploading a PDB file, you will see “add hydrogen” in the online interface.
  3. HAAD: (a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures)
  4. PyMOL (Win/Linux/Mac)
  5. SPDB (Swiss PDB Viewer)

In my own test, WHATIF is more friendly for other CNS/Xplor-NIH/Haddock-related works because WHATIF generates CNS/Xplor compatible PDB format.

Molprobity generates PDB with added hydrogens but the added hydrogens are ALL numbered as “0”. Thus I have to use other program to reset all atom numbers.

PyMOL adds hydrogens,too (object -> A -> hydrogens -> add) but the nomenclature of hydrogens in proteins seems weird (see below). The hydrogens are named as H01, H02, H03.. etc. I don’t think CNS/Xplor-NIH can take it for further calculation purposes.

February 22, 2012

Things must be changed before Protein-RNA docking using Haddock

Filed under: xplor/xplor-nih/cns — kpwu @ 8:10 pm
Tags: , ,

Just a note for RNA-protein docking using Haddock 2.1

System: Mac OS 10.6.8, CNS 1.3, Haddock 2.1

1. RNA (or DNA) nomenclature in CNS is not same as the names in PDB.

e.g. ACU in PDB = ADE CYT URI in CNS

The “nucleic acid builder” developed in David  Case group can generate template structure 100% satisfied to CNS format

2. change all paramenters/toppar file from version 5.3 to 5.4 (if using Mac/CNS 1.3)

3. Assume molecule B is RNA/DNA, then in

A. “filenames”, change {===>} dna_B=false; to {===>} dna_B=true (for DNA);

B. “DNA-RNA restraints”, change {===>} dnarest_on=false;  to {===>} dnarest_on=true;
also copy file “dna-rna_restraints.def” to run1/data/sequence (if it’s run1 in your path)

The “dan-rna_restraints.def” can be found in the Haddock example folder — see 3cro
–> change the resid numbers at lines 30, 35
=== example ===
{========================== base planarity ===========================}

{* Nucleic acid residues to have base planarity restrained. This selection
must only include nucleotide residues *}
{===>} bases_planar=(resid 1:11 and segid B);

{========================== sugar puckers ============================}

{* residues with sugar pucker restrained – group 1 *}
{===>} pucker_1=(resid 1:11 and segid B);


C. “topology and parameter files”, change

C1. prot_top_B=”” to prot_top_B=”
C2. prot_link_B=”topallhdg5.4.pep to  to prot_link_B=”
C3.  prot_par_B=”” to prot_par_B=”dna-rna-allatom-hj-opls-1.3.param

February 14, 2012

[web server] RNA Frabase 2.0

Filed under: servers — kpwu @ 8:48 pm

My colleague asked me to know if I can generate/model 3D structure of a short, single chain RNA. I know there are some servers doing such task but I am not sure how reliable the de novo structures are.

Instead of de novo structure model, I found there is a nice website called “RNA Frabase 2.0” ( which provides easy-to-use interface.

For example, I put a short RNA sequence “UAUUC” to search the published RNA structures. I got a lot of hits:

The outputs provide very detail information include “secondary structure”, “chain”, “position of start and end in matched sequence”, “method of structure determination”, “source of RNA (class)”, and “resolution”.

From this search and quickly inspect the structure from the Jmol plugin, users can decide  and pick up which RNA structure fragment best fits to their purpose (e.g. linear, circular…).

February 8, 2012

water refinement in Xplor-NIH

Filed under: xplor/xplor-nih/cns — kpwu @ 1:23 pm

Starting at Xplor-NIH 2.26 (now it’s version 2.29 on Feb. 8th, 2012), official Xplor-NIH package provides an example script doing explicit solvent refinement. The short description made by Xplor-NIH author:

refinement with explicit solvent and full electrostatics. Includes rdcs, noes, jcoupling terms and dihedral restraints. This is a work-in-progress. Please compare with other protocols. In particular, this protocol seems to result in structures for which the DIHE term is large.

Note on J-coupling violations:

Calculated structures exhibit at least four consistently violated J-coupling restraints. These restraints are at or near mobile loop regions where the single structure approximation breaks down. In these regions an ensemble of structures must be used to fit all experimental data. Please see the gb3_ensemble directory for an example of ensemble refinement.

The script can be found (after version 2.26) at : XPLOR-NIH HOME/eginput/gb1_rdc

I did a quick try using a 90-aa protein–a small protein I am working on determining the solution structure. The input structure was originally refined by the refinement script provided by Xplor-NIH (with NOE, CDIH, RDC) from simulated annealed  templates. The structural quality after regular refinement has been improved a lot ( by checking the Ramachandran plot: from ~60% to 85%). But the water refinement makes the solution structure better (85% –> 95%) although a lot of DIHE violations are noted by Xplor-NIH (same issue as issued by the author).

Here is the analysis done by Molprobity ( showing improved scores and structural quality.

1. Ramachandran plot of structure refined by NOE, CDIH and RDC only.

2. Structure in #1 was refined by water refinement

3. Molprobity analysis of structures in 1 (up) and 2 (down) (click to see full sized snapshots)

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