ProMol+Project


 * ProMol Project**

Ruifei

Goals: install and become competent in using ProMol put on the 6 laptops in lab (Windows) and install on the Linux distribution on one of the laptops too

Read some papers, websites, etc. on how to implement ProMol.

03/09/13

Tried installing ProMol on correct PyMol 1.3, but still nothing happens when I click on the ProMol plugin.

03/07/13

Error when installing ProMol on clean installation of PyMol 1.3r2 on Histidine laptop (resolved: use PyMol 1.3)

This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. Exception in plugin 'ProMol' -- Traceback follows... Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py", line 156, in initialize_plugins __builtin__.__import__(mod_name) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\__init__.py", line 5, in ? from pmg_tk.startup.ProMol.promolglobals import VERSION File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\promolglobals.py", line 777 self.widget.columnconfigure(0, weight=leftWeight if someOfEach else 1) ^ SyntaxError: invalid syntax Error: unable to initialize plugin 'ProMol'.

02/16/13 -

Another error when opening ProMol:

Error: 2  Exception in Tk callback Function:  (type: ) Args: Traceback (innermost last): File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/__init__.py", line 18, in command = lambda p=pymol:GUI.__init__(p)) File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/__init__.py", line 43, in __init__ from pmg_tk.startup.ProMol.GUI import welcome, ez_viz, motifs, \ File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/motifs.py", line 5, in from pmg_tk.startup.treewidgets import widget, node, texttree : No module named treewidgets

Cannot find any 'treewidgets' file

Ruifei installed updated ProMol on personal laptop, running into error when installing ProMol:

Exception in plugin 'ProMol' -- Traceback follows... Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pmg_tk/PMGApp.py", line 315, in initializePlugins __builtin__.__import__(mod_name) File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/__init__.py", line 11, in from pmg_tk.startup.ProMol import GUI File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/__init__.py", line 7, in from pmg_tk.startup.remote_pdb_load import FetchPDB as showFetchDialog ImportError: No module named remote_pdb_load Error: unable to initialize plugin 'ProMol'.

FIX: copy contents of 'startup' directory from another directory if the current 'startup' directory does not contain the 'remote_pdb_load' file.

020713 - Ruifei and Dr. B met with Dr. Paul Craig about ProMol Latest Version of ProMol is uploaded to Google Docs/Misc/Software/ProMOL_notPyMol ProMOL-194.zip Unzip this to the appropriate folder

2 ProMol Websites
@http://www.rit.edu/cos/ezviz/ProMOL_dl.html

This one has updated version of ProMol @http://www.promol.org/

Link to ProMol User Guide


ToDo: Add specific instructions on how to install ProMol on a Windows computer

NOTE: the older ProMOL (not the 194 version) worked better with older version of PyMol (not the Schrodinger version - but rather the DeLano Scientific version)

Catalytic Binding Site Atlas:
@http://www.ebi.ac.uk/thornton-srv/databases/CSA/

PART 1:
Purpose: send PDB ID's and/or E.C. numbers of our enzymes to Dr. Paul Craig at RIT (Rochester Institute of Technology). He will have his students work on them.

INSTRUCTIONS:

- Mark each target as either: OR
 * Homology Model needed
 * PDB structure available

If structure available, list PDB

If Homology Model needed, use SWISS-Model to find template, then use ICM to generate Homology Model.

Identities =, Positives =


 * PDB Identifier**

2012 Targets
//Leishmania// Target-serine-threonine protein phosphatase (Leishmania major) Homology Model needed ---Joey--- DONE Template: 2nppf Sequence Identities = 207/284 (72%), Positives = 239/284 (84%) Template: Clash score, Molprobity score = 51.32, 3.47 Model: Clash score, Molprobity score = 18.24, 3.11

//Wolbachia// endosymbiont of //Brugia malayi (//see Wolbachia Targets page too//)// Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia) Homology Model needed - Dr. B - DONE Template: 1R0k Sequence Identities = 42.34%, Positives = 63% Template: Clash score, Molprobity score = 13.66, 1.77 Model: Clash score, Molprobity score = 3.85, 2.11

Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia) Homology Model needed - JC - DONE Template: 3K31-A Sequence Identities = 66% 169/256, Positives = 214/256 83% Template: Clash score, Molprobity score = 4.08, 1.40 Model: Clash score, Molprobity score = 0.00, 1.36

//Yersinia// Target - Fab V (Yersinia Pestis) PDB: 3ZU5 - Sadhana - DONE Model: Clash score, Molprobity score = 11.63, 1.92

Target- Protein Tyrosine Phosphate (Yersinia Enterocolitica) Homology Model needed - Sadhana - DONE Template:1YWF-A Sequence Identities = 28%, Positives = 42% Template: Clash score, Molprobity score = 5.1, 2.03 Model: Clash score, Molprobity score = 13.04, 3.03

//Francisella tularensis// Homology Model needed - Christina - DONE Template: 3ANM Sequence Identities = 48%, Positives = 66% Template: Clash score = 17.46, Molprobity score = 2.35 Model: Clash score = 8.26, Molprobity score = 2.42
 * Target -1-deoxy-D-xylulose 5-phosphate reductoisomerase (Francisella Tularensis)**

//Trypanosoma brucei// Homology Model needed - Christina (Larry -- Finished first so the one in the folder is Larry's) - DONE Template:1auia Sequence Identities =44%, Positives = 62% Template: Clash score = 14.64, Molprobity score = 2.42 Model: Clash score = 4.07, Molprobity score = 2.29
 * Target- Protein Phosphatase 2B**

//Plasmodium falciparans// Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum)- PDB = 3AU8, 3AU9, 3AUA - SADHANA - DONE

Clash score, Molprobity score = 10.48, 1.99 Clash score, Molprobity score = 8.29, 1.98 Clash score, Molprobity score = 11.65, 2.11

//Staphylococcus agalactiae -// Neonatal Septicemia Target - S. agalactiae serine-threonine phosphatase STP1 PDB structure available = 2PK0 - Sadhana - DONE 2PK0 Clash score, Molprobity score = 7.53, 1.89

//Listeria monocytogenes// Homology Model needed (Larry) - DONE Template: 1ywfa, Sequence Identities = 27%, Positives = 46% Template: Clash score, Molprobity score = 5.1, 2.03 Model: Clash score, Molprobity score = 0.77, 2.03
 * Target - Protein Tyrosine Phosphatase (Listeria monocytogenes)**

//Candida albicans// Target - Methionine Synthase (PDB exist) No need. Template: Sequence Identities = ? , Positives = ? Homology Model needed OR PDB structure available? Template: Clash score, Molprobity score = ???, ??? Model: Clash score, Molprobity score = ???, ???

2011 Targets
Target-Histidine Phosphatase (Francisella Tularensis) Target-MPTPB(Mycobacterium Tuberculosis) H37Rv Target - Protein-Tyrosine Phosphatase Yersinia pestis YopH (Bubonic Plague) Target-Mycobacterium Tuberculosis PSTP Target - Carbonic Anhydrase IX (Homo sapiens) Target- Carbonic Anhydrase YadF and cynT(E. coli) Target - PTP1b (Homo sapiens)