Structure Refinement Using XPLOR-NIH - Revision history

TheresaRamelot at 19:32, 30 November 2009

2009-11-30T19:32:39Z

← Older revision		Revision as of 19:32, 30 November 2009
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	Download the script [[Media:Mkpsf_prot.inp\|mkpsf_prot.inp]].<br> Edit the script with your sequence and to match your input xplor PDB files:		Download the script [[Media:Mkpsf_prot.inp\|mkpsf_prot.inp]].<br> Edit the script with your sequence and to match your input xplor PDB files:

	#Have chain A or no chain ID to match your input PDB file.		#Have chain A or no chain ID to match your input PDB file.
	#Add the TOPPAR:toph19.pep line if your input structures have ~~NH3~~+ and COO- at the N- and C-~~term~~ with the atoms HT1, HT2, HT3 and OT1, OT2, respectively.		#Add the TOPPAR:toph19.pep line if your input structures have NH<sup>3+</sup> and COO- at the N- and C-termini with the atoms HT1, HT2, HT3 and OT1, OT2, respectively.
	#Fix the Histidine patch to match the protonation state / tautomer.		#Fix the Histidine patch to match the protonation state / tautomer.
	#If you protein sequence starts at residues 43, for example, add extra residues to the sequence and uncomment the "dele sele (resid 1:42)" line by removing the "!".		#If you protein sequence starts at residues 43, for example, add extra residues to the sequence and uncomment the "dele sele (resid 1:42)" line by removing the "!".
	#Add cis Proline patch if you have any cis Prolines.<br>		#Add cis Proline patch if you have any cis Prolines.<br>

TheresaRamelot at 19:32, 30 November 2009

2009-11-30T19:32:01Z

← Older revision		Revision as of 19:32, 30 November 2009
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	==== The input PDB files should be in Xplor-NIH format<br> ====		==== The input PDB files should be in Xplor-NIH format<br> ====

	One way to convert them from another format, such as Cyana or CNS is using ~~PDBStat (references)~~		One way to convert them from another format, such as Cyana or CNS is using [[PdbStat]]

	=== Creating protein structure file, (psf) ===		=== Creating protein structure file, (psf) ===

TheresaRamelot at 19:31, 30 November 2009

2009-11-30T19:31:38Z

← Older revision		Revision as of 19:31, 30 November 2009
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	==== The NMR restraints should be in Xplor/CNS format. ====		==== The NMR restraints should be in Xplor/CNS format. ====

	If you have restraint files in another format, one way to convert is using [PdbStat]		If you have restraint files in another format, one way to convert is using [[PdbStat]]

	==== The input PDB files should be in Xplor-NIH format<br> ====		==== The input PDB files should be in Xplor-NIH format<br> ====

TheresaRamelot at 19:31, 30 November 2009

2009-11-30T19:31:16Z

← Older revision		Revision as of 19:31, 30 November 2009
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	==== The NMR restraints should be in Xplor/CNS format. ====		==== The NMR restraints should be in Xplor/CNS format. ====

	If you have restraint files in another format, one way to convert is using ~~PDBStat (reference)~~		If you have restraint files in another format, one way to convert is using [PdbStat]

	==== The input PDB files should be in Xplor-NIH format<br> ====		==== The input PDB files should be in Xplor-NIH format<br> ====

TheresaRamelot at 19:30, 30 November 2009

2009-11-30T19:30:01Z

← Older revision		Revision as of 19:30, 30 November 2009
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	#Edit the radius of gyration line for your "core" residues.		#Edit the radius of gyration line for your "core" residues.

	For example, if your core residues are 13-92 , then the number of ordered residues, N<sup>residues</sup> is 80.  Use the equation below to determine the radiue of gyration.  In this case R<sub>gyr</sub> = 11.6.		For example, if your core residues are 13-92 , then the number of ordered residues, N<sub><sup>residues</sup></sub> is 80.  Use the equation below to determine the radiue of gyration.  In this case R<sub>gyr</sub> = 11.6.
	<pre> Rgyr = 2.2 * (~~N<sub>residues</sub>~~^ 0.38)		<pre> Rgyr = 2.2 * (Nresidues^ 0.38)
	</pre>		</pre>
	The line in the prot_sa_refine.inp script should look like this:		The line in the prot_sa_refine.inp script should look like this:
	<pre> assign ( resid 13:92 ) 50.0 11.6		<pre> assign ( resid 13:92 ) 50.0 11.6
	</pre>		</pre>
	The number 50 is a scaling constant, so don't change it.		The number 50 is a scaling constant, so don't change it.

	==== Run the Xplor-NIH refinement<br> ====		==== Run the Xplor-NIH refinement<br> ====

TheresaRamelot at 19:28, 30 November 2009

2009-11-30T19:28:44Z

← Older revision		Revision as of 19:28, 30 November 2009
Line 54:		Line 54:
	Download the script [[Media:Mkpsf_prot.inp\|mkpsf_prot.inp]].<br> Edit the script with your sequence and to match your input xplor PDB files:		Download the script [[Media:Mkpsf_prot.inp\|mkpsf_prot.inp]].<br> Edit the script with your sequence and to match your input xplor PDB files:

	#Have chain A or no chain ID to match your input PDB file		#Have chain A or no chain ID to match your input PDB file.
	#Add the TOPPAR:toph19.pep line if your input structures have NH3+ and COO- at the N- and C-term with the atoms HT1, HT2, HT3 and OT1, OT2, respectively.		#Add the TOPPAR:toph19.pep line if your input structures have NH3+ and COO- at the N- and C-term with the atoms HT1, HT2, HT3 and OT1, OT2, respectively.
	#Fix the Histidine patch to match the protonation state / tautomer		#Fix the Histidine patch to match the protonation state / tautomer.
	#If you protein sequence starts at residues 43, for example, add extra residues to the sequence and uncomment the "dele sele (resid 1:42)" line by removing the~~ ~~!.		#If you protein sequence starts at residues 43, for example, add extra residues to the sequence and uncomment the "dele sele (resid 1:42)" line by removing the "!".
	#Add cis Proline patch if you have any		#Add cis Proline patch if you have any cis Prolines.<br>

	~~<br>~~ <br>

	=== Edit and run the simulated annealing script<br> ===		=== Edit and run the simulated annealing script<br> ===

TheresaRamelot at 19:27, 30 November 2009

2009-11-30T19:27:56Z

← Older revision		Revision as of 19:27, 30 November 2009
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	The number 50 is a scaling constant, so don't change it.		The number 50 is a scaling constant, so don't change it.

	==== Run the ~~script:~~ ====		==== Run the Xplor-NIH refinement<br> ====

	Edit the number of structures that your are  refining and run like this:		Edit the number of structures that your are  refining and run like this:

TheresaRamelot at 19:27, 30 November 2009

2009-11-30T19:27:26Z

← Older revision		Revision as of 19:27, 30 November 2009
Line 39:		Line 39:
	==== The NMR restraints should be in Xplor/CNS format. ====		==== The NMR restraints should be in Xplor/CNS format. ====

	If you have restraint files in another format, one way to convert is using PDBStat (reference)		If you have restraint files in another format, one way to convert is using PDBStat (reference)



	==== The input PDB files should be in Xplor-NIH format<br> ====		==== The input PDB files should be in Xplor-NIH format<br> ====

TheresaRamelot at 19:26, 30 November 2009

2009-11-30T19:26:54Z

← Older revision		Revision as of 19:26, 30 November 2009
Line 47:		Line 47:
	One way to convert them from another format, such as Cyana or CNS is using PDBStat (references)		One way to convert them from another format, such as Cyana or CNS is using PDBStat (references)

	==== Creating protein structure file, (psf)~~, using~~ mkpsf_prot.inp script ====		=== Creating protein structure file, (psf) ===

			==== Editing and running the mkpsf_prot.inp script ====

	The X-Plor psf file specifies the atom parameters and connectivity for all amino acids.  The xplor script mkpsf_prot.inp is edited with the protein sequence in three letter code and used to generate the psf files by running:		The X-Plor psf file specifies the atom parameters and connectivity for all amino acids.  The xplor script mkpsf_prot.inp is edited with the protein sequence in three letter code and used to generate the psf files by running:
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	#Add cis Proline patch if you have any		#Add cis Proline patch if you have any

	<br>		<br> <br>
	<br>

	=== Edit and run the simulated annealing script<br> ===		=== Edit and run the simulated annealing script<br> ===

TheresaRamelot at 19:25, 30 November 2009

2009-11-30T19:25:55Z

@@ Line 60: / Line 60: @@
 #Add cis Proline patch if you have any
-==== Edit simulated annealing script  ====
+<br>
 <br>