PDB and BMRB Deposition - Revision history

Alex: /* Preparing files for BMRB depostion */

2010-09-22T16:09:11Z

Preparing files for BMRB depostion

← Older revision		Revision as of 16:09, 22 September 2010
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	write bmrb XXXX.bmrb # write out the BMRB file </onlyinclude>		write bmrb XXXX.bmrb # write out the BMRB file </onlyinclude>

	Using any text editor rename all non-standard residues, such as <tt>HIST</tt> or <tt>HIS+</tt> to <tt>HIS</tt>, and <tt>cPRO</tt> to <tt>PRO</tt> in the tt>XXXX.bmrb</tt> file.		Using any text editor rename all non-standard residues, such as <tt>HIST</tt> or <tt>HIS+</tt> to <tt>HIS</tt>, and <tt>cPRO</tt> to <tt>PRO</tt> in the <tt>XXXX.bmrb</tt> file.

	== '''Creating an NMR structure record in SPINE''' ==		== '''Creating an NMR structure record in SPINE''' ==

Alex: /* Preparing files for BMRB depostion */

2010-09-22T16:08:51Z

Preparing files for BMRB depostion

← Older revision		Revision as of 16:08, 22 September 2010
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	pseudo=2 # use H* labels for pseudoatoms		pseudo=2 # use H* labels for pseudoatoms
	write bmrb XXXX.bmrb # write out the BMRB file </onlyinclude>		write bmrb XXXX.bmrb # write out the BMRB file </onlyinclude>

			Using any text editor rename all non-standard residues, such as <tt>HIST</tt> or <tt>HIS+</tt> to <tt>HIS</tt>, and <tt>cPRO</tt> to <tt>PRO</tt> in the tt>XXXX.bmrb</tt> file.

	== '''Creating an NMR structure record in SPINE''' ==		== '''Creating an NMR structure record in SPINE''' ==

Alex: /* Preparing files for BMRB depostion */

2010-09-22T16:03:21Z

Preparing files for BMRB depostion

← Older revision		Revision as of 16:03, 22 September 2010
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	<br>		<br>

			Creating a BMRB file from CYANA

			<onlyinclude>
			read prot XXXX-final.prot # read the latest atom list
			finalstereo # stereospecific assignments (to set proper ambiguity codes)
			translate bmrb # use BMRB nomenclature
			pseudo=2 # use H* labels for pseudoatoms
			write bmrb XXXX.bmrb # write out the BMRB file </onlyinclude>

	== '''Creating an NMR structure record in SPINE''' ==		== '''Creating an NMR structure record in SPINE''' ==

Alex: /* Preparing files for BMRB depostion */

2010-09-22T15:34:45Z

Preparing files for BMRB depostion

← Older revision		Revision as of 15:34, 22 September 2010
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	*Chemical shifts (BMRB file) - '''required'''.		*Chemical shifts (BMRB file) - '''required'''.
	*NOESY peaklists - '''~~strongly recommended~~'''.		*NOESY peaklists - '''required'''.
	*Raw NMR Data - '''~~strongly recommended~~'''. Due to its size usually uploaded as a single archive to the FTP server of BMRB after the deposition is submitted.		*Raw NMR Data - '''NOESY FIDs required'''. Due to its size usually uploaded as a single archive to the FTP server of BMRB after the deposition is submitted.

	#Create a new directory (like <tt>structure/deposit/bmrb</tt>). Copy the following files from the last CYANA 2.1 manual structure calculation:<br>		#Create a new directory (like <tt>structure/deposit/bmrb</tt>). Copy the following files from the last CYANA 2.1 manual structure calculation:<br>
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	#You may have to rename non-standard residues in <tt>XXXX.bmrb</tt>, such as <tt>HIST</tt> or <tt>HIS+</tt> to <tt>HIS</tt>, and <tt>cPRO</tt> to <tt>PRO</tt>. Use any text editor.<br>		#You may have to rename non-standard residues in <tt>XXXX.bmrb</tt>, such as <tt>HIST</tt> or <tt>HIS+</tt> to <tt>HIS</tt>, and <tt>cPRO</tt> to <tt>PRO</tt>. Use any text editor.<br>

	<br>		<br>

	== '''Creating an NMR structure record in SPINE''' ==		== '''Creating an NMR structure record in SPINE''' ==

Alex: /* Converting PDB file with PDBStat and MAXIT */

2010-09-22T15:32:11Z

Converting PDB file with PDBStat and MAXIT

← Older revision		Revision as of 15:32, 22 September 2010
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	You can optionally choose the desired orientation for the resulting molecular bundle. Open the <tt>overlay.pdb</tt> in MOLMOL, find the desired orientation and save with '''File''' -> '''Write Transform...''', for example, as <tt>rotation_matrix.mac</tt>. Start PDBStat again and enter the following commands:		You can optionally choose the desired orientation for the resulting molecular bundle. Open the <tt>overlay.pdb</tt> in MOLMOL, find the desired orientation and save with '''File''' -> '''Write Transform...''', for example, as <tt>rotation_matrix.mac</tt>. Start PDBStat again and enter the following commands:
	<onlyinclude>		<onlyinclude>
	read coor overlay.pdb #read file with concatenated CNS pdb files		read coor pdb overlay.pdb #read file with concatenated CNS pdb files
	all #select all the models		all #select all the models
	rotate file rotation_matrix.mac #apply rotation matrix		rotate file rotation_matrix.mac #apply rotation matrix

Alex at 15:33, 20 September 2010

2010-09-20T15:33:23Z

← Older revision		Revision as of 15:33, 20 September 2010
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	<pre>		<pre>
	sed "s/O''/OXT/g" ordered.pdb > deposit.pdb</pre>		sed "s/O''/OXT/g" ordered.pdb > deposit.pdb</pre>

	~~=== '''Using MolMol''' ===~~

	~~#Copy the resulting file of the water bath refinement (e.g. <tt>All_KKK_cns.pdb</tt>) in a new directory, preferably <tt>structure/deposit/pdb</tt>.~~
	~~#Download the [http://deposit.rcsb.org/pdbformat/chainsub.py chainsub.py] script from RCSB web site.~~
	~~#Download the [[Media:PBD_patch.sh\|patch.sh]] script (see below).~~
	#Download the [[Media:Pdbfit.mac\|pdbfit.mac]] macro for MOLMOL (see below). Modify it to specify the input PDB file and the residue range of secondary structure elements used to superimpose the structure (consult the output of PSVS).
	~~#Start MOLMOL and execute the <tt>pdbfit.mac</tt>. Ignore the warning about incorrect atoms. It should produce a <tt>deposit.pdb</tt> file.~~

	=== '''Precheck and Validation''' ===		=== '''Precheck and Validation''' ===

Alex: /* Using PDBStat and MAXIT */

2010-09-20T15:32:14Z

Using PDBStat and MAXIT

← Older revision		Revision as of 15:32, 20 September 2010
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	Prior to deposition individual conformers should be superimposed to minimize backbone atom RMSD of the folded region. Also, since structure calculation programs such as CYANA or CNS/XPLOR utilize custom atom nomenclature, the PDB coordinate file has to be converted to conform to the RCSB nomenclatuere. The procedure below describes how this can be done with PDBStat and [http://sw-tools.pdb.org/apps/MAXIT/index.html MAXIT].		Prior to deposition individual conformers should be superimposed to minimize backbone atom RMSD of the folded region. Also, since structure calculation programs such as CYANA or CNS/XPLOR utilize custom atom nomenclature, the PDB coordinate file has to be converted to conform to the RCSB nomenclatuere. The procedure below describes how this can be done with PDBStat and [http://sw-tools.pdb.org/apps/MAXIT/index.html MAXIT].

	=== '''~~Using~~ PDBStat and MAXIT''' ===		=== '''Converting PDB file with PDBStat and MAXIT''' ===

	Start PDBStat and enter the following commands:		Start PDBStat and enter the following commands:

Alex: /* Files deposited */

2010-09-20T15:31:09Z

Files deposited

← Older revision		Revision as of 15:31, 20 September 2010
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	*PDB coordinate file - '''required'''.		*PDB coordinate file - '''required'''.
	*Constraint files used in the calculation - '''~~recommended~~'''.		*Constraint files used in the calculation - '''required'''.
	**NOE constraints ~~(UPL file)~~.		**NOE distance constraints.
	**~~ACO~~ constraints (e.g. from TALOS).		**Dihedral angle constraints (e.g. from TALOS).
	**H-bond constraints		**Hydrogen bond constraints
			**RDC constraints

	~~Constraint~~ files ~~can be taken from~~ the latest ~~manual~~ refined ~~structure~~ calculation.		Please deposit constraint files that were used to generate the deposited coordinates in latest refined calculation cycle. For example, assuming that constrained refinement in explicit water bath using CNS was performed, the corresponding constraints in CNS format should be deposited.

	~~Here we assume that you are depositing~~ the ~~coordinate file after refinement in explicit water bath~~. ~~You will need to convert~~ the ~~resulting~~ PDB file to ~~use proper PDB atom names. You can use either PDBstat or Molmol~~ to ~~superimpose your ensemble~~.		Prior to deposition individual conformers should be superimposed to minimize backbone atom RMSD of the folded region. Also, since structure calculation programs such as CYANA or CNS/XPLOR utilize custom atom nomenclature, the PDB coordinate file has to be converted to conform to the RCSB nomenclatuere. The procedure below describes how this can be done with PDBStat and [http://sw-tools.pdb.org/apps/MAXIT/index.html MAXIT].

	The procedure below ~~requires that you install~~ [http://sw-tools.pdb.org/apps/MAXIT/index.html ~~maxit~~] ~~from the RCSB web site~~.

	=== '''Using PDBStat and MAXIT''' ===		=== '''Using PDBStat and MAXIT''' ===

Alex: /* Using PDBStat */

2010-09-17T22:33:50Z

Using PDBStat

@@ Line 25: / Line 25: @@
 The procedure below requires that you install [http://sw-tools.pdb.org/apps/MAXIT/index.html maxit] from the RCSB web site.
-=== '''Using PDBStat'''  ===
+=== '''Using PDBStat and MAXIT'''  ===
-#Start [[PdbStat|<tt>pdbstat</tt>]] and use the following commands<br> <tt>read coord pdb All_KKK_cns.pdb</tt> <br> <tt>classify</tt> <br> <tt>order 0.9</tt> <br> <tt>rmsd best backbone</tt> <br> <tt>write coord pdb ordered</tt> <br> These commands will sort the conformers in the order of lowest to highest [[NESG:CNS|CNS]] energy, superimpose them automatically based on the ordered regions and report RMSD.
+Start PDBStat and enter the following commands:
-#Run <tt>patch2.sh</tt> script. It use Maxit to fix atom nomenclature and runs <tt>sed</tt> to rename C-terminal <tt></tt>''to <tt>OXT</tt>.''
+<onlyinclude>
 === '''Using MolMol'''  ===

Jma at 16:57, 5 January 2010

2010-01-05T16:57:30Z

← Older revision		Revision as of 16:57, 5 January 2010
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	== '''Introduction''' ==		== '''Introduction''' ==

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	#Create a new directory (like <tt>structure/deposit/bmrb</tt>). Copy the following files from the last CYANA 2.1 manual structure calculation:<br>		#Create a new directory (like <tt>structure/deposit/bmrb</tt>). Copy the following files from the last CYANA 2.1 manual structure calculation:<br>

	*<span style="display: none;~~" id="1257278398860S~~"> </span><tt>init.cya</tt>		*<span id="1257278398860S" style="display: none;"> </span><tt>init.cya</tt>
	*<tt>XXXX.seq</tt>		*<tt>XXXX.seq</tt>
	*<tt>XXXX.prot</tt>		*<tt>XXXX.prot</tt>
	*Stereospecific assignment file (e.g. <tt>finalstereo.cya</tt>) <br> <span style="display: none;~~" id="1257278398974E~~"> </span><br> Make sure you have added the following missing CG2 atoms of Val and CD2 of Leu, Phe and Tyr in residues, where they are degenerate with CG1 and CD1, respectively. The proton list <tt>XXXX.prot</tt> should have stereoassigned atoms swapped. The stereospecific assignment file is needed to properly set the ambiguity codes in the resulting BMRB file.		*Stereospecific assignment file (e.g. <tt>finalstereo.cya</tt>) <br> <span id="1257278398974E" style="display: none;"> </span><br> Make sure you have added the following missing CG2 atoms of Val and CD2 of Leu, Phe and Tyr in residues, where they are degenerate with CG1 and CD1, respectively. The proton list <tt>XXXX.prot</tt> should have stereoassigned atoms swapped. The stereospecific assignment file is needed to properly set the ambiguity codes in the resulting BMRB file.

	#Download the [[Media:Bmrb_dep.cya\|bmrb_dep.cya]] script and set the tolerances appropriate for you project (see below).<br>		#Download the [[Media:Bmrb_dep.cya\|bmrb_dep.cya]] script and set the tolerances appropriate for you project (see below).<br>
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	*The first value in the <tt>tolerance</tt> list the <sup>1</sup>H chemical shift tolerance. The last value is the <sup>13</sup>C/<sup>15</sup>N tolerance. The second value is ignored.		*The first value in the <tt>tolerance</tt> list the <sup>1</sup>H chemical shift tolerance. The last value is the <sup>13</sup>C/<sup>15</sup>N tolerance. The second value is ignored.
	*Here <tt>stereofound</tt> declares stereospecific assignments so the ambiguity codes appropriately in the resulting BMRB file.		*Here <tt>stereofound</tt> declares stereospecific assignments so the ambiguity codes appropriately in the resulting BMRB file.
			<br>
	<br>

	~~-- GaohuaLiu - 17 Feb 2007~~

	~~--Edited by JimAramini - 03 Nov 2009~~

	<br>		<br>