Hello Charles,
Thank you for your quick reply.
There are still some errors.
I defined three atoms in my PDB as three different metal centers:
ATOM 1209 TM+3 TM3 A 77 5.123 0.823 -30.478 1.00 0.00 TM
ATOM 1210 TM+3 TM3 A 78 21.082 6.942 -4.665 1.00 0.00 TM
ATOM 1211 TM+3 TM3 A 79 7.788 5.347 6.577 1.00 0.00 TM
For my tbl.files, I have the following format:
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 77 and name TM+3 )
( resid 69 and name HN) -0.02600 0.02000
This time, the restraints seems be right for Xplor-NIH input.
but there are new errors appeared as following:
----------------------------------------------------------------------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/Xplor/xplor-nih-2.49/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "refinePCS.py", line 37, in <module>
protocol.loadPDB('model+3.pdb')
File "/usr/local/Xplor/xplor-nih-2.49/python/protocol.py", line 552, in
loadPDB
**kwargs)
File "/usr/local/Xplor/xplor-nih-2.49/python/psfGen.py", line 1188, in
pdbToPSF
customRename=customRename, sync=False)
File "/usr/local/Xplor/xplor-nih-2.49/python/psfGen.py", line 806, in seqToPSF
if seqType=='auto': seqType = deduceSeqType(seq)
File "/usr/local/Xplor/xplor-nih-2.49/python/psfGen.py", line 574, in
deduceSeqType
(res,ret,`seq`))
Exception: residue TM3 not of type protein in ['MET', 'GLN', 'ILE', 'PHE',
'VAL', 'LYS', 'THR', 'ALA', 'THR', 'GLY', 'LYS', 'THR', 'ILE', 'THR', 'LEU',
'GLU', 'VAL', 'GLU', 'PRO', 'SER', 'ASP', 'THR', 'ILE', 'GLU', 'ASN', 'VAL',
'LYS', 'ALA', 'LYS', 'ILE', 'GLN', 'ASP', 'LYS', 'GLU', 'GLY', 'ILE', 'PRO',
'PRO', 'ASP', 'GLN', 'GLN', 'ARG', 'LEU', 'ALA', 'PHE', 'ALA', 'GLY', 'LYS',
'GLN', 'LEU', 'GLU', 'ASP', 'GLY', 'ARG', 'THR', 'LEU', 'SER', 'ASP', 'TYR',
'ASN', 'ILE', 'GLN', 'LYS', 'GLU', 'SER', 'THR', 'LEU', 'HIS', 'LEU', 'ALA',
'LEU', 'ARG', 'PRO', 'ARG', 'ALA', 'ALA', 'TM3', 'TM3', 'TM3']
PyInterp::command: error executing: >execfile('refinePCS.py')<
------------------------------------------------------------------------------------------------------------------------------------
I am not sure whether the error is coming from my pdb files. My lanthanide tag
is Tm complex with a DOTA-like derivative, should I patch the tag, instead of
defining pdb file directly?
Also, I am still not so clear about the "rdc.setLocalTensor" setting, in my
case, the 1H-PCS and 15N-PCS from three different metal position are separately
read by xplor-nih, should I set 6 subsets for this part? How should I edit?
Thanks for your time,
HOU
________________________________
From: Charles Schwieters <[email protected]>
Sent: 06 January 2020 23:33
To: Xplor-NIH mailing list <[email protected]>
Cc: [email protected] <[email protected]>
Subject: Re: refinement with multiple PCSs
Hello HOU--
> I am trying to use a modified version of refine.py ( eginput/gb1_rdc) to
> refine a structure using PCSs only. I have three experimental PCS data-sets
> from three different positions.
>
> There are many error messages when I run the script:
> ---------------------------------------------------------------------------------------------------------------------------------------------
> return _rdcPot.RDCPot1_addRestraints(self, *args, **kwargs)
> SystemError: xplor-nih error: error reading restraint: selection string resid
> 500 and name OO selects no atoms
> PyInterp::command: error executing: >execfile('refinePCS.py')<
> --------------------------------------------------------------------------------------------------------------------------------------------------
> My restraint file is in Xplor format from Numbat:
> assign ( resid 500 and name OO )
> ( resid 500 and name Z )
> ( resid 500 and name X )
> ( resid 500 and name Y )
> ( resid 69 and name H ) -0.02600 0.20000
Apparently, Numbat restraints aren't quite right for Xplor-NIH input.
> For rdcPot, it seems that the Assign command must be followed by six
> selections, but for PCS, only five selections have been generated by Numbat.
> In RDC restraints, the fifth line should be the coupled nuclues, and the sixth
> line is detected nuclues. What I should set in PCS?
In RDCPot, the first 4 atom selections are actually ignored, and can
be anything (but the 4 sets of parentheses are still required).
> Perhaps the OO position( paramagneitc center postion). so I tried again by the
> restraint file as following:
> My restraint file is in Xplor format from Numbat:
> assign ( resid 500 and name OO )
> ( resid 500 and name Z )
> ( resid 500 and name X )
> ( resid 500 and name Y )
> ( resid 500 and name OO )
> ( resid 69 and name H ) -0.02600 0.20000
I suggest that the alignment tensor be completely separate from the
paramagnetic center, and that you instead include the atom explicitly
(like TM+3) in the PSF. A simpler restraint format can be used if you
utilize the rdcPotTools.spaceSeparatedToRestraint function to do the
conversion on input. e.g.
from rdcPotTools import spaceSeparatedToRestraint
restraints = spaceSeparatedToRestraint(open("restraints.txt").read(),
atom1Name='TM+3',
atom2Name='HN',
residCol=1, rdcCol=2, errCol=3)
rdc = create_RDCPot("%s_%s"%(medium,expt),restraints=restraints,
media[medium])
If the local environment of the paramagnetic tags are identical, it
may be useful to use a single alignment tensor with the local
environment defined for each tag. This can be achieved using
rdc.setLocalTensors( [(a1,b1,c1), ...] )
where the argument is a list of three atoms for each tag site,
defining the local coordinate system.
I hope this helps some--
Charles
########################################################################
To unsubscribe from the XPLOR-NIH list, click the following link:
http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
