Dear Charles...
First thanks for your reply.
I tried your script, and Code 1 works. But it changed coordinates too much.
So I tried to specify the regions to refine covalent geometry at Code 2. But I
got error message as follows:
"PyInterp::command: error executing: >execfile('fix_11.py')"
Could you check my output of Code 2?
Hyun.
1) Code1:
import protocol
protocol.loadPDB('AAA.pdb')
protocol.addUnknownAtoms('AAA.pdb')
protocol.fixupCovalentGeom(useVDW=True)
protocol.writePDB('BBB.pdb')
Output of Code 1:
Number of violations greater 2.000: 30
RMS deviation= 0.572
(violations: bond: 0 angle: 810 improper: 30)
addUnknownAtoms_fast: covalent exceptions:
Covalent geometry still violated after fixupCovalentGeom
(violations: bond: 0 angle: 810 improper: 30)
Try increasing maxIters.
fix_1.py(4): protocol.fixupCovalentGeom(useVDW=True)
fix_1.py(5): protocol.writePDB('BBB.pdb')
2) Code 2:
import protocol
protocol.loadPDB('AAApdb')
protocol.addUnknownAtoms('AAA.pdb')
protocol.fixupCovalentGeom(useVDW=True,sel=AtomSel('(segid A and (resid 48 or
resid 66 or resid 176 or resid 184 or resid 256 or resid 48 or resid 63 or
resid 65 or resid 66 or resid 108 or resid 109 or resid 226 or resid 243 or
resid 244 or resid 333 or resid 334 or resid 365 or resid 366 or resid 372 or
resid 373 or resid 374)) or (segid B and (resid 459 or resid 461 or resid 503
or resid 579 or resid 698 or resid 766 or resid 767 or resid 400 or resid 401
or resid 448 or resid 458 or resid 459 or resid 502 or resid 503 or resid 621
or resid 638 or resid 639 or resid 759 or resid 760 or resid 761 or resid 767
or resid 768))'), maxIters=1000)
protocol.writePDB('BBB.pdb')
Output of Code 2:
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/lib/xplor-nih-2.26/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "fix_11.py", line 4, in <module>
protocol.fixupCovalentGeom(useVDW=True,sel=AtomSel('(segid A and (resid 48
or resid 66 or resid 176 or resid 184 or resid 256 or resid 48 or resid 63 or
resid 65 or resid 66 or resid 108 or resid 109 or resid 226 or resid 243 or
resid 244 or resid 333 or resid 334 or resid 365 or resid 366 or resid 372 or
resid 373 or resid 374)) or (segid B and (resid 459 or resid 461 or resid 503
or resid 579 or resid 698 or resid 766 or resid 767 or resid 400 or resid 401
or resid 448 or resid 458 or resid 459 or resid 502 or resid 503 or resid 621
or resid 638 or resid 639 or resid 759 or resid 760 or resid 761 or resid 767
or resid 768))'), maxIters=1000)
File "/usr/local/lib/xplor-nih-2.26/python/regularize.py", line 490, in
fixupCovalentGeom
printViolsAndRaiseException(xSim,minState)
File "/usr/local/lib/xplor-nih-2.26/python/regularize.py", line 416, in
printViolsAndRaiseException
raise CovalentViolation(mess)
regularize.CovalentViolation: Covalent geometry still violated after
fixupCovalentGeom
(violations: bond: 35 angle: 62 improper: 34)
Try increasing maxIters.
PyInterp::command: error executing: >execfile('fix_11.py')<
_______________________________________
From: Charles at Schwieters.org [[email protected]]
Sent: Thursday, October 28, 2010 4:33 PM
To: Song, Hyundeok (songhk)
Cc: Xplor-nih at nmr.cit.nih.gov
Subject: Re: [Xplor-nih] question about refinement
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello Hyun--
>
> I am new to XPLOR-NIH. After reading Xplor-NIH Documentation, I have one
> question.
> I built one pdb structure by homology modelling.
> When I checked the model structure by some programs, I found some warnings
> about unusal bond angle, chirality deviations. I want to fix them.
>
> Can I fix those warnings about bond angles, chirality by XPLOR-NIH
> refinement ?
Probably. The simplest thing to do is to try this simple script:
import protocol
protocol.loadPDB('in.pdb')
protocol.fixupCovalentGeom(useVDW=True)
protocol.writePDB('out.pdb')
In the likely event that this changes your coordinates too much,
something more sophisticated will be needed, and you will have to
specify which parts (and how much) to allow portions of your structure
to change.
best regards--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/>
iEYEARECAAYFAkzJ3i0ACgkQPK2zrJwS/lYUVQCePuvB1ppgvPw72Ztm+bwO7ooN
OE8AnR3ksLB84je2+dgMr/0w6mAfDNzZ
=Spon
-----END PGP SIGNATURE-----
