headers
Charles | 4 Nov 2010 16:01

Re: Fwd: One question about adding NOE constraints


Hello Yawen--

Regarding your question:

> 
> I am currently using X-plor doing calculations based on 2D NMR spectra data
> , in order to get a 3D structure of the peptide of interest.
> 
> The peptide has a ACE at the N-terminus, and I observed a cross-peak of the
>  ACE to other residues. I don't know how can I add this NOE to my NOE const
> raints. Can anyone help me?
> 

I think all you need is to introduce the ACE residue at the beginning of
your sequence. You can then generate coordinates and psf using
e.g. eginput/PSF_generation/addAtoms.py in the Xplor-NIH distribution.

best regards--
Charles
Permalink | Reply | 0 comments |
headers
Si Yan | 8 Nov 2010 17:34
Picon
Favicon

A few questions of PASD Protocol for structure determination.

Hello Charles,

    I'm trying to use PASD for automated assignment and structure determination for my protein. But I encountered several problems:
   The first problem is about the format of peaks location table (the .shifts file and .PCK file). In the paper J. Biom. NMR(2008), we know that PIPP, nmrPipe, or XEASY format will work. We only have nmrPipe. So I selected peaks in nmrDraw and made the peak table (the .PCK file) in nmrPipe format. However, when I use the scripts in tutorial folders, it always shows "header mistake". 
 
    PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for axis X_AXIS aren't in ppm.
   PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for axis X_AXIS aren't in ppm. while executing "error "PIPP header in file $fname indicates peak positions for axis $axis aren't in ppm.""
    Should I change my input file or somewhere in the initMatch3dC.tcl script?  

   The second problem is about understanding language of the scripts. The example scripts are written for 3D noe restraints. But for my solid-state data, we have a series of 2D C-C correlation spectra with different mixing times. So I need to change some sentences in the scripts. However, I'm not familiar with tcl language, and I can not find some instructions for pasd module in the xplor-nih manual.

  The next question is for the parallel calculation with multiple processors. I tried to run the example of cvn protein on our cluster which has 24 processors. I modified the machine_name_file and I wrote the host name of the cluster on each line (20 lines in total). I typed this sentence
           xplor -tcl -parallel -machines machine_name_file sa_pass2.tcl>sa_pass2.out

It can run the simulation, but it also shows:
        ssh_exchange_identification:Connection closed by remote host

   The last question is about the .exceptions file. Is it necessary to make them?

I'm sorry that I have so many questions. Your answer will be very helpful for us.
Thank you!


Best
Si

_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
Permalink | Reply | 1 comment |
headers
Charles | 8 Nov 2010 20:59

Re: A few questions of PASD Protocol for structure determination.


Hello Si--

> 
>     I'm trying to use PASD for automated assignment and structure
> determination for my protein. But I encountered several problems:
>    The first problem is about the format of peaks location table (the
> .shifts file and .PCK file). In the paper J. Biom. NMR(2008), we know that
> PIPP, nmrPipe, or XEASY format will work. We only have nmrPipe. So I
> selected peaks in nmrDraw and made the peak table (the .PCK file) in nmrPipe
> format. However, when I use the scripts in tutorial folders, it always shows
> "header mistake".
> 
>     *PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for
> axis X_AXIS aren't in ppm.
>    PIPP header in file ./13cap_500ms_peak.PCK indicates peak positions for
> axis X_AXIS aren't in ppm. while executing "error "PIPP header in file
> $fname indicates peak positions for axis $axis aren't in ppm.""
>     *Should I change my input file or somewhere in the initMatch3dC.tcl
> script? *  *

If you could send me your headers I should be able to figure out what's
going on.

> 
>    The second problem is about understanding language of the scripts. The
> example scripts are written for 3D noe restraints. But for my solid-state
> data, we have a series of 2D C-C correlation spectra with different mixing
> times. So I need to change some sentences in the scripts. However, I'm not
> familiar with tcl language, and I can not find some instructions for pasd
> module in the xplor-nih manual.

My apologies that it is not better documented. Currently, 2D import is
only supported for the xeasy format, but I probably could fix this
rather quickly. If you upload your tables (or maybe only a small subset of
them) via http://nmr.cit.nih.gov/xplor-nih/download.cgi, I should get to
this shortly.

> 
>   The next question is for the parallel calculation with multiple
> processors. I tried to run the example of cvn protein on our cluster which
> has 24 processors. I modified the machine_name_file and I wrote the host
> name of the cluster on each line (20 lines in total). I typed this sentence
>            *xplor -tcl -parallel -machines machine_name_file
> sa_pass2.tcl>sa_pass2.ou*t
> 
> It can run the simulation, but it also shows:
>         *ssh_exchange_identification:Connection closed by remote host

From your description, I'm not certain whether there was any
problem. Did the job successfully execute on 20 cores? If so, the
message can be ignored.

Also, if you're running PBS, rather than specifying 
 -parallel -machines machine_name_file 
you might use something like:

 pbsxplor -l nodes=20 -tcl -o sa_pass2.out sa_pass2.tcl

> *
>    The last question is about the .exceptions file. Is it necessary to make
> them?
> 

These are generated automatically by the initMatch scripts.

best regards--
Charles
Permalink | Reply | 0 comments |
headers
Charles | 10 Nov 2010 21:06

Re: xplor-nih question


Hello Ranjani--

> I am using XPLOR-NIH to simulate some SANS data (using bin/calcSAXS in
> version 2.26) and had a question re how the data is simulated --
> 
> -- the script calcSAXS describes that solvent background is added to the
> simulated data for easier comparison with experimental data, and I noticed
> that the term 'scat.bg' is added to the calc(i) and expt(i) terms.
> 
> 1. Does this addition of the bkgd occur only if the background is
> specified using the -background option? In other words, if no -background
> value is specified, can one directly compare the simulated and background
> subtracted experimental data?

for SANS data, an optimal background value is computed automatically if
you specify the -fit flag (and this requires an experimental SANS
curve). An isotropic background is not normally computed for SAXS data.

> 
> 2. In what cases does the 'background' value have to be specified? How is
> it different from specifying the 'fractionD2O'?

The fraction of D2O should always be specified (if it is not the default
value of 1). The background is a fit parameter which takes into account
inaccuracies in the subtraction of isotropic background from the
experimental curve.

best regards--
Charles
Permalink | Reply | 0 comments |
headers
Song, Hyundeok (songhk | 12 Nov 2010 07:20
Picon

Re: question about refinement

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 [Charles <at> Schwieters.org]
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-----
Permalink | Reply | 2 comments |
headers
Charles | 12 Nov 2010 15:34

Re: question about refinement


Hello Hyun--

> 
> 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')"
> 

You might try this:

import protocol, regularize
protocol.loadPDB('AAApdb')
protocol.addUnknownAtoms('AAA.pdb')
try:
  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)
except regularize.CovalentViolation:
  pass
protocol.writePDB('BBB.pdb')

This should at least write out the structure. If the violations are
still too many, or too large, a more sophisticated fix-up procedure can
be used in which we allow atom positions to move, but not too much.

best regards--
Charles
Permalink | Reply | 1 comment |
headers
Joshua Ward | 15 Nov 2010 21:27
Picon
Favicon

XPLOR maximum RDC setting

Good day,

I am trying to refine a structure of ubiquitin using some very large  
RDCs (several > 100 Hz). During refinement, the rdc energy becomes  
very large, and final structures are yielding 10 out of 40 rdcs  
violated. Looking at the list, all violated residues have observed RDC  
greater than 100 and a calculated RDC of exactly 100, so it looks like  
you have a maximum value limit in place. All other RDCs are modeled  
quite well.

Is there indeed an upper limit restriction on RDC_calc, and is there a  
way that I can increase it? I haven't spotted an appropriate keyword  
in the examples and docs yet.

Thanks,
Josh

Joshua M Ward
Post Doctoral Research Associate
Wetherill Laboratory of Chemistry, Room 352
Department of Chemistry
Purdue University
560 Oval Drive Box 207
West Lafayette IN 47907-2084 USA
phone: (765) 496-3324
Permalink | Reply | 5 comments |
headers
Charles | 15 Nov 2010 21:40

Re: XPLOR maximum RDC setting


Hello Jos--

> I am trying to refine a structure of ubiquitin using some very large  
> RDCs (several > 100 Hz). During refinement, the rdc energy becomes  
> very large, and final structures are yielding 10 out of 40 rdcs  
> violated. Looking at the list, all violated residues have observed RDC  
> greater than 100 and a calculated RDC of exactly 100, so it looks like  
> you have a maximum value limit in place. All other RDCs are modeled  
> quite well.
> 
> Is there indeed an upper limit restriction on RDC_calc, and is there a  
> way that I can increase it? I haven't spotted an appropriate keyword  
> in the examples and docs yet.
>

There is indeed an upper bound for Da which can be adjusted using the
setDaMax method of VarTensor. For example, the setup of the alignment
tensor object in eginput/gb1_rdc/refine.py can be modified as below to
set a maximum Da value to 200 Hz. This is documented here:
http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensor.html
and the default value of DaMax is 50.

best regards--
Charles

#                        medium  Da   rhombicity
for (medium,Da,Rh) in [ ('t',   -6.5, 0.62),
                        ('b',   -9.9, 0.23) ]:
    oTensor = create_VarTensor(medium)
    oTensor.setDaMax(200)
    oTensor.setDa(Da)
    oTensor.setRh(Rh)
    media[medium] = oTensor
    pass
Permalink | Reply | 4 comments |
headers
Mueller, Geoffrey (NIH/NIEHS) [E] | 15 Nov 2010 22:05
Picon
Favicon

Re: XPLOR maximum RDC setting

Clearly that was a problem.

Another issue may be if you have very large couplings you may also create very large forces on the atoms, and
you will need to rebalance (probably lower) the RDC force constants.  You may need to make the time step
shorter, and refine longer, similar to Choy et al.  Journal of Biomolecular NMR, 21: 31-40, 2001.

Cheers,
Geoff

On 11/15/10 4:40 PM, "Charles <at> schwieters.org" <Charles <at> schwieters.org> wrote:

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello Jos--

> I am trying to refine a structure of ubiquitin using some very large
> RDCs (several > 100 Hz). During refinement, the rdc energy becomes
> very large, and final structures are yielding 10 out of 40 rdcs
> violated. Looking at the list, all violated residues have observed RDC
> greater than 100 and a calculated RDC of exactly 100, so it looks like
> you have a maximum value limit in place. All other RDCs are modeled
> quite well.
>
> Is there indeed an upper limit restriction on RDC_calc, and is there a
> way that I can increase it? I haven't spotted an appropriate keyword
> in the examples and docs yet.
>

There is indeed an upper bound for Da which can be adjusted using the
setDaMax method of VarTensor. For example, the setup of the alignment
tensor object in eginput/gb1_rdc/refine.py can be modified as below to
set a maximum Da value to 200 Hz. This is documented here:
http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensor.html
and the default value of DaMax is 50.

best regards--
Charles

#                        medium  Da   rhombicity
for (medium,Da,Rh) in [ ('t',   -6.5, 0.62),
                        ('b',   -9.9, 0.23) ]:
    oTensor = create_VarTensor(medium)
    oTensor.setDaMax(200)
    oTensor.setDa(Da)
    oTensor.setRh(Rh)
    media[medium] = oTensor
    pass
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/><http://mailcrypt.sourceforge.net/>

iEYEARECAAYFAkzhmskACgkQPK2zrJwS/lYXjQCfbo7hJQ0tv0soWOtiACeb+PeC
IDsAn07sAMAIBz00bCBkNUZQ3vM2Gc+T
=MVFI
-----END PGP SIGNATURE-----
_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih

--
Geoffrey A. Mueller, Ph.D.
Staff Scientist, NIEHS
919-541-3872
mueller3 <at> niehs.nih.gov
Permalink | Reply | 3 comments |
headers
Joshua Ward | 15 Nov 2010 22:40
Picon
Favicon

Re: XPLOR maximum RDC setting

 <at>  Charles
Thanks for the feedback. I saw the setting but it didn't quite sink in  
that it would fix the problem. Guess my thought pattern was stuck in a  
local minimum.

 <at>  Geoff
A good thought. I managed to avoid exploding forces at least, and the  
dynamics were actually completing. I'll give the force constant  
adjustment a try anyway and see how it goes.

Josh

On Nov 15, 2010, at 4:05 PM, Mueller, Geoffrey (NIH/NIEHS) [E] wrote:

> Clearly that was a problem.
>
> Another issue may be if you have very large couplings you may also  
> create very large forces on the atoms, and you will need to  
> rebalance (probably lower) the RDC force constants.  You may need to  
> make the time step shorter, and refine longer, similar to Choy et  
> al.  Journal of Biomolecular NMR, 21: 31-40, 2001.
>
> Cheers,
> Geoff
>
>
> On 11/15/10 4:40 PM, "Charles <at> schwieters.org"  
> <Charles <at> schwieters.org> wrote:
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> Hello Jos--
>
>> I am trying to refine a structure of ubiquitin using some very large
>> RDCs (several > 100 Hz). During refinement, the rdc energy becomes
>> very large, and final structures are yielding 10 out of 40 rdcs
>> violated. Looking at the list, all violated residues have observed  
>> RDC
>> greater than 100 and a calculated RDC of exactly 100, so it looks  
>> like
>> you have a maximum value limit in place. All other RDCs are modeled
>> quite well.
>>
>> Is there indeed an upper limit restriction on RDC_calc, and is  
>> there a
>> way that I can increase it? I haven't spotted an appropriate keyword
>> in the examples and docs yet.
>>
>
> There is indeed an upper bound for Da which can be adjusted using the
> setDaMax method of VarTensor. For example, the setup of the alignment
> tensor object in eginput/gb1_rdc/refine.py can be modified as below to
> set a maximum Da value to 200 Hz. This is documented here:
> http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensor.html
> and the default value of DaMax is 50.
>
> best regards--
> Charles
>
> #                        medium  Da   rhombicity
> for (medium,Da,Rh) in [ ('t',   -6.5, 0.62),
>                        ('b',   -9.9, 0.23) ]:
>    oTensor = create_VarTensor(medium)
>    oTensor.setDaMax(200)
>    oTensor.setDa(Da)
>    oTensor.setRh(Rh)
>    media[medium] = oTensor
>    pass
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.10 (GNU/Linux)
> Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/ 
> ><http://mailcrypt.sourceforge.net/>
>
> iEYEARECAAYFAkzhmskACgkQPK2zrJwS/lYXjQCfbo7hJQ0tv0soWOtiACeb+PeC
> IDsAn07sAMAIBz00bCBkNUZQ3vM2Gc+T
> =MVFI
> -----END PGP SIGNATURE-----
> _______________________________________________
> Xplor-nih mailing list
> Xplor-nih <at> nmr.cit.nih.gov
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
>
>
>
> --
> Geoffrey A. Mueller, Ph.D.
> Staff Scientist, NIEHS
> 919-541-3872
> mueller3 <at> niehs.nih.gov
Permalink | Reply | 2 comments |

Gmane