Pararestraints help needed

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Deviation from ideal geometry

Hi *

I just finished a structure calculation using the xplor-nih software, 
and  I'm making the final structural statistics table for a set of 
structures, so common in the NMR field.

One quick question from a NMR newbie.
How do you guys calculate the "deviations from the ideal geometry", for 
a set of obtained pdb's?. Does the xplor-nih scripts calculate this?

Best,
Léon Salgado

Re: Pararestraints help needed

Hello Hong--

>      I want to refine my protein structure using paramagnetism-based
>     constraints (PCS, RDC). The module I used for the calculation is
>     Pararestraints in Xplor. I try to follow those two sample scripts
>     from Dr. Bertini's website. One question to me is that why they
>     define two different tensors (two sets of pseudo atoms) for PCSs
>     and RDCs. As I know, if the PCS is measured by comparison the
>     difference of chemical shifts between diamagnetic and paramagnetic
>     samples. The order tensors for PCS should be the same as that for
>     RDCs. 

Dr. Bertini and his coworkers are welcome to comment in this forum, but
if you find no answer here you may have to contact his group directly.

>     The other question is that how to calculate the coefficients for
>     XPCS and XRDC?  If the protein structure is known but the metal
>     ion is unknown, can we just use RDCs to determine the order
>     tensors? What program do you use to calculate the order tensors? I
>     used our own program REDCAT but the definition of the order
>     tensors might be different. 
>    

You might be able to use eginput/protG/calcTensor.py in the Xplor-NIH
distribution. 

best regards--
Charles

Re: Deviation from ideal geometry

Hello Léon--

> One quick question from a NMR newbie.
> How do you guys calculate the "deviations from the ideal geometry", for 
> a set of obtained pdb's?. Does the xplor-nih scripts calculate this?
> 

The output of Xplor-NIH does contain some metrics- look at violations of
the BOND, ANGL, DIHE and VDW terms. Howeverm it may be best to use an
independent program, such as WhatIF for these calculations - as an
independent check. If there are large discrepencies between the two
programs, we'd like to know about it.

best regards--
Charles

Standard formats of PDB ??

Hi,

Perhaps this is a stupid question, but I do wonder why
- Xplor cannot read PDBs as provided by the protein databank?
- Xplor output is not PDB standard as required for submission to the
protein databank.

Example, an Xplor-pdb ATOM line looks like:

ATOM      7 H5'' GUA     1     305.922  17.032 -97.545  1.00  0.00
EDHB

The last element is the segment ID.

Wheras the line for the protein databank looks like (taken from another
PDB from the databank):
ATOM     22 2H5*   G A   1     -12.277 -10.770   5.000  1.00  0.00
H  

Or is there an easy way to change the output to PDB(tm) standard, which
I may have overlooked ?

Regards,
Ramon

Re: Standard formats of PDB ??

Hello Ramon--

> 
> Perhaps this is a stupid question, but I do wonder why
> - Xplor cannot read PDBs as provided by the protein databank?

protocol.loadPDB does a pretty good job of reading PDBs, particularly
for proteins. If you have a problem with a specific PDB entry, please
send us the ID>

> - Xplor output is not PDB standard as required for submission to the
> protein databank.
> 
> Example, an Xplor-pdb ATOM line looks like:
> 
> ATOM      7 H5'' GUA     1     305.922  17.032 -97.545  1.00  0.00
> EDHB
> 
> The last element is the segment ID.
> 
> Wheras the line for the protein databank looks like (taken from another
> PDB from the databank):
> ATOM     22 2H5*   G A   1     -12.277 -10.770   5.000  1.00  0.00
> H  
> 

PDBTool in the upcoming Xplor-NIH release has an option writeChainID,
which will write the segid to the chainID field, if it's a single
character.

best regards--
Charles

Re: Standard formats of PDB ??

Hi,

Jut to expand on Charles's answer a bit,

On Oct 3, 2007, at 4:22 AM, R.M. van der Werf wrote:

> Hi,
>
> Perhaps this is a stupid question, but I do wonder why
> - Xplor cannot read PDBs as provided by the protein databank?
> - Xplor output is not PDB standard as required for submission to the
> protein databank.

The two major differences between xplor-standard PDBs and PDB-standard
PDBs are the atom names and the absence of the segid field in the PDB  
standard.

Xplor has used nonstandard atom names for a long time because they  
greatly facilitate
atom selections.  The PDB's standard atom names for, for example, leu  
delta protons
are 1HD1, 1HD2, etc.  Xplor's are HD11, HD12, etc.  With xplor's atom  
names, you can
do selections like (resn leu and name h*) that cover all the atoms in  
the residue.

As an aside, lots of our scripts (in Python, TCL, and in the classic  
xplor language)
are dependent upon the xplor atom naming convention.  So changing  
naming conventions
would require changes to a lot of stuff.

The second major difference between xplor and PDB-standard PDB files  
is xplor's addition
of the segid field.  As far as I can tell, Axel added the segid  
because the PDB standard's
chainID is only one character long.

As Charles said, we have some pretty good tools for reading and  
writing PDB-standard
PDB files, but we're always looking for cases where xplor's tools  
don't yet work.
So please email us if you find such a case.

--JK

nested while loops in XPLOR-NIH

Dear XPLOR-NIH users:

I am (finally) moving from X-PLOR to XPLOR-NIH, and I've ecountered a 
problem with legacy scripts containing nested while loops. The nesting 
worked in XPLOR 98.1 under UNIX, but gives errors when the exact same 
script is run in XPLOR-NIH 2.15.0 under Linux.

The follwing are excerpts from a log file generated with XPLOR 98.1 run 
under UNIX:

 X-PLOR>while ($lasti GE $currenti) loop main
 NEXTCD: condition evaluated as true

 X-PLOR>while ($rcon  < 0.1) loop stg2
 NEXTCD: condition evaluated as true

When run using XPLOR-NIH 1.15.0 under Linux, the first (outer) while 
loop works fine, but the inner loop fails:

 X-PLOR>while ($lasti GE $currenti) loop main
 NEXTCD: condition evaluated as true

 X-PLOR>while ($rcon  < 0.1) loop stg2
 %X-PLOR-ERR: unrecognized command:
 while
 ^^^^^

Has anyone enountered problems with nested while loops when running 
legacy XPLOR scripts with XPLOR-NIH? If anyone knows of a simple way to 
fix this,  I would very much appreciate your help. I could re-write my 
legacy scripts based on the examples provided with XPLOR-NIH, but a 
quick fix would be a big time saver it it is possible. Thank you very much.

    Keith Constantine

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Re: nested while loops in XPLOR-NIH

Hello Keith--

> 
> I am (finally) moving from X-PLOR to XPLOR-NIH, and I've ecountered a
> problem with legacy scripts containing nested while loops. The nesting
> worked in XPLOR 98.1 under UNIX, but gives errors when the exact same
> script is run in XPLOR-NIH 2.15.0 under Linux.
> 

It would be quite helpful if you could send a very short example script
which exhibits the problem.

Nested while loops are used extensively in legacy XPLOR scripts, and
they should work fine. Do note that Xplor-NIH maintains compatibilty
with X-PLOR 3.851 and it's conceivable that there are slight differences
with XPLOR 98.1, but should be easily worked around.

best regards--
Charles

Re: nested while loops in XPLOR-NIH

{ ************************************************************************** }
{    A straight minimization procedure for a familu of structures.           }
{                                                                            }
{ ************************************************************************** }

parameter  
! {===>}    <at> ../top/parall_kc.pro 
{===>}    <at> ../top/parall_kc_fixarg.pro
          <at> $ligparfile
   nbfix  S    S    462  13.6  462  13.6   
end

set echo=off end
set message=off end

{===>} structure  <at> $psffile1  <at> $psffile2 end                      { read structure files }

evaluate ($currenti = $firsti )

{ ************************************************************************** }
{  Construct pdb file names. Read in coordinates.                            }
{ ************************************************************************** }

while ($lasti GE $currenti) loop main

   evaluate ( $pdb1 = $pdbfilein + encode($currenti) + ".pdb" )
   coordinates  <at>  <at> $pdb1                   { read the coordinates }

{ ************************************************************************** }
{  Read in noe constraints and set up energy functions.                      }
{ ************************************************************************** }

evaluate ($knoe  = 50.0)        { set constants for the experimental energy   }

flags
  include noe cdih elec
  exclude dihe
end

noe                                                     { read NOE restraints }
  reset
  nrestraints = 8000                                 { allocate space for NOEs }
  ceiling = 100                      { maximum force constant that is allowed }

  class      all  <at>  <at> $noefile                        { NOE restraint file }
                  <at>  <at> $disulfides    {  disulfide bond distance restraints }

  averaging  all sum
  potential  all square
  scale      all $knoe                           
  sqconstant all 1.0
  sqexponent all 2
end

{ ************************************************************************** }
{  Read in torsion constraints and set up energy functions.                  }
{ ************************************************************************** }

restraints dihedral               { next 4 lines should eliminate NASS error }
  reset
  nassign = 2000
end

 <at>  <at> $anglefile                         { read NMR torsion angle restraints }         

{===>}  <at>  <at> $fixfile         

parameters                                  { setup the repulsive energy term }
  nbonds
    cutnb = 8.5   {changed from 8.0} 
    ctofnb = 7.5
    ctonnb = 6.5
    rdiel
    eps = 4.0      {changed from 2.0}
    switch vswitch
    nbxmod = 5
    tolerance 0.3
    repel  =  0.0
    rexp   =  2                        { exponents in (r^irex - R0^irex)^rexp }
    irex   =  2
    rcon   =  4                                  { actually set the vdW weight }
  end
end 

{ ************************************************************************** }
{    Stage 1: The initial minimization ensures the geometry of the initial   }
{             structure is good.                                             }
{ ************************************************************************** }

 { mini abnr nstep=2000 end } 

mini powell nstep=2000 drop = 10.0 end 

{ ************************************************************************** }
{   Write out final coordinates.  Get next file.                             }
{ ************************************************************************** }

evaluate ( $pdb2 = $pdbfileout + encode($currenti) + ".pdb" )
write coordinates output=$pdb2  end         { write coordinates }

evaluate ( $currenti=$currenti+1 )

end loop main

stop

evaluate ( $psffile1 = "a.psf" )
evaluate ( $psffile2 = "b.xpsf" )
evaluate ( $ligparfile = "b.xprm")
evaluate ( $pdbfilein = "c_" )
evaluate ( $pdbfileout = "d_" )
evaluate ( $firsti = 1 )
evaluate ( $lasti = 2 ) 
evaluate ( $noefile = "noe.tbl")
evaluate ( $disulfides = "null.file")
evaluate ( $anglefile = "dih.tbl")
evaluate ( $fixfile = "fixnone.tbl")
evaluate ( $numstep = 2000)
 <at> ../input/minelec_sum_prot_lig.inp

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