user queries for the Xplor-NIH biomolecular structure determination program

Charles | 1 Jun 2006 23:36

Re: Problem creating talos variable in marvin


> 
> I am trying to use marvin in xplor-nih-2.14 to generate restraints for
> a small alpha helical protein.   When running the sa_pass1.tcl script,
> the following error is obtained:
> 

A new version of xplor-nih-2.14-Linux_2.4_i686 has been posted at the
download site. This fixes the issue you are having with the TCL
interface. The packages for other architectures do not suffer this
problem.

regards--
Charles

Peter Teriete | 5 Jun 2006 19:37

Problems Generating the template.pdb

Hi all,

Started using Xplor-NIH for some structure calculations (used CNS
previously, tough that was some time ago). I have troubles generating a
useful template.pdb structure or my protein using the mkpsf.inp scripts in
the eginput directory (i.e. modifying the protG_mkpsf.inp). It generates a
psf file which looks correct, although I don't seem to see the connect
information for the peptide bonds, and a pdb file where the peptide bonds
are missing. All the residues are placed along the x-axis, as anticipated,
but the distances between the residues is too large for the peptide bonds to
be recognised. I ran the unmodified perotG-mkpsf.inp and have the same
problem. Any advice on what I'm doing wrong?

The calculations are performed using Xplor-NIH 2.13 build for Darwin 7.9.0
on a Mac G5 operating OSX 10.3.9

Thanks,

Peter

--

-- 
Peter Teriete
The Burnham Institute
10901 N Torrey Pines Rd
La Jolla, CA, 92037
+1 858 646 3100 ext.3724

Charles | 5 Jun 2006 21:58

Re: Problems Generating the template.pdb


Hello Peter--

> 
> Started using Xplor-NIH for some structure calculations (used CNS
> previously, tough that was some time ago). I have troubles generating a
> useful template.pdb structure or my protein using the mkpsf.inp scripts in
> the eginput directory (i.e. modifying the protG_mkpsf.inp). It generates a
> psf file which looks correct, although I don't seem to see the connect
> information for the peptide bonds, and a pdb file where the peptide bonds
> are missing. All the residues are placed along the x-axis, as anticipated,
> but the distances between the residues is too large for the peptide bonds to
> be recognised. I ran the unmodified perotG-mkpsf.inp and have the same
> problem. Any advice on what I'm doing wrong?

please try running eginput/protG/protG_gen.py. Like in the XPLOR, you
specify sequence, then run with
xplor -py protG_gen.py

I'll be happy to fix any problems you might have with this.

regards--
Charles

dgnorman | 14 Jun 2006 15:05

Picon

Intel Mac

Hi,
  Has anyone made an Xplor-NIH binary for the Intel Mac?
Thanks
David

David Norman Ph.D.
Nucleic Acid Structure Research Group
School of Life Sciences
MSI/WTB Complex
University of Dundee
Dow Street
Dundee DD1 5EH
Tel: +44 (0)1382 344798
Email: dgnorman <at> lifesci.dundee.ac.uk

Charles | 15 Jun 2006 15:28

Re: Intel Mac


Hi David--

>   Has anyone made an Xplor-NIH binary for the Intel Mac?

not to my knowledge. Is there a mechanism to run x86 linux binaries on
those machines? 

Charles

Franz Hagn | 22 Jun 2006 13:28

Picon

MTSL parameter and topology files

Hi,

I am using Xplor-NIH Version 2.9.4 without python interface.
I want to define a Cystein-MTSL spin label residue for incorporating 
this residue into my protein with psfgen.inp.
Does anybody have these files or know how to make it ??
Thanks so far !

Franz

Charles | 22 Jun 2006 16:16

Re: MTSL parameter and topology files


Hello Franz--

> I am using Xplor-NIH Version 2.9.4 without python interface.
> I want to define a Cystein-MTSL spin label residue for incorporating
> this residue into my protein with psfgen.inp.
> Does anybody have these files or know how to make it ??
> Thanks so far !
> 

An example of adding Cys-MTSL is given in 
eginput/PSF_generation/addAtoms.py
in Xplor-NIH version 2.9.12 and higher. While this script is Python, it
is quite simple to modify. 

regards--
Charles

--

-- 
Charles Schwieters     email:   Charles <at> Schwieters.org
		       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt

igor barsukov | 28 Jun 2006 12:53

Picon

Picon

SuSe 10.1

Hi,

It's probably something very simple. XPLOR-NIH runs fine on SuSe10.0,
but when I tried it on 10.1 I got the error message:

/igb/prog/xplor_nih/xplor-nih-2.14/bin.Linux_2.4_i686/xplor: error while
loading shared libraries: libpthread.so.0: cannot open shared object
file: No such file or directory

As far as I can see I have the same files for the libraries in 10.0 and
10.1:

In /usr/lib :
/usr/lib/libpthread.a  /usr/lib/libpthread_nonshared.a
/usr/lib/libpthread.so

In /lib:
-rwxr-xr-x 1 root root 100331 2006-04-29 00:20 /lib/libpthread-2.4.so
lrwxrwxrwx 1 root root     17 2006-06-26 15:57 /lib/libpthread.so.0 ->
libpthread-2.4.so

/usr/lib/libpthread.so contains:

/* GNU ld script
   Use the shared library, but some functions are only in
   the static library, so try that secondarily.  */
OUTPUT_FORMAT(elf32-i386)
GROUP ( /lib/libpthread.so.0 /usr/lib/libpthread_nonshared.a )

The main difference is the version of /lib/libpthread.

(Continue reading)

andrea spitaleri | 28 Jun 2006 14:16

Picon

Re: SuSe 10.1

Hi,
probably xplor is looking that file somewhere else, not in standard path. try to use strace and 
ldconfig to trace where xplor is trying to load the lib.

I hope this help

Regards

Andrea

igor barsukov wrote:
> Hi,
> 
> It's probably something very simple. XPLOR-NIH runs fine on SuSe10.0,
> but when I tried it on 10.1 I got the error message:
> 
> /igb/prog/xplor_nih/xplor-nih-2.14/bin.Linux_2.4_i686/xplor: error while
> loading shared libraries: libpthread.so.0: cannot open shared object
> file: No such file or directory
> 
> As far as I can see I have the same files for the libraries in 10.0 and
> 10.1:
> 
> In /usr/lib :
> /usr/lib/libpthread.a  /usr/lib/libpthread_nonshared.a
> /usr/lib/libpthread.so
> 
> In /lib:
> -rwxr-xr-x 1 root root 100331 2006-04-29 00:20 /lib/libpthread-2.4.so
> lrwxrwxrwx 1 root root     17 2006-06-26 15:57 /lib/libpthread.so.0 ->

(Continue reading)

Charles | 28 Jun 2006 15:16

Re: SuSe 10.1


Hi Igor--

> It's probably something very simple. XPLOR-NIH runs fine on SuSe10.0,
> but when I tried it on 10.1 I got the error message:
> 
> /igb/prog/xplor_nih/xplor-nih-2.14/bin.Linux_2.4_i686/xplor: error while
> loading shared libraries: libpthread.so.0: cannot open shared object
> file: No such file or directory
> 

it may be the same LD_ASSUME problem that struck Fedora Core 5. Please see
http://nmr.cit.nih.gov/xplor-nih/faq.html#node0947.txt

There also may be something wrong with the path setup. Please send the
output of:
ldd bin.*/xplor

regards--
Charles

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