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Valerie A. Villareal | 24 Mar 2009 17:50

Adding CYS and MTSL to PDB

Hello group.

I am trying to change a residue (e.g., LYS) to CYS-MTSL. This was
previously discussed; however, what should I do if the pdb (X-ray
structure downloaded from pdb.org) does not have the CYS present
already? Is executing the addAtoms.py script supposed to work in this
case? The output generated from addAtoms.py and addAtoms2.py (this
fixes covalent geometry) from Xplor v. 2.22 is an incorrectly folded
structure. The demo works, so it must be my input info. I also tried
adding protocol.genExtendedStructure(sel="not known") or (sel="resid
xx"). Unfortunately, the tertiary structure is still incorrect.

I have not done any modifications to the downloaded pdb; could this be
the problem?

Thanks,
Valerie
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Charles | 24 Mar 2009 19:08

Re: Adding CYS and MTSL to PDB


Hello Valerie--

> I am trying to change a residue (e.g., LYS) to CYS-MTSL. This was
> previously discussed; however, what should I do if the pdb (X-ray
> structure downloaded from pdb.org) does not have the CYS present
> already? Is executing the addAtoms.py script supposed to work in this
> case? The output generated from addAtoms.py and addAtoms2.py (this
> fixes covalent geometry) from Xplor v. 2.22 is an incorrectly folded
> structure. The demo works, so it must be my input info. I also tried
> adding protocol.genExtendedStructure(sel="not known") or (sel="resid
> xx"). Unfortunately, the tertiary structure is still incorrect.
> 

eginput/PSF_generation/addAtoms2.py should work for you in this
case. Note, the comment above the definition of fixGeom is incorrect:
only atoms in fixGeom are moved.

> I have not done any modifications to the downloaded pdb; could this be
> the problem?
> 

It should work fine.

If you still have problems, I'd like to see the output of the script, so
I can figure out what's going on.

best regards--
Charles
(Continue reading)

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Valerie A. Villareal | 25 Mar 2009 00:16

Re: Adding CYS and MTSL to PDB

Hi Charles.

Thanks for the help and clarifying the use of fixGeom. It looks like
using addAtoms2.py worked only when I converted the downloaded pdb
(X-ray structure) into a pdb in which the HETATOMS and water were
removed and selenomet was changed to MET. I used both pdbs and the
only correct output pdb was the one in which the converted pdb was
used.

Valerie

On Tue, Mar 24, 2009 at 10:08 AM,  <Charles <at> schwieters.org> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
>
> Hello Valerie--
>
>> I am trying to change a residue (e.g., LYS) to CYS-MTSL. This was
>> previously discussed; however, what should I do if the pdb (X-ray
>> structure downloaded from pdb.org) does not have the CYS present
>> already? Is executing the addAtoms.py script supposed to work in this
>> case? The output generated from addAtoms.py and addAtoms2.py (this
>> fixes covalent geometry) from Xplor v. 2.22 is an incorrectly folded
>> structure. The demo works, so it must be my input info. I also tried
>> adding protocol.genExtendedStructure(sel="not known") or (sel="resid
>> xx"). Unfortunately, the tertiary structure is still incorrect.
>>
>
> eginput/PSF_generation/addAtoms2.py should work for you in this
(Continue reading)

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Nir London | 25 Mar 2009 17:29

Rosetta Academic Training Webinar

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. 

What: Protein-Protein Docking

When: May 4th 2009, 0800-1000 AM EST

Where: Your office!

Click here for more details and registration

(For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en ) 

Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version.

Hope to see you there, 

Nir London. 

Rosetta Design Group | http://rosettadesigngroup.com/

_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
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Charles | 27 Mar 2009 12:17

Re: Adding CYS and MTSL to PDB


Hello Valerie--

My apologies for the sluggish response.

> Thanks for the help and clarifying the use of fixGeom. It looks like
> using addAtoms2.py worked only when I converted the downloaded pdb
> (X-ray structure) into a pdb in which the HETATOMS and water were
> removed and selenomet was changed to MET. I used both pdbs and the
> only correct output pdb was the one in which the converted pdb was
> used.
> 

HETATOM records should be ignored, and strange residue names should not
matter in that script, unless you added them to the sequence passed to
seqToPSF. If you found different behavior, I would be quite grateful if
you would send me your input so I might fix things up.

thanks--
Charles
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Jurgen F. Doreleijers | 30 Mar 2009 12:14
Picon

Announcing NMR validation web interface iCing

Hi there,

We are happy to announce the iCing web interface to CING
(http://nmr.cmbi.ru.nl/cing) that can validate your NMR data &
structures online, running tools such as What If, Procheck, Wattos,
ShiftX, etc..

Please direct your browser to: https://nmr.cmbi.ru.nl/icing

You can send in your data using a simple PDB file that has only
coordinates or a CCPN or CING project file (.tgz) with experimental
data such as chemical shifts and restraints included.

To create a CCPN project file please visit the CCPN project web pages
at; http://www.ccpn.ac.uk/

There are YouTube tutorials available here:
http://nmr.cmbi.ru.nl/cing/Tutorials/Tutorials.html
They show how to create input and how to use iCing in a variety of
ways online or locally.

Finally, almost all of the over 4,000 PDB entries with experimental
NMR data in BMRB are already run through CING and were put into a site
called NRG-CING here: http://nmr.cmbi.ru.nl/NRG-CING

Please take a look if you find a PDB entry of your interest there!

Cheers,
Jurgen Doreleijers, Alan W.S. da Silva, and Geerten Vuister
--
Jurgen F. Doreleijers
Centre for Molecular & Biomolecular Informatics, NCMLS &
Protein Biophysics, Institute for Molecules & Materials
Radboud University of Nijmegen
Visitors: NCMLS Research building, room 0.25, Geert-Grooteplein 26-28,
6525 GA Nijmegen, The Netherlands
Mail: Protein Biophysics 260, PO Box 9101, 6500 HB Nijmegen, The
Netherlands
Tel: +31 24 3619674
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Ben Eisenbraun | 31 Mar 2009 16:59
Picon

OS X bug in tcl/noe_reporting.tcl


Howdy,

In tcl/noe_reporting.tcl, line 2104 is:

   exec ln --symbolic $oldname $newname

The long option '--symbolic' is a GNU-ism and doesn't work with the
BSD-based ln command in OS X.

The short form -s option is in the POSIX standard, so it should be fairly
portable.

-ben

--
Ben Eisenbraun
Structural Biology Grid                           Harvard Medical School
http://sbgrid.org                                 http://hms.harvard.edu
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Charles | 31 Mar 2009 17:15

Re: OS X bug in tcl/noe_reporting.tcl


Hi Ben--

> 
> In tcl/noe_reporting.tcl, line 2104 is:
> 
>    exec ln --symbolic $oldname $newname
> 
> The long option '--symbolic' is a GNU-ism and doesn't work with the
> BSD-based ln command in OS X.
> 
> The short form -s option is in the POSIX standard, so it should be fairly
> portable.
> 

thanks for catching this. It'll be fixed in the next version.

best regards--
Charles
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David A. Horita | 31 Mar 2009 17:37
Favicon

setting fixDa/fixRh for specific data sets


Hi,
How do I set setFreedom("fixDa, fixRh") for specific data sets?
I have three rdc media and they're not co-fitting well.  Part of it seems to be high rhombicity in some sets
(0.5-0.66) and +/- for Da.  I'd like to be able to fix Da and Rh for some of my sets and refine Da and Rh for others.

with 

for m in media.values():
    m.setFreedom("varyDa,varyRh")

I can fix/float all of them, but what is m relative to my media?  I have media defined as t g and c but
t.setFreedom doesn't work.

As a general question, how do I tell what a variable's value is in the python interface, and specifically, m
is in media.values()?
  print m gives an error

Thanks,
David Horita
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Charles | 31 Mar 2009 19:49

Re: setting fixDa/fixRh for specific data sets


Hello David--

> How do I set setFreedom("fixDa, fixRh") for specific data sets?
> I have three rdc media and they're not co-fitting well.  Part of it
> seems to be high rhombicity in some sets (0.5-0.66) and +/- for Da.
> I'd like to be able to fix Da and Rh for some of my sets and refine Da
> and Rh for others. 
> 
> with 
> 
> for m in media.values():
>     m.setFreedom("varyDa,varyRh")
> 
> I can fix/float all of them, but what is m relative to my media?  I
> have media defined as t g and c but t.setFreedom doesn't work. 

this should work:

media['t'].setFreedom("fixDa, fixRh")

> 
> As a general question, how do I tell what a variable's value is in the
> python interface, and specifically, m is in media.values()? 

media is a Python dictionary, so the key values can be obtained using
the keys() method:

print media.keys()

I hope this help--
Charles
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Gmane