Re: [PyMOL] protein active site

[pymol . 20 . beantownboy]

Hello Vijay,

Check the following:

Pockets: http://sts.bioengr.uic.edu/castp/  (Castp server)

Protein functional sites:

Qsite: http://www.bioinformatics.leeds.ac.uk/qsitefinder/

SARIG: http://bioinfo2.weizmann.ac.il/~pietro/SARIG/V3/index.html

THEMATICS from Mary Jo Ondrechen at Northeastern University is very 
good. Unfortunately, there is no
web server as of yet that I am aware off. However, they are very 
helpful. If you have a structure of interest

you can write to her and ask them to run it through their program.

In all the above methods the only necessary input is the structure of 
the protein in
PDB format. Thus, they are very good when you have novel or orphan 
(no homology to
others) structures . There are several methods that rely on 
comparison with known structures. You can check:


http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure

for a summary.

Hope this helps.

Maurizzio

At 07:12 AM 7/18/2006, you wrote:

hello,

   Can anyone pl tell me programs which can find the 
protein surface properties such as pockets, different potential 
surfaces and active sites.

thanks in advance.

Regards,
vijay


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[PyMOL] Can PyMOL read amber8 trajectory files?

[Michael Lerner]

I have some stuff from an amber8 (sander) MD run that I'd like to
visualize in PyMOL.  When I load it up, PyMOL says something like
"assuming amber6 format" and dies.  I'm using fink/pymol-py24 on an
intel macbook pro.  I always forget how to load amber files anyway, so
I could easily be screwing something up.  I call my topology file
"something.top" and here's what happens:

PyMOL>load something.top
ObjectMolecule: Assuming this is an Amber6 topology file.
TOPStrToCoordSet-Error: Error reading atom types
/sw/bin/pymol: line23:Bus error

I made that file with amber8.

Thanks,

-michael

[PyMOL] workaround for 'atom name problem with apbs plugin'

[Daniel Rigden]

Dear all

After following the suggestion to try apbs at the command line and some
googling, I found that the problem was that new-ish apbs 0.4 was
expecting a new keyword 'sdens' that my slightly old apbs plugin for
PyMol was not outputting.

http://sourceforge.net/mailarchive/forum.php?thread_id=9502914&forum_id=46597
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6140.html

With the new version of apbs plugin this issue is resolved so can get it
to work with *externally generated* pqr files.  However, the self-made
pqr files *still* come with the unassigned atom problem I mentioned
before.  Any help on that very welcome.

Daniel

On Tue, 2006-07-18 at 09:32 -0400, Peter Adrian Meyer wrote:
> Hi,
> 
> It's good to hear that you got things working, or are at least one step
> closer.  Other than the usual troubleshooting steps that you've probably
> alread tried (checking to make sure that the file exists, path is correct,
> running apbs from the command line to make sure it's happy, etc), I don't
> have any other ideas.
> 
> Good luck,
> 
> Pete
> 
> > Hi Pete
> >
> > Thanks for the idea.  In fact adding a chain ID doesn't make any
> > difference in this case.
> >
> > Based on a mail from Kostas Tripsianes I successfully used the pdb2pqr
> > server to get a pqr file independently to feed to the plug-in.  I got a
> > good looking pqr file but when I try to run apbs, after setting the
> > grid, I now get this error message
> >
> > ObjectMapLoadDXFile-Error: Unable to open file!
> >
> > Does anyone know why that is?
> >
> > Thanks again
> >
> > Daniel
> >
> > On Mon, 2006-07-17 at 14:51 -0400, Peter Adrian Meyer wrote:
> >> Hi Daniel,
> >>
> >> Based on your atom lines, it looks like the pdb -> pqr conversion may
> >> not
> >> be happy about not having a chain ID in the pdb file (this might not be
> >> the problem, but it's worth a shot).  You could test this with a pdb
> >> file
> >> that has chain IDs, or assign them to the pdb file you're working with.
> >>
> >> > ATOM   1191  N   TRP   157 -19.981  10.079  -4.038  1.00  0.00
> >> > ATOM   1192  CA  TRP   157 -21.189  10.376  -3.276  1.00  0.00
> >> > ATOM   1193  C   TRP   157 -20.891  11.323  -2.118  1.00  0.00
> >> > ATOM   1194  O   TRP   157 -21.507  11.233  -1.056  1.00  0.00
> >> > ATOM   1195  CB  TRP   157 -21.787   9.092  -2.697  1.00  0.00
> >> > ATOM   1196  CG  TRP   157 -20.856   8.356  -1.783  1.00  0.00
> >> > ATOM   1197  CD1 TRP   157 -19.931   7.417  -2.137  1.00  0.00
> >>
> >> If this doesn't resolve things, hopefully one of the apbs guru's will be
> >> able to tell you what's going on.
> >>
> >> Pete
> >>
> >>
> >>
> >> Pete Meyer
> >> Fu Lab
> >> BMCB grad student
> >> Cornell University
> >>
> > --
> > Dr Daniel John Rigden Tel:(+44) 151 795 4467
> > School of Biological Sciences FAX:(+44) 151 795 4406
> > Room 101, Biosciences Building
> > University of Liverpool
> > Crown St.,
> > Liverpool L69 7ZB, U.K.
> >
> >
> > -
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share
> > your
> > opinions on IT & business topics through brief surveys -- and earn cash
> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > ___
> > PyMOL-users mailing list
> > PyMOL-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
> 
-- 
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.

[PyMOL] protein active site

[vijay]

hello,
   
 Can anyone pl tell me programs which can find the protein surface 
properties such as pockets, different potential surfaces and active sites.
  thanks in advance.
   
  Regards,
  vijay


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Re: [PyMOL] atom name problem with apbs plugin

[Daniel Rigden]

Hi Pete

Thanks for the idea.  In fact adding a chain ID doesn't make any
difference in this case.

Based on a mail from Kostas Tripsianes I successfully used the pdb2pqr
server to get a pqr file independently to feed to the plug-in.  I got a
good looking pqr file but when I try to run apbs, after setting the
grid, I now get this error message

ObjectMapLoadDXFile-Error: Unable to open file!

Does anyone know why that is?

Thanks again

Daniel

On Mon, 2006-07-17 at 14:51 -0400, Peter Adrian Meyer wrote:
> Hi Daniel,
> 
> Based on your atom lines, it looks like the pdb -> pqr conversion may not
> be happy about not having a chain ID in the pdb file (this might not be
> the problem, but it's worth a shot).  You could test this with a pdb file
> that has chain IDs, or assign them to the pdb file you're working with.
> 
> > ATOM   1191  N   TRP   157 -19.981  10.079  -4.038  1.00  0.00
> > ATOM   1192  CA  TRP   157 -21.189  10.376  -3.276  1.00  0.00
> > ATOM   1193  C   TRP   157 -20.891  11.323  -2.118  1.00  0.00
> > ATOM   1194  O   TRP   157 -21.507  11.233  -1.056  1.00  0.00
> > ATOM   1195  CB  TRP   157 -21.787   9.092  -2.697  1.00  0.00
> > ATOM   1196  CG  TRP   157 -20.856   8.356  -1.783  1.00  0.00
> > ATOM   1197  CD1 TRP   157 -19.931   7.417  -2.137  1.00  0.00
> 
> If this doesn't resolve things, hopefully one of the apbs guru's will be
> able to tell you what's going on.
> 
> Pete
> 
> 
> 
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
> 
-- 
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.