pymol-users

[PyMOL] Problem reading multiframe pdb file for animation

[<Pet...@we...>]

Dear PyMol experts:

When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has
40 coordinate sets (each is one frame in an animation) each beginning
with:
HEADER  Output iset=     n "xxxx_G=r_0_01"
then a list of the pdb coordinates
and ending with:
ENDMDL
"n" ranges from 0 to 39.
This results in the following output:
HEADER  Output iset=     0  "xxxx_G=r_0_01"
HEADER  Output iset=     1  "xxxx_G=r_0_01"
 ObjectMolReadPDBStr: read MODEL 1
 ObjectMolReadPDBStr: read MODEL 2
etc. ...
 ObjectMolReadPDBStr: read MODEL 39
 ObjectMolReadPDBStr: read MODEL 40
 CmdLoad: "/home/psstern/pymol/xxxx_G=r_0_01.pdb" loaded as "xxxx_G=r_0_01".

This then displays one molecule with 40 frames and the animation can be
activated by clicking on the red arrow.

However, when using Open-Source PyMOL 1.3 the same file results in
different behavior.  Instead of reading in one object with 40 frames
it reads in 40 different objects and displays all of them.  The output
I get is:
HEADER  Output iset=     0  "xxxx_G=r_0_01"
HEADER  Output iset=     1  "xxxx_G=r_0_01"
HEADER  Output iset=     2  "xxxx_G=r_0_01"
etc. ...
HEADER  Output iset=    38  "xxxx_G=r_0_01"
HEADER  Output iset=    39  "xxxx_G=r_0_01"
 CmdLoad: loaded 40 objects from "/home/psstern/pymol/xxxx_G=r_0_01.pdb".

Is this a bug or am I missing some parameter which is set differently
by default for the two versions?  I couldn't find a solution in the
on-line documentation.

Regards,
Peter Stern

Re: [PyMOL] Problem reading multiframe pdb file for animation

[Jason V. <jas...@sc...>]

Hi Peter,

If you could send me the PDB (or one like it) I'd like to see it.

The known flags for controlling how PyMOL loads multi-state files are:

 discrete= 0 or 1
  If 0, then all states must have the same number of atoms and similar
connectivity
  If 1, then all states are treated as different molecular structures,
so can have differing numbers of atoms and bonds

 multiplex= 0 or 1
  If 0, then load the N-state file as one N-state object
  If 1, then load the N-state file as N one-state objects


So, what happens in v1.3 if you write:

load fileName.pdb, multiplex=0


Cheers,

-- Jason



On Wed, Mar 16, 2011 at 10:23 AM,  <Pet...@we...> wrote:
> Dear PyMol experts:
>
> When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has
> 40 coordinate sets (each is one frame in an animation) each beginning
> with:
> HEADER  Output iset=     n "xxxx_G=r_0_01"
> then a list of the pdb coordinates
> and ending with:
> ENDMDL
> "n" ranges from 0 to 39.
> This results in the following output:
> HEADER  Output iset=     0  "xxxx_G=r_0_01"
> HEADER  Output iset=     1  "xxxx_G=r_0_01"
>  ObjectMolReadPDBStr: read MODEL 1
>  ObjectMolReadPDBStr: read MODEL 2
> etc. ...
>  ObjectMolReadPDBStr: read MODEL 39
>  ObjectMolReadPDBStr: read MODEL 40
>  CmdLoad: "/home/psstern/pymol/xxxx_G=r_0_01.pdb" loaded as "xxxx_G=r_0_01".
>
> This then displays one molecule with 40 frames and the animation can be
> activated by clicking on the red arrow.
>
> However, when using Open-Source PyMOL 1.3 the same file results in
> different behavior.  Instead of reading in one object with 40 frames
> it reads in 40 different objects and displays all of them.  The output
> I get is:
> HEADER  Output iset=     0  "xxxx_G=r_0_01"
> HEADER  Output iset=     1  "xxxx_G=r_0_01"
> HEADER  Output iset=     2  "xxxx_G=r_0_01"
> etc. ...
> HEADER  Output iset=    38  "xxxx_G=r_0_01"
> HEADER  Output iset=    39  "xxxx_G=r_0_01"
>  CmdLoad: loaded 40 objects from "/home/psstern/pymol/xxxx_G=r_0_01.pdb".
>
> Is this a bug or am I missing some parameter which is set differently
> by default for the two versions?  I couldn't find a solution in the
> on-line documentation.
>
> Regards,
> Peter Stern
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

[PyMOL] Adding Hydrogens

[Martin H. <ma...@bl...>]

Dear All
I would like to ask if the PyMOL function to add hydrogens to an entire 
protein also has options, meaning is it possible to set the protonation 
state of individual residues specifically? Like in a list or something?
h_add, His202:+1 or so?
And, it can be relevant at what atom a residue gets protonated: His can 
be protonated at Nd, or Ne or both. Is there a way to control this?

On a more general note: what other smart hydrogen adding tools are there 
out there anyway? Does anyone know a really smart tool for this? I know 
OpenBabel has a pH parameter. But on the other hand OpenBabel just 
appends the hydrogens to the PDB file, whereas PyMOL really writes them 
within the block of atoms corresponding to one residue.
Also, AutoDock can add hydrogens and it even has an option for the 
protonation state of histidine, but it doesn't seem to work in my case.

Thanks for your answers and input.
martin

Re: [PyMOL] Adding Hydrogens

[Michael L. <mgl...@gm...>]

I've had good results with MolProbity (
http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15)
in the past.

I had a script that would let me cycle through all of the HIS residues, add
hydrogens, and cycle between states. It's broken at the moment. The trick
was that PyMOL doesn't care about the name of the residue, so you have to
manually cycle the valences.

On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger <ma...@bl...> wrote:

> Dear All
> I would like to ask if the PyMOL function to add hydrogens to an entire
> protein also has options, meaning is it possible to set the protonation
> state of individual residues specifically? Like in a list or something?
> h_add, His202:+1 or so?
> And, it can be relevant at what atom a residue gets protonated: His can
> be protonated at Nd, or Ne or both. Is there a way to control this?
>
> On a more general note: what other smart hydrogen adding tools are there
> out there anyway? Does anyone know a really smart tool for this? I know
> OpenBabel has a pH parameter. But on the other hand OpenBabel just
> appends the hydrogens to the PDB file, whereas PyMOL really writes them
> within the block of atoms corresponding to one residue.
> Also, AutoDock can add hydrogens and it even has an option for the
> protonation state of histidine, but it doesn't seem to work in my case.
>
> Thanks for your answers and input.
> martin
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Adding Hydrogens

[Martin H. <ma...@bl...>]

Dear all, thanks for the feedback, I'll definitely give it a try.





On 16.03.11 16:50, Michael Lerner wrote:
> I've had good results with MolProbity 
> (http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15 
> <http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15>) 
> in the past.
>
> I had a script that would let me cycle through all of the HIS 
> residues, add hydrogens, and cycle between states. It's broken at the 
> moment. The trick was that PyMOL doesn't care about the name of the 
> residue, so you have to manually cycle the valences.
>
> On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger <ma...@bl... 
> <mailto:ma...@bl...>> wrote:
>
>     Dear All
>     I would like to ask if the PyMOL function to add hydrogens to an
>     entire
>     protein also has options, meaning is it possible to set the
>     protonation
>     state of individual residues specifically? Like in a list or
>     something?
>     h_add, His202:+1 or so?
>     And, it can be relevant at what atom a residue gets protonated:
>     His can
>     be protonated at Nd, or Ne or both. Is there a way to control this?
>
>     On a more general note: what other smart hydrogen adding tools are
>     there
>     out there anyway? Does anyone know a really smart tool for this? I
>     know
>     OpenBabel has a pH parameter. But on the other hand OpenBabel just
>     appends the hydrogens to the PDB file, whereas PyMOL really writes
>     them
>     within the block of atoms corresponding to one residue.
>     Also, AutoDock can add hydrogens and it even has an option for the
>     protonation state of histidine, but it doesn't seem to work in my
>     case.
>
>     Thanks for your answers and input.
>     martin
>
>     ------------------------------------------------------------------------------
>     Colocation vs. Managed Hosting
>     A question and answer guide to determining the best fit
>     for your organization - today and in the future.
>     http://p.sf.net/sfu/internap-sfd2d
>     _______________________________________________
>     PyMOL-users mailing list (PyM...@li...
>     <mailto:PyM...@li...>)
>     Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>     Archives:
>     http://www.mail-archive.com/pym...@li...
>
>
>
>
> -- 
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Problem reading multiframe pdb file for animation

[Jason V. <jas...@sc...>]

Hi Peter,

> When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has
> 40 coordinate sets (each is one frame in an animation) each beginning
> with:
> HEADER  Output iset=     n "xxxx_G=r_0_01"

Please replace your HEADER stamps with REMARK in your PDB file.  Then
load with multiplex=0.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120