date:20111206

Re: [PyMOL] Electrostatic calculations with ligand bound

2011-12-06 Thread Troels Emtekær Linnet

Hi Andrew.

I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin

During my trials, I notified two things for autodock.
It did not like "funny atom names" or "Alternative configuration"

Could this be a case for your protein / ligand?
I don't know if is the same for the APBS plugin, but you could try?
http://www.pymolwiki.org/index.php/Autodock_plugin#Example_1_-_Rename_of_funny_atom_names

Some of the "preparation" scripts for both plugins are coming from the same
research groups.
I think they both use: pdb2pqr or something.

Best
Troels

2011/12/7 Michael Lerner 

> Hi Andrew,
>
> The main limitation for problems like this is that you need to have
> parameters for the ligand. Making sure that you have "good" parameters
> is often an expert-level topic, and you're probably best served by the
> APBS or PDB2PQR listservs as well as the literature ... but, you can
> get a decent start on things with PDB2PQR itself. See
> http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization
> for some good starting instructions. Once you have a PQR file that
> includes both the protein and the ligand, the PyMOL/APBS plugin should
> do everything that you need.
>
> If that doesn't solve your problem, please let me know.
>
> Cheers,
> -Michael
>
> On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew
>  wrote:
> > Hey guys,
> >
> > I am trying to calculate electrostatics with a ligand bound to my
> molecule using ABPS.  I am not having success.  Everything I've read seems
> to say that this is a normal limitation with APBS, and I've tried other
> programs to no avail.  I have not been able to rebuild my molecule in the
> "correct format" either.  Any help here is greatly appreciated.
> >
> > Andrew
> > UMass Med School, Worcester, MA
> >
> >
> --
> > All the data continuously generated in your IT infrastructure
> > contains a definitive record of customers, application performance,
> > security threats, fraudulent activity, and more. Splunk takes this
> > data and makes sense of it. IT sense. And common sense.
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> --
> Michael Lerner
> Department of Physics and Astronomy
> Earlham College - Drawer 111
> 801 National Road West
> Richmond, IN   47374-4095
>
>
> --
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Re: [PyMOL] Electrostatic calculations with ligand bound

2011-12-06 Thread Michael Lerner

Hi Andrew,

The main limitation for problems like this is that you need to have
parameters for the ligand. Making sure that you have "good" parameters
is often an expert-level topic, and you're probably best served by the
APBS or PDB2PQR listservs as well as the literature ... but, you can
get a decent start on things with PDB2PQR itself. See
http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization
for some good starting instructions. Once you have a PQR file that
includes both the protein and the ligand, the PyMOL/APBS plugin should
do everything that you need.

If that doesn't solve your problem, please let me know.

Cheers,
-Michael

On Tue, Nov 29, 2011 at 11:44 AM, Malaby, Andrew
 wrote:
> Hey guys,
>
> I am trying to calculate electrostatics with a ligand bound to my molecule 
> using ABPS.  I am not having success.  Everything I've read seems to say that 
> this is a normal limitation with APBS, and I've tried other programs to no 
> avail.  I have not been able to rebuild my molecule in the "correct format" 
> either.  Any help here is greatly appreciated.
>
> Andrew
> UMass Med School, Worcester, MA
>
> --
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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-- 
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Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095

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Re: [PyMOL] H-bonds representation

2011-12-06 Thread James Starlight

Dear all :)

I want to find Hbonds beetween different helices in the membrane receptor (
H bonds beetween sidechains only)

I know possible way to do it wihin selection if I defined different helixes
but is there any way to find almost all Hbonds between polar sidecains
groups ?

Could I use

 find-> polar contact-> sidechain only
for this purpose ?

James

2011/11/30 Jason Vertrees 

> James,
>
> > It works quite well in case of not very compliated ligands ( e.g bonds
> > beetween aa-tRNA and the  aa-tRNA syntase were correct ) but in the
> > sugar-bound enzyme there were some mistakes in representation of the
> H-bonds
> > netween water/ligand/active center ( some water also partisipate in the
> > ligand binding but in case where water and some residues of the active
> sites
> > were positioned iclosely the bonds were incorect ). So a I understood I
> can
> > fix this mistakes only manually ?
>
> Please ask the pymol-users about this.
>
>
> > By the way, on what assumptions helix elements of my proteins were
> colored
> > after representation of the ligand binding with the cartoons ?
>
> It's colored rainbow from start to end.
>
>
> > Finally how I could represent ionic contacts in the ion-binding proteins
> ?
> > E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've
> > tried to represent bonds beetwen some polar residues of the active site
> with
> > the ligand but failed :(
>
> Please ask the pymol-users about this.
>
> I'm gearing up for the PyMOL v1.5.0 release, so I won't have time
> right now to personally answer your questions. Please keep relying on
> the pymol-users list--they're very knowledgeable about PyMOL.
>
> Cheers,
>
> -- Jason
>
>
>
>
> > 2011/11/29 Jason Vertrees 
> >>
> >> James,
> >>
> >> > Is there any semi-avtomated way to find ligand binding pocket and do
> all
> >> > such things ?
> >>
> >> For your given object, click A > preset > ligands sites > cartoon. Try
> >> other options under that menu.
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >>
> >> > 2011/11/28 Thomas Holder 
> >> >>
> >> >> Hi James,
> >> >>
> >> >> most trivial manner:
> >> >>
> >> >> as cartoon
> >> >> show sticks, resn LEU+ILE+VAL
> >> >> set cartoon_side_chain_helper
> >> >>
> >> >> and eventually something like this:
> >> >>
> >> >> show spheres, resn LEU+ILE+VAL and not name N+O+C
> >> >> set sphere_transparency, 0.5
> >> >>
> >> >>
> >> >> Cheers,
> >> >>  Thomas
> >> >>
> >> >> On 11/28/2011 02:58 PM, James Starlight wrote:
> >> >>>
> >> >>> Another question also linked with the non-covalent interaction.
> >> >>>
> >> >>> In particular I wounder to know how i Could represent all
> hydrophobic
> >> >>> (
> >> >>> Ley Ile Val etc) sidechains in my proteins in most trivial manner?
> I'd
> >> >>> like to represent the hydrophobic core of the proteins made from
> those
> >> >>> residues.
> >> >>>
> >> >>> Thanks,
> >> >>>
> >> >>> James
> >> >>
> >> >> --
> >> >> Thomas Holder
> >> >> MPI for Developmental Biology
> >> >> Spemannstr. 35
> >> >> D-72076 Tübingen
> >> >
> >> >
> >> >
> >> >
> --
> >> > All the data continuously generated in your IT infrastructure
> >> > contains a definitive record of customers, application performance,
> >> > security threats, fraudulent activity, and more. Splunk takes this
> >> > data and makes sense of it. IT sense. And common sense.
> >> > http://p.sf.net/sfu/splunk-novd2d
> >> > ___
> >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >> >
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
> >
> >
> >
> >
> --
> > All the data continuously generated in your IT infrastructure
> > contains a definitive record of customers, application performance,
> > security threats, fraudulent activity, and more. Splunk takes this
> > data and makes sense of it. IT sense. And common sense.
> > http://p.sf.net/sfu/splunk-novd2d
> > ___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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Re: [PyMOL] Electron Density

2011-12-06 Thread Dirk Kostrewa


Hi Manas Sule,

this is a bit more complicated:

For PyMOL, you usually calculate an electron density map covering your 
molecule. As far as I understand PyMOL, the sigma is taken directly from 
your input map.


For Coot, this is completely different. Coot tries to reconstruct from 
your input map the complete map for the unit cell taking the 
crystallographic symmetry into account (using it for displaying an 
"infinite" map), and calculates the sigma from the unit cell map. This 
already might be different to the sigma within the box that you used to 
cover your molecule. However, if the reconstruction fails, either 
because the symmetry of your map is wrong (i.e., P1), or the input box 
is too small to allow reconstruction of the whole unit cell, the rest of 
the unit cell is filled with "0", resulting in much smaller sigma values!
If this happens, you have to display the input map at a much higher 
sigma level in Coot to get the same absolute electron density value and 
thus appearance. Apparently, this is the case for your map.


To get the sigma value right, you should calculate a map covering either 
the asymmetric unit with the right symmetry or covering the whole unit 
cell. Then, run a peak search program, like CCP4 peakmax, or play 
visually with the sigma value using that map - it should be same in 
PyMOL and in Coot, then.


Best regards,

Dirk.

Am 06.12.11 15:12, schrieb Manas Sule:

Is there a difference in the sigma values assigned by pymol and coot
I am able to see the density at 8 sigma in coot for the Fo-Fc map but 
can go to maximum at 4.5 sigma in pymol after which it disappears


On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett > wrote:


I think the isomesh command will let you set whatever contour
level you wish, e.g.:

isomesh map, mymap.map, X.X, maparea

Where map is the name of the mesh object, mymap.map is the map
file name, X.X is the desired contour level, and maparea, is the
selection about which you would like to see the electron density
mesh. I haven't tested the contour limits, but it's larger than 10.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu 

On 12/5/2011 12:49 PM, Manas Sule wrote:

I have tried that...but i can see the density in coot at  even 8
sigma.. however the maximum i can go to in pymol is 4.5 simga on
a F0-Fc map
Can u suggest any method to see the same density at 6 sigma

Manas

On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer mailto:pame...@mcw.edu>> wrote:

isomesh [mesh name], [map name], 6.0





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***
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G

Re: [PyMOL] Electron Density

2011-12-06 Thread Thomas Holder

Hi Manas,

have you tried turning the normalize_* setting off?

set normalize_ccp4_maps, off
set normalize_o_maps, off
set normalize_grd_maps, off

http://pymolwiki.org/index.php/Normalize_ccp4_maps
http://pymolwiki.org/index.php/Display_CCP4_Maps#User_Notes

Cheers,
   Thomas

On 12/06/2011 03:12 PM, Manas Sule wrote:
> Is there a difference in the sigma values assigned by pymol and coot
> I am able to see the density at 8 sigma in coot for the Fo-Fc map but
> can go to maximum at 4.5 sigma in pymol after which it disappears

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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Re: [PyMOL] Electron Density

2011-12-06 Thread Manas Sule

Is there a difference in the sigma values assigned by pymol and coot
I am able to see the density at 8 sigma in coot for the Fo-Fc map but can
go to maximum at 4.5 sigma in pymol after which it disappears

On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett  wrote:

>  I think the isomesh command will let you set whatever contour level you
> wish, e.g.:
>
> isomesh map, mymap.map, X.X, maparea
>
> Where map is the name of the mesh object, mymap.map is the map file name,
> X.X is the desired contour level, and maparea, is the selection about which
> you would like to see the electron density mesh. I haven't tested the
> contour limits, but it's larger than 10.
>
> ___
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: rrowl...@colgate.edu
>
> On 12/5/2011 12:49 PM, Manas Sule wrote:
>
> I have tried that...but i can see the density in coot at  even 8 sigma..
> however the maximum i can go to in pymol is 4.5 simga on a F0-Fc map
> Can u suggest any method to see the same density at 6 sigma
>
>  Manas
>
> On Mon, Dec 5, 2011 at 11:14 PM, Pete Meyer  wrote:
>
>> isomesh [mesh name], [map name], 6.0
>>
>>
>>
>
> --
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common 
> sense.http://p.sf.net/sfu/splunk-novd2d
>
>
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
>
> --
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
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Re: [PyMOL] mmView - a tool for mmCIF exploration

2011-12-06 Thread Daniel Svozil

Hi Troels,

mmView is intended as a web-based viewer (and nothing more) of the
textual mmCIF format, which i used by the PDB database as its archival
format. mmCIF offers, with its flexible syntax, much better solution
for storing biomolecular structures than the PDB format. However,
mmCIF format is primarily intended for automatic processing, and is
thus, in contrary to PDB format, much less readable by human.

The data in the mmCIF format are stored as database tables (called
categories), and our tool tries to facilitate the work with mmCIF
files. All data shown by mmView are taken from the mmCIF file with the
only exception, which is the abstract of the structure citation that
is downloaded automatically from Pubmed database.

Sure there is overlap with Proteopedia, however Proteopedia's aim is
apparently to provide as much information about the given structure as
possible (and there is much much more information in Proteopedia than
in mmView, and certainly some information in Proteopedia is obtained
from the mmCIF or PDB file). The aim of mmView is to present mmCIF
categories in more readable form, and in addition some information
about the structure we regard as interesting is aggregated from more
categorie and presented in a summary form.

We use mmView in the classes of structural biology and structural
bioinformatics, and our experience shows that students grasp much
easily basic principles of the mmCIF format if it is presented this
way.

More information about mmView you can find in the BMC Rasearch Notes
journal: http://www.biomedcentral.com/content/pdf/1756-0500-4-121.pdf.

Regards
  Daniel

2011/12/6 Troels Emtekær Linnet :
> That reminds me of:
>
> http://www.proteopedia.org/wiki/index.php/4ins
>
> What is the difference between the two web pages?
>
> Best
> Troels
>
>
> 2011/12/6 Daniel Svozil 
> mailto:daniel.svo...@vscht.cz>>
> Dear colleagues,
>
> We would like to announce the availability of mmView - the web-based
> application which allows to comfortably explore the structural data of
> biomacromolecules stored in the mmCIF (macromolecular Crystallographic
> Information File) format. The mmView software system is primarily
> intended for educational purposes but it can also serve as an
> auxiliary tool for working with biomolecular structures.
>
> The mmView application is offered in two flavors: as a publicly
> available web server http://ich.vscht.cz/projects/mmview/, and as an
> open-source stand-alone application (available from
> http://sourceforge.net/projects/mmview) that can be installed on the
> user’s computer.
>
> Petr Cech and Daniel Svozil
>
> --
> Daniel Svozil, PhD
> Head of Laboratory of Informatics and Chemistry
> Institute of Chemical Technology
> Czech Republic
>
> phone: +420 220 444 391
> http://ich.vscht.cz/~svozil
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point of
> discussion for anyone considering optimizing the pricing and packaging model
> of a cloud services business. Read Now!
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> ___
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> (PyMOL-users@lists.sourceforge.net)
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-- 
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Head of Laboratory of Informatics and Chemistry
Institute of Chemical Technology
Czech Republic

phone: +420 220 444 391
http://ich.vscht.cz/~svozil

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Re: [PyMOL] mmView - a tool for mmCIF exploration

2011-12-06 Thread Troels Emtekær Linnet

That reminds me of:

http://www.proteopedia.org/wiki/index.php/4ins

What is the difference between the two web pages?

Best
Troels


2011/12/6 Daniel Svozil 

> Dear colleagues,
>
> We would like to announce the availability of mmView - the web-based
> application which allows to comfortably explore the structural data of
> biomacromolecules stored in the mmCIF (macromolecular Crystallographic
> Information File) format. The mmView software system is primarily
> intended for educational purposes but it can also serve as an
> auxiliary tool for working with biomolecular structures.
>
> The mmView application is offered in two flavors: as a publicly
> available web server http://ich.vscht.cz/projects/mmview/, and as an
> open-source stand-alone application (available from
> http://sourceforge.net/projects/mmview) that can be installed on the
> user’s computer.
>
> Petr Cech and Daniel Svozil
>
> --
> Daniel Svozil, PhD
> Head of Laboratory of Informatics and Chemistry
> Institute of Chemical Technology
> Czech Republic
>
> phone: +420 220 444 391
> http://ich.vscht.cz/~svozil
>
>
> --
> Cloud Services Checklist: Pricing and Packaging Optimization
> This white paper is intended to serve as a reference, checklist and point
> of
> discussion for anyone considering optimizing the pricing and packaging
> model
> of a cloud services business. Read Now!
> http://www.accelacomm.com/jaw/sfnl/114/51491232/
> ___
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[PyMOL] mmView - a tool for mmCIF exploration

2011-12-06 Thread Daniel Svozil

Dear colleagues,

We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
intended for educational purposes but it can also serve as an
auxiliary tool for working with biomolecular structures.

The mmView application is offered in two flavors: as a publicly
available web server http://ich.vscht.cz/projects/mmview/, and as an
open-source stand-alone application (available from
http://sourceforge.net/projects/mmview) that can be installed on the
user’s computer.

Petr Cech and Daniel Svozil

-- 
Daniel Svozil, PhD
Head of Laboratory of Informatics and Chemistry
Institute of Chemical Technology
Czech Republic

phone: +420 220 444 391
http://ich.vscht.cz/~svozil

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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-06 Thread grantaka36

Dear Thomas,

Thanks for good pointing for the weird problem, which I couldn't notice at all.

> You do compile with -D_FORTIFY_SOURCE=2, could you remove that?
I'm afraid, I know not related PyMOL itself, but I wish to know how to
do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with
the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches.

And Zhijian and Andreas,

Thank you for advices through your experiences, I will pursue at first
as Thomas advised.

Regards,
Masataka


2011/12/5 Andreas Förster :
> Dear Masataka,
>
> a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1.  If
> version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I
> would urge you, to upgrade as well.  RHEL and CentOS are rock-solid
> operating systems, but their libraries and dependencies show their age.
>
>
> Andreas
>
>
>
> On 05/12/2011 1:50, grantaka36 wrote:
>>
>> Hi, Marius, Troels and David,
>>
>> I appreciate very much for guiding, tried in three ways but no success
>> currently.
>>
>> - I also think some difference on distributions (CentOS 5 here,) trapped
>> at
>>>
>>> function 'IsosurfGetRange'
>>
>> Does anyone have information to workaround?
>> - Do you think if any dependency on Python version (2.4.3 here)?
>>
>> Attached '20111205_script_and_error.zip' is for information sharing:
>> - 'install_pymol.sh' : followed by below, some package name modified for
>> CentOS
>>
>> http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
>> - 'install_pymol_sh_error.txt'
>>>
>>> layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro
>>> "fprintf"
>>> layer0/Isosurf.c: In function 'IsosurfGetRange':
>>
>>
>> - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5
>> instead of 4.4
>> - 'install_pymol_gcc45_sh_error.txt'
>>>
>>> layer0/Isosurf.c: In function 'IsosurfGetRange':
>>> layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
>>> "fprintf"
>>
>>
>> - 'compile_pymol.sh' : again by initial trying
>> http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source
>> - 'compile_pymol_sh_error.txt'
>>>
>>> layer0/Isosurf.c: In function 'IsosurfGetRange':
>>> layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro
>>> "fprintf"
>>
>>
>>
>> Regards,
>> Masataka
>>
>>
> --
>        Andreas Förster, Research Associate
>        Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>            http://www.msf.bio.ic.ac.uk

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Re: [PyMOL] Electrostatic calculations with ligand bound

Re: [PyMOL] Electrostatic calculations with ligand bound

Re: [PyMOL] H-bonds representation

Re: [PyMOL] Electron Density

Re: [PyMOL] Electron Density

Re: [PyMOL] Electron Density

Re: [PyMOL] mmView - a tool for mmCIF exploration

Re: [PyMOL] mmView - a tool for mmCIF exploration

[PyMOL] mmView - a tool for mmCIF exploration

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

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