pymol-users Mailing List for PyMOL Molecular Graphics System

Hi James,

retarding ordering of atoms, set this before loading the file:

set retain_order, 1

See also:
http://pymolwiki.org/index.php/Retain_order

The atom names should actually not be changed, what did you do exactly?

Cheers,
   Thomas

James Starlight wrote, On 06/28/12 09:50:
> Dear Pymol Users!
> 
> I've forced with the problem of missing correct atom numbering order 
> during processing of my pbd structure.
> 
> 
> E.g I had a mollecule of caffein where each atoms had its own number ( 
> e.g N1 or N3 etc)
> 
> HETATM 2252  N1  CFF A 330       9.174 -33.156 -31.881  
> 1.00147.73           N 
> HETATM 2253  C2  CFF A 330       9.511 -33.973 -32.948  
> 1.00148.15           C 
> HETATM 2254  C10 CFF A 330      10.180 -32.790 -30.862  
> 1.00138.32           C 
> HETATM 2255  C6  CFF A 330       7.880 -32.698 -31.748  
> 1.00147.40           C 
> HETATM 2256  N3  CFF A 330       8.560 -34.329 -33.882  
> 1.00149.30           N 
> HETATM 2257  O11 CFF A 330      10.781 -34.432 -33.079  
> 1.00142.40           O 
> HETATM 2258  C12 CFF A 330       8.923 -35.204 -35.004  
> 1.00147.42           C 
> HETATM 2259  C4  CFF A 330       7.287 -33.864 -33.735  
> 1.00146.85           C 
> HETATM 2260  C5  CFF A 330       6.925 -33.068 -32.699  
> 1.00145.81           C 
> HETATM 2261  N9  CFF A 330       6.240 -34.112 -34.550  
> 1.00147.23           N 
> HETATM 2262  O13 CFF A 330       7.552 -31.908 -30.705  
> 1.00147.52           O 
> HETATM 2263  N7  CFF A 330       5.617 -32.775 -32.828  
> 1.00147.22           N 
> HETATM 2264  C8  CFF A 330       5.235 -33.422 -33.954  
> 1.00148.06           C 
> HETATM 2265  C14 CFF A 330       4.727 -31.975 -31.994  
> 1.00145.92           C 
> 
> as the consequence I've obtained pdb of this molecule with changing atom 
> order and (that is expesiaaly crusial ) missing atom names
> 
> ATOM   3076  N   CFF A 309      34.653  29.507  62.240  1.00  
> 0.00           N 
> ATOM   3077  N   CFF A 309      34.101  31.995  64.970  1.00  
> 0.00           N 
> ATOM   3078  N   CFF A 309      34.561  30.167  66.245  1.00  
> 0.00           N 
> ATOM   3079  N   CFF A 309      34.804  28.565  64.396  1.00  
> 0.00           N 
> ATOM   3080  C   CFF A 309      34.394  30.795  62.724  1.00  
> 0.00           C 
> ATOM   3081  C   CFF A 309      34.844  28.368  63.031  1.00  
> 0.00           C 
> ATOM   3082  C   CFF A 309      34.674  29.255  60.791  1.00  
> 0.00           C 
> ATOM   3083  C   CFF A 309      34.304  30.906  64.146  1.00  
> 0.00           C 
> ATOM   3084  C   CFF A 309      33.873  33.404  64.619  1.00  
> 0.00           C 
> ATOM   3085  C   CFF A 309      34.302  31.471  66.198  1.00  
> 0.00           C 
> ATOM   3086  C   CFF A 309      34.489  29.789  64.952  1.00  
> 0.00           C 
> ATOM   3087  C   CFF A 309      34.554  27.304  65.108  1.00  
> 0.00           C 
> ATOM   3088  O   CFF A 309      33.999  31.682  61.969  1.00  
> 0.00           O 
> ATOM   3089  O   CFF A 309      35.172  27.317  62.481  1.00  
> 0.00           O 
> ATOM   3090  H   CFF A 309      34.383  32.108  67.079  1.00  
> 0.00           H 
> 
> in the second example you can see that all Nitrogens are just N without 
> numbers etc.
> 
> 1- Does it possible to resutn to the second pdb file initial correct 
> atom numbering ?
> 2- How I could prevent in future deleating of such numbers ? (It's 
> occured after I add missing Hydrogens and connect enties to my mollecule 
> by PYMOL)
> 
> 
> Thanks for help,
> 
> James

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

Dear Pymol Users!


I've forced with the problem of missing correct atom numbering order during
processing of my pbd structure.


E.g I had a mollecule of caffein where each atoms had its own number ( e.g
N1 or N3 etc)

HETATM 2252  N1  CFF A 330       9.174 -33.156 -31.881
1.00147.73           N
HETATM 2253  C2  CFF A 330       9.511 -33.973 -32.948
1.00148.15           C
HETATM 2254  C10 CFF A 330      10.180 -32.790 -30.862
1.00138.32           C
HETATM 2255  C6  CFF A 330       7.880 -32.698 -31.748
1.00147.40           C
HETATM 2256  N3  CFF A 330       8.560 -34.329 -33.882
1.00149.30           N
HETATM 2257  O11 CFF A 330      10.781 -34.432 -33.079
1.00142.40           O
HETATM 2258  C12 CFF A 330       8.923 -35.204 -35.004
1.00147.42           C
HETATM 2259  C4  CFF A 330       7.287 -33.864 -33.735
1.00146.85           C
HETATM 2260  C5  CFF A 330       6.925 -33.068 -32.699
1.00145.81           C
HETATM 2261  N9  CFF A 330       6.240 -34.112 -34.550
1.00147.23           N
HETATM 2262  O13 CFF A 330       7.552 -31.908 -30.705
1.00147.52           O
HETATM 2263  N7  CFF A 330       5.617 -32.775 -32.828
1.00147.22           N
HETATM 2264  C8  CFF A 330       5.235 -33.422 -33.954
1.00148.06           C
HETATM 2265  C14 CFF A 330       4.727 -31.975 -31.994
1.00145.92           C

as the consequence I've obtained pdb of this molecule with changing atom
order and (that is expesiaaly crusial ) missing atom names

ATOM   3076  N   CFF A 309      34.653  29.507  62.240  1.00
0.00           N
ATOM   3077  N   CFF A 309      34.101  31.995  64.970  1.00
0.00           N
ATOM   3078  N   CFF A 309      34.561  30.167  66.245  1.00
0.00           N
ATOM   3079  N   CFF A 309      34.804  28.565  64.396  1.00
0.00           N
ATOM   3080  C   CFF A 309      34.394  30.795  62.724  1.00
0.00           C
ATOM   3081  C   CFF A 309      34.844  28.368  63.031  1.00
0.00           C
ATOM   3082  C   CFF A 309      34.674  29.255  60.791  1.00
0.00           C
ATOM   3083  C   CFF A 309      34.304  30.906  64.146  1.00
0.00           C
ATOM   3084  C   CFF A 309      33.873  33.404  64.619  1.00
0.00           C
ATOM   3085  C   CFF A 309      34.302  31.471  66.198  1.00
0.00           C
ATOM   3086  C   CFF A 309      34.489  29.789  64.952  1.00
0.00           C
ATOM   3087  C   CFF A 309      34.554  27.304  65.108  1.00
0.00           C
ATOM   3088  O   CFF A 309      33.999  31.682  61.969  1.00
0.00           O
ATOM   3089  O   CFF A 309      35.172  27.317  62.481  1.00
0.00           O
ATOM   3090  H   CFF A 309      34.383  32.108  67.079  1.00
0.00           H

in the second example you can see that all Nitrogens are just N without
numbers etc.

1- Does it possible to resutn to the second pdb file initial correct atom
numbering ?
2- How I could prevent in future deleating of such numbers ? (It's occured
after I add missing Hydrogens and connect enties to my mollecule by PYMOL)


Thanks for help,

James

Hi Thomas,


I wounder to know what corrections should I add to the below selection in
case of multi state object

remove solvent beyond 3.5 of polymer

e.g I'm working with the MD trajectory saved in PDB format. I've decided to
deleate all solvent from all 100 frames simultaneously but the above
command works fine only in case of 1 state object .


James


2012/4/26 Thomas Holder <sp...@us...>

> Hi Martin & James,
>
> is it just a coincident that you both ask almost the same question?
>
> You could remove all water atoms with few protein contacts or with a small
> surface area. For example:
>
> remove solvent beyond 3.5 of polymer
> set dot_solvent
> get_area solvent, load_b=1
> remove solvent and b > 20
>
> Hope that helps.
>
> Cheers,
>  Thomas
>
> On 04/26/2012 10:55 AM, James Starlight wrote:
>
>> Another question- I have my protein.pdb with some inserted crystall
>> waters within protein interiour as well as water surrounded of my
>> protein. I want to remove only sorrounding water but prevent internal
>> water ( wich could be functional relevant ).
>>
>> How I could to select such surrounded water ( e.g via some cutoff
>> radius relative my protein etc) wich I'd like to remove further ?
>>
>
> On 04/25/2012 05:34 PM, Martin Hediger wrote:
>
>> In a crystal structure, there are usually a number of relevant crystal
>> waters, as well as water molecules on the surface. In our approach, we
>> model the protein structure within a dielectric continuum, so surface
>> water molecules are not required (to save computer time). However,
>> waters in the interior should remain in our model. How could we discard
>> the surface waters while keeping the internal waters?
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

Dear Christian,

thank you for infromation- I'll examine this software. In particular I'm
looking for possible modules for pymol because as I've found previously
it's a good visualisation of the surfaces wich have been already included
in PyMol.



2012/6/28 Christian Roth <chr...@bb...>

>
>
> By the way, there are already comments about the internal waters from the
> pose-view group?
>

yes, I've told with the pose view developers and they said that there have
no options to include buried water yet. So the LigProt software is the best
sollution for 2D diaagrams as yet.

Dear James.

I found the hollow script and/or Castp quite useful for this. There exist also 
a program called surfplot, from Roman Laskowski again. It is integrated in the 
pdbsum interface and creates ther surfaces. You may look there for examples. 
Another possibility is Voidoo from Uppsala. 

By the way, there are already comments about the internal waters from the 
pose-view group?

Best Regards 

Christian

Am Donnerstag 28 Juni 2012 07:53:31 schrieb James Starlight:
> I've obtained accademical licence on LigProt and I found that this
> softwatre is most handfull in the 2d analysis of protein-ligand
> interactions. Is it possible to integrate it into pymol  what have been
> done in case of Pose view ? )
> 
> By the way does anybody know any another intresting software or pymol
> modules for the analysis of protein-ligand interactions. In particular I'd
> like to obtain 3d surfaces of vdw as well as electrosctatics profiles of
> the active sites of my proteins as well as analysing of H-bonds ?
> 
> 
> James
> 
> 2012/6/26 James Starlight <jms...@gm...>
> 
> > I'm still waiting for accademical license on lig prot. By the way it's
> > very strange that PoseView have not been accompanied with 'internal water
> > detector' ;) i've sent  the letter to developers with this question and
> > hope they can help
> >
> > James
> >
> > 2012/6/26 Thomas Holder <sp...@us...>
> >
> >> Hi James,
> >>
> >> hm, looks like PoseView ignores all water molecules :(
> >>
> >> Have you tried LigPlot? It has a "-w" option to include waters.
> >>
> >> Cheers,
> >>  Thomas
> >>
> >> On 06/26/2012 05:11 PM, James Starlight wrote:
> >>> Thomas,
> >>> Its really great )
> >>> Could you tell me if you find a possible way to take into account
> >>> burried water from the protein interiour in the Pose View
> >>> protein-ligand interaction 2D plots ?
> >>> Most of my proteins consist of such internal water ( like a het atoms
> >>> in the protein.pdb ) but pose view didnt take this mollecules into
> >>> account so the final plot lack of many crussial h_bonds between ligand
> >>> and protein itself.
> >>> James
> >>> 2012/6/26 Thomas Holder <sp...@us...
> >>> <mailto:speleo3@users.**sourceforge.net
> >>> <sp...@us...>>>
> >>>
> >>>
> >>>
> >>>    Hi all,
> >>>
> >>>    I thought it would be nice to run such tools directly from PyMOL. So
> >>>    there is a PoseView wrapper on the PyMOLWiki now:
> >>>
> >>>   
> >>> http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.ph
> >>>p/PoseView>
> >>>
> >>>    A LigPlot wrapper may follow...
> >>>
> >>>    Cheers,
> >>>       Thomas
> >>>
> >>>    On 06/26/2012 10:13 AM, James Starlight wrote:
> >>>     > Christian,
> >>>     > Also I've found the same software- pose view (in that article
> >>>
> >>>    I've also
> >>>
> >>>     > found link on it). Its very friendly but I've noticed some erorrs
> >>>
> >>>    during
> >>>
> >>>     > representation of the non-covalent contacts partly in case of the
> >>>
> >>> vdw
> >>>
> >>>     > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw
> >>>
> >>>    but some
> >>>
> >>>     > crussial interactions could not be visualized)
> >>>     > And the main disadvantage of that software is that it does not
> >>>
> >>>    take into
> >>>
> >>>     > account burrial water and it's h-bond networks within protein.
> >>>     > I've ordered free license on the lig prot and hope that this
> >>>
> >>> software
> >>>
> >>>     > will be better ;)
> >>>     > James
> >>>     > 2012/6/26 Christian Roth
> >>>     > <chr...@bb...-**leipzig.de<chr...@bb...-leipz
> >>>     >ig.de>
> >>>
> >>>   
> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...-leip
> >>>zig.de>
> >>>
> >>>     > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...
> >>>     >i-leipzig.de>
> >>>
> >>>   
> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...-leip
> >>>zig.de>
> >>>
> >>>     >     Hi James,
> >>>     >
> >>>     >     LigPlot is free for academic users. You just have to verify
> >>>
> >>>    that you
> >>>
> >>>     >     are a
> >>>     >     academic user. MOE does a simimlar representiation but is
> >>>
> >>>    definitely
> >>>
> >>>     >     not free.
> >>>     >
> >>>     >     Christian
> >>
> >> --
> >> Thomas Holder
> >> MPI for Developmental Biology
> >> Spemannstr. 35
> >> D-72076 Tübingen
> 


-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319

I've obtained accademical licence on LigProt and I found that this
softwatre is most handfull in the 2d analysis of protein-ligand
interactions. Is it possible to integrate it into pymol  what have been
done in case of Pose view ? )

By the way does anybody know any another intresting software or pymol
modules for the analysis of protein-ligand interactions. In particular I'd
like to obtain 3d surfaces of vdw as well as electrosctatics profiles of
the active sites of my proteins as well as analysing of H-bonds ?


James

2012/6/26 James Starlight <jms...@gm...>

> I'm still waiting for accademical license on lig prot. By the way it's
> very strange that PoseView have not been accompanied with 'internal water
> detector' ;) i've sent  the letter to developers with this question and
> hope they can help
>
> James
>
> 2012/6/26 Thomas Holder <sp...@us...>
>
>> Hi James,
>>
>> hm, looks like PoseView ignores all water molecules :(
>>
>> Have you tried LigPlot? It has a "-w" option to include waters.
>>
>> Cheers,
>>  Thomas
>>
>>
>> On 06/26/2012 05:11 PM, James Starlight wrote:
>>
>>> Thomas,
>>> Its really great )
>>> Could you tell me if you find a possible way to take into account
>>> burried water from the protein interiour in the Pose View protein-ligand
>>> interaction 2D plots ?
>>> Most of my proteins consist of such internal water ( like a het atoms in
>>> the protein.pdb ) but pose view didnt take this mollecules into account
>>> so the final plot lack of many crussial h_bonds between ligand and
>>> protein itself.
>>> James
>>> 2012/6/26 Thomas Holder <sp...@us...
>>> <mailto:speleo3@users.**sourceforge.net <sp...@us...>>>
>>>
>>>
>>>
>>>    Hi all,
>>>
>>>    I thought it would be nice to run such tools directly from PyMOL. So
>>>    there is a PoseView wrapper on the PyMOLWiki now:
>>>
>>>    " rel="nofollow">http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.php/PoseView>
>>>
>>>    A LigPlot wrapper may follow...
>>>
>>>    Cheers,
>>>       Thomas
>>>
>>>    On 06/26/2012 10:13 AM, James Starlight wrote:
>>>     > Christian,
>>>     > Also I've found the same software- pose view (in that article
>>>    I've also
>>>     > found link on it). Its very friendly but I've noticed some erorrs
>>>    during
>>>     > representation of the non-covalent contacts partly in case of the
>>> vdw
>>>     > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw
>>>    but some
>>>     > crussial interactions could not be visualized)
>>>     > And the main disadvantage of that software is that it does not
>>>    take into
>>>     > account burrial water and it's h-bond networks within protein.
>>>     > I've ordered free license on the lig prot and hope that this
>>> software
>>>     > will be better ;)
>>>     > James
>>>     > 2012/6/26 Christian Roth <chr...@bb...-**leipzig.de<chr...@bb...>
>>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>> >
>>>     > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>>
>>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>> >>>
>>>     >
>>>     >     Hi James,
>>>     >
>>>     >     LigPlot is free for academic users. You just have to verify
>>>    that you
>>>     >     are a
>>>     >     academic user. MOE does a simimlar representiation but is
>>>    definitely
>>>     >     not free.
>>>     >
>>>     >     Christian
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>

Martin,

Are you looking for a structure validator or a PDB file format validator?

Cheers,

-- Jason

On Wed, Jun 27, 2012 at 6:00 AM, Martin Hediger <ma...@bl...> wrote:
> Dear PyMOL users
> Does anybody know a script to verify that a file contains valid a valid
> PDB formatted structure?
> The file extension alone obviously does not provide sufficient validation.
>
> Thanks for any feedback.
> Martin
>
> ------------------------------------------------------------------------------
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> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

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

Hi Martin,

I might be missing something but a little more information might help as to what you want to do. agreed, a file extension can be changed to anything but viewing the text file should tell you the type (of coordinate file). If you are doing this in batch mode then I guess a script would help!

Joel

-----Original Message-----
From: Martin Hediger [mailto:ma...@bl...] 
Sent: Wednesday, 27 June 2012 10:01 p.m.
To: pym...@li...
Subject: [PyMOL] Verify PDB format

Dear PyMOL users
Does anybody know a script to verify that a file contains valid a valid PDB formatted structure?
The file extension alone obviously does not provide sufficient validation.

Thanks for any feedback.
Martin

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Hi,

What is the current status of Pymol with respect to O1P or OP1 atom labels in nucleic acid ?
The current PDB convention is OP1 and OP2.
Is there an option in pymol to save the coordinates with this convention ?

Thanks,

Pascal

-----
Pascal Auffinger
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex

p.a...@ib...
-----

Dear PyMOL users
Does anybody know a script to verify that a file contains valid a valid 
PDB formatted structure?
The file extension alone obviously does not provide sufficient validation.

Thanks for any feedback.
Martin

I'm still waiting for accademical license on lig prot. By the way it's very
strange that PoseView have not been accompanied with 'internal water
detector' ;) i've sent  the letter to developers with this question and
hope they can help

James

2012/6/26 Thomas Holder <sp...@us...>

> Hi James,
>
> hm, looks like PoseView ignores all water molecules :(
>
> Have you tried LigPlot? It has a "-w" option to include waters.
>
> Cheers,
>  Thomas
>
>
> On 06/26/2012 05:11 PM, James Starlight wrote:
>
>> Thomas,
>> Its really great )
>> Could you tell me if you find a possible way to take into account
>> burried water from the protein interiour in the Pose View protein-ligand
>> interaction 2D plots ?
>> Most of my proteins consist of such internal water ( like a het atoms in
>> the protein.pdb ) but pose view didnt take this mollecules into account
>> so the final plot lack of many crussial h_bonds between ligand and
>> protein itself.
>> James
>> 2012/6/26 Thomas Holder <sp...@us...
>> <mailto:speleo3@users.**sourceforge.net <sp...@us...>>>
>>
>>
>>
>>    Hi all,
>>
>>    I thought it would be nice to run such tools directly from PyMOL. So
>>    there is a PoseView wrapper on the PyMOLWiki now:
>>
>>    " rel="nofollow">http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.php/PoseView>
>>
>>    A LigPlot wrapper may follow...
>>
>>    Cheers,
>>       Thomas
>>
>>    On 06/26/2012 10:13 AM, James Starlight wrote:
>>     > Christian,
>>     > Also I've found the same software- pose view (in that article
>>    I've also
>>     > found link on it). Its very friendly but I've noticed some erorrs
>>    during
>>     > representation of the non-covalent contacts partly in case of the
>> vdw
>>     > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw
>>    but some
>>     > crussial interactions could not be visualized)
>>     > And the main disadvantage of that software is that it does not
>>    take into
>>     > account burrial water and it's h-bond networks within protein.
>>     > I've ordered free license on the lig prot and hope that this
>> software
>>     > will be better ;)
>>     > James
>>     > 2012/6/26 Christian Roth <chr...@bb...-**leipzig.de<chr...@bb...>
>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>> >
>>     > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>>
>>    <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...>
>> >>>
>>     >
>>     >     Hi James,
>>     >
>>     >     LigPlot is free for academic users. You just have to verify
>>    that you
>>     >     are a
>>     >     academic user. MOE does a simimlar representiation but is
>>    definitely
>>     >     not free.
>>     >
>>     >     Christian
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

Hi James,

hm, looks like PoseView ignores all water molecules :(

Have you tried LigPlot? It has a "-w" option to include waters.

Cheers,
   Thomas

On 06/26/2012 05:11 PM, James Starlight wrote:
> Thomas,
> Its really great )
> Could you tell me if you find a possible way to take into account
> burried water from the protein interiour in the Pose View protein-ligand
> interaction 2D plots ?
> Most of my proteins consist of such internal water ( like a het atoms in
> the protein.pdb ) but pose view didnt take this mollecules into account
> so the final plot lack of many crussial h_bonds between ligand and
> protein itself.
> James
> 2012/6/26 Thomas Holder <sp...@us...
> <mailto:sp...@us...>>
>
>     Hi all,
>
>     I thought it would be nice to run such tools directly from PyMOL. So
>     there is a PoseView wrapper on the PyMOLWiki now:
>
>     http://pymolwiki.org/index.php/PoseView
>
>     A LigPlot wrapper may follow...
>
>     Cheers,
>        Thomas
>
>     On 06/26/2012 10:13 AM, James Starlight wrote:
>      > Christian,
>      > Also I've found the same software- pose view (in that article
>     I've also
>      > found link on it). Its very friendly but I've noticed some erorrs
>     during
>      > representation of the non-covalent contacts partly in case of the vdw
>      > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw
>     but some
>      > crussial interactions could not be visualized)
>      > And the main disadvantage of that software is that it does not
>     take into
>      > account burrial water and it's h-bond networks within protein.
>      > I've ordered free license on the lig prot and hope that this software
>      > will be better ;)
>      > James
>      > 2012/6/26 Christian Roth <chr...@bb...
>     <mailto:chr...@bb...>
>      > <mailto:chr...@bb...
>     <mailto:chr...@bb...>>>
>      >
>      >     Hi James,
>      >
>      >     LigPlot is free for academic users. You just have to verify
>     that you
>      >     are a
>      >     academic user. MOE does a simimlar representiation but is
>     definitely
>      >     not free.
>      >
>      >     Christian

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

Thomas,

Its really great )

Could you tell me if you find a possible way to take into account burried
water from the protein interiour in the Pose View protein-ligand
interaction 2D plots ?
Most of my proteins consist of such internal water ( like a het atoms in
the protein.pdb ) but pose view didnt take this mollecules into account so
the final plot lack of many crussial h_bonds between ligand and protein
itself.


James
2012/6/26 Thomas Holder <sp...@us...>

> Hi all,
>
> I thought it would be nice to run such tools directly from PyMOL. So
> there is a PoseView wrapper on the PyMOLWiki now:
>
> http://pymolwiki.org/index.php/PoseView
>
> A LigPlot wrapper may follow...
>
> Cheers,
>   Thomas
>
> On 06/26/2012 10:13 AM, James Starlight wrote:
> > Christian,
> > Also I've found the same software- pose view (in that article I've also
> > found link on it). Its very friendly but I've noticed some erorrs during
> > representation of the non-covalent contacts partly in case of the vdw
> > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some
> > crussial interactions could not be visualized)
> > And the main disadvantage of that software is that it does not take into
> > account burrial water and it's h-bond networks within protein.
> > I've ordered free license on the lig prot and hope that this software
> > will be better ;)
> > James
> > 2012/6/26 Christian Roth <chr...@bb...
> > <mailto:chr...@bb...>>
> >
> >     Hi James,
> >
> >     LigPlot is free for academic users. You just have to verify that you
> >     are a
> >     academic user. MOE does a simimlar representiation but is definitely
> >     not free.
> >
> >     Christian
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi all,

I thought it would be nice to run such tools directly from PyMOL. So 
there is a PoseView wrapper on the PyMOLWiki now:

http://pymolwiki.org/index.php/PoseView

A LigPlot wrapper may follow...

Cheers,
   Thomas

On 06/26/2012 10:13 AM, James Starlight wrote:
> Christian,
> Also I've found the same software- pose view (in that article I've also
> found link on it). Its very friendly but I've noticed some erorrs during
> representation of the non-covalent contacts partly in case of the vdw
> interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some
> crussial interactions could not be visualized)
> And the main disadvantage of that software is that it does not take into
> account burrial water and it's h-bond networks within protein.
> I've ordered free license on the lig prot and hope that this software
> will be better ;)
> James
> 2012/6/26 Christian Roth <chr...@bb...
> <mailto:chr...@bb...>>
>
>     Hi James,
>
>     LigPlot is free for academic users. You just have to verify that you
>     are a
>     academic user. MOE does a simimlar representiation but is definitely
>     not free.
>
>     Christian

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

Christian,

Also I've found the same software- pose view (in that article I've also
found link on it). Its very friendly but I've noticed some erorrs during
representation of the non-covalent contacts partly in case of the vdw
interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some
crussial interactions could not be visualized)
And the main disadvantage of that software is that it does not take into
account burrial water and it's h-bond networks within protein.

I've ordered free license on the lig prot and hope that this software will
be better ;)


James
2012/6/26 Christian Roth <chr...@bb...>

> Hi James,
>
> LigPlot is free for academic users. You just have to verify that you are a
> academic user. MOE does a simimlar representiation but is definitely not
> free.
>
> Christian
>

Hi James,

LigPlot is free for academic users. You just have to verify that you are a 
academic user. MOE does a simimlar representiation but is definitely not free.  

Christian

Hi Christian!

As I understood that LigPlot is not free for accademical ussage isnt?

By the way in that paper
http://onlinelibrary.wiley.com.sci-hub.org/doi/10.1002/minf.201000167/pdf
there is exhaustive comparison of three different packages for such 2D
diagram generation. Have anybody used such software else ?


James

2012/6/26 Christian Roth <chr...@bb...>

> Hi James,
>
> the program you can use for this is ligplot from Roman Laskowski at the
> EBI.
> the solvent accessability shading is done with the help of naccess.
>
>
> Best Regards
>
> Christian
> Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie:
> > By the way
> >
> > in some papers I've seen  2D schematic diagrams of the protein-ligand
> > interactions.
> > The exapmle of such maps could be found here
> >
> http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-g
> > r4.jpg
> >
> >  Could you tell me examples of software wich could produce such maps?
> >
> >
> > Thanks
> >
> > James
> >
> > 2012/6/15 James Starlight <jms...@gm...>
> >
> > > Thomas, thanks this works perfect.
> > >
> > >
> > > Jason,  I've tested  this script on my system ( this is the membrane
> > > protein inserted in the bilayer surrounded by two water layers ( up and
> > > down ). During simulation individual water mollecules move into the
> > > protein interiour ( in that case protein like a water pore althought
> it's
> > > the receptor ) so I want to visualise only that buried water.
> > >
> > > I've tried to do it via find_buried_waters script both via ASA as well
> as
> > > in case when I've used small cutoffs ( 0.1) but the script selected too
> > > many waters ( e.g virtually all waters from up and down layers have
> been
> > > selected ). How I could specify this selection more carefully ?
> > >
> > > find_buried_waters 1, 0.1
> > >
> > >
> > > James
> > >
> > >
> > > 2012/6/12 Thomas Holder <sp...@us...>
> > >
> > >> This will show them in the same slot in group mode.
> > >>
> > >>
> > >> sorry, not "group mode" but "grid mode" of course.
> > >>
> > >>
> > >> --
> > >> Thomas Holder
> > >> MPI for Developmental Biology
> > >> Spemannstr. 35
> > >> D-72076 Tübingen
> >
>
>
>

Hi James,

the program you can use for this is ligplot from Roman Laskowski at the EBI. 
the solvent accessability shading is done with the help of naccess. 


Best Regards

Christian
Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie:
> By the way
> 
> in some papers I've seen  2D schematic diagrams of the protein-ligand
> interactions.
> The exapmle of such maps could be found here
> http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-g
> r4.jpg
> 
>  Could you tell me examples of software wich could produce such maps?
> 
> 
> Thanks
> 
> James
> 
> 2012/6/15 James Starlight <jms...@gm...>
> 
> > Thomas, thanks this works perfect.
> >
> >
> > Jason,  I've tested  this script on my system ( this is the membrane
> > protein inserted in the bilayer surrounded by two water layers ( up and
> > down ). During simulation individual water mollecules move into the
> > protein interiour ( in that case protein like a water pore althought it's
> > the receptor ) so I want to visualise only that buried water.
> >
> > I've tried to do it via find_buried_waters script both via ASA as well as
> > in case when I've used small cutoffs ( 0.1) but the script selected too
> > many waters ( e.g virtually all waters from up and down layers have been
> > selected ). How I could specify this selection more carefully ?
> >
> > find_buried_waters 1, 0.1
> >
> >
> > James
> >
> >
> > 2012/6/12 Thomas Holder <sp...@us...>
> >
> >> This will show them in the same slot in group mode.
> >>
> >>
> >> sorry, not "group mode" but "grid mode" of course.
> >>
> >>
> >> --
> >> Thomas Holder
> >> MPI for Developmental Biology
> >> Spemannstr. 35
> >> D-72076 Tübingen
> 

By the way

in some papers I've seen  2D schematic diagrams of the protein-ligand
interactions.
The exapmle of such maps could be found here
http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-gr4.jpg

 Could you tell me examples of software wich could produce such maps?


Thanks

James

2012/6/15 James Starlight <jms...@gm...>

> Thomas, thanks this works perfect.
>
>
> Jason,  I've tested  this script on my system ( this is the membrane
> protein inserted in the bilayer surrounded by two water layers ( up and
> down ). During simulation individual water mollecules move into the protein
> interiour ( in that case protein like a water pore althought it's the
> receptor ) so I want to visualise only that buried water.
>
> I've tried to do it via find_buried_waters script both via ASA as well as
> in case when I've used small cutoffs ( 0.1) but the script selected too
> many waters ( e.g virtually all waters from up and down layers have been
> selected ). How I could specify this selection more carefully ?
>
> find_buried_waters 1, 0.1
>
>
> James
>
>
> 2012/6/12 Thomas Holder <sp...@us...>
>
>> This will show them in the same slot in group mode.
>>>
>>
>> sorry, not "group mode" but "grid mode" of course.
>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>

Thank you, Jason. I have a pml script that creates a fairly long (3000
states) movie. There are several morphed proteins that are loaded at
different states, and I was hoping to fine tune the camera views and
clipping planes at key points. My computer runs out of memory after
~500 states, and although I can render the movie on the university
cluster and look at the png-s, it is a bit of a pain.

Vitaly

On Sat, Jun 23, 2012 at 2:21 AM, Jason Vertrees
<jas...@sc...> wrote:
> Vitaly,
>
> Despite the documentation, you cannot save a single state to a
> session; you can, however, save a single state to a pdb:
>
> save ~/state5.pdb, my_object, 5
>
> Why are you deleting objects instead of hiding them (using scenes)?
> Name collisions? Something else?
>
> Cheers,
>
> -- Jason
>
> On Mon, Jun 18, 2012 at 2:40 PM, V.V. <vv...@gm...> wrote:
>> Hello,
>>
>> I have a 60-state session file that contains three objects: one of
>> them has a single state, while other two have several. In the first
>> state of the session objects #1 and #2 are loaded, and halfway through
>> object #2 is deleted and object #3 is loaded.
>> Is it possible to save the individual states as a session, discarding
>> the others? I thought of using split_states and deleting the
>> multi-state objects, but in this case the object #1 is discarded.
>>
>> This is what it looks like:
>>
>> mset 1 -60
>> #obj01 = 1-state object
>> #obj02 = 20-state object
>> #obj03 = 40-state object
>>
>> load obj01, obj01, 1
>> load obj02, obj02, 1
>>
>> mdo 21: load obj03, obj03, 41 ; delete obj 02
>>
>> Thank you,
>> Vitaly
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> 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
> Schrödinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Vitaly,

Despite the documentation, you cannot save a single state to a
session; you can, however, save a single state to a pdb:

save ~/state5.pdb, my_object, 5

Why are you deleting objects instead of hiding them (using scenes)?
Name collisions? Something else?

Cheers,

-- Jason

On Mon, Jun 18, 2012 at 2:40 PM, V.V. <vv...@gm...> wrote:
> Hello,
>
> I have a 60-state session file that contains three objects: one of
> them has a single state, while other two have several. In the first
> state of the session objects #1 and #2 are loaded, and halfway through
> object #2 is deleted and object #3 is loaded.
> Is it possible to save the individual states as a session, discarding
> the others? I thought of using split_states and deleting the
> multi-state objects, but in this case the object #1 is discarded.
>
> This is what it looks like:
>
> mset 1 -60
> #obj01 = 1-state object
> #obj02 = 20-state object
> #obj03 = 40-state object
>
> load obj01, obj01, 1
> load obj02, obj02, 1
>
> mdo 21: load obj03, obj03, 41 ; delete obj 02
>
> Thank you,
> Vitaly
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> 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
Schrödinger, LLC

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

Hi.

I'm sorry I didn't respond earlier. I wasn't well.

Thank you for all of your replays. Jeff Van Voorst's solution was the one I
was looking for.

Again. Thank and sorry

Yotam

On Mon, Jun 18, 2012 at 6:00 PM, Jeffrey Van Voorst <van...@um...>wrote:

> Hello Yotam,
>
> You can place the commands you would otherwise type in the pymol command
> window in a .pml file.  Supposing you have a script called
> my_script.pml, you can run the script by typing "pymol my_script.pml"
> when you start pymol or if you have pymol already running you may use
> "@my_script.pml" (without the quotes).
>
> One place this information may be found is:
> http://pymol.sourceforge.net/newman/user/S0210start_cmds.html
>
> --Jeff Van Voorst
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
My other email account has a "professional" signature.

hi,
i think i am missing something simple.
i open my pdb files, then auto open an mtz file
which draws the map far away from my pdb.
how do i center and redraw the map ?
is there a gui way or should i isomesh etc ?
thanks
jpd

Hi Martin,

I don't know the MOPAC format and couldn't find a specification ad hoc.
But the attached script will produce output which is equivalent to your
example. Use the "zero" argument to specify the selection of "+0" 
flagged atoms.

Cheers,
    Thomas

On 06/21/2012 11:27 PM, Martin Hediger wrote:
> Dear PyMOL users
> I'm using MOPAC to do quantum chemical calculations of enzymes.
> I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
> An example of this format is here:
>
>      C(     1 LEU  24)   9.04500000 +0   4.94400000 +0  19.45600000 +0                     0.4527
>      O(     2 LEU  24)   8.05600000 +1   5.59200000 +1  19.15100000 +1                    -0.5188
>      H(     3 LEU  24)  10.04000000 +1   5.40500000 +1  19.57200000 +1                     0.1090
>      N(     4 ASP  25)   9.08100000 +1   3.59500000 +1  19.71600000 +1                    -0.4910
>      C(     5 ASP  25)   7.89300000 +1   2.76600000 +1  19.57800000 +1                    -0.0307
>      C(     6 ASP  25)   7.70800000 +0   1.88300000 +0  20.81000000 +0                     0.3465
>      O(     7 ASP  25)   8.44900000 +1   0.95600000 +1  21.12200000 +1                    -0.4321
>      C(     8 ASP  25)   7.97500000 +1   1.90500000 +1  18.33900000 +1                    -0.4663
>      C(     9 ASP  25)   6.66900000 +1   1.15400000 +1  18.28400000 +1                     0.7179
>      O(    10 ASP  25)   5.64600000 +1   1.70700000 +1  18.79700000 +1                    -0.7657
>      O(    11 ASP  25)   6.69700000 +1   0.02300000 +1  17.72800000 +1                    -0.6565
>      H(    12 ASP  25)   7.03100000 +1   3.43800000 +1  19.54700000 +1                     0.1841
>      H(    13 ASP  25)   8.81500000 +1   1.20200000 +1  18.39200000 +1                     0.1979
>      H(    14 ASP  25)   8.10000000 +1   2.50700000 +1  17.43400000 +1                     0.1919
>      H(    15 ASP  25)   9.95700000 +1   3.14300000 +1  19.95300000 +1                     0.2791
>      H(    16 ASP  25)   6.98200000 +1   2.29500000 +1  21.52500000 +1                     0.1043
>
> What I'm especially interested in is the "+0" and "+1" flags, which
> sometimes are required but are quite inconvenient to find for single
> atoms in a large file, it's also very error prone. The parenthesis after
> the atom type can be omitted, also the very last column (0.4527, ...)
> Would it be possible to write a PyMOL plugin, where single atoms could
> be added to a selection (using point-and-click) and when saving to the
> MOPAC file, the selected atoms would be written with the "+0" flags?
> Any hints on what part of the API to look at are very appreciated.
>
> Best regards
> Martin

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

Dear PyMOL users
I'm using MOPAC to do quantum chemical calculations of enzymes.
I'm wondering if PyMOL could be used to output a PDB file in MOPAC format.
An example of this format is here:

    C(     1 LEU  24)   9.04500000 +0   4.94400000 +0  19.45600000 +0                     0.4527
    O(     2 LEU  24)   8.05600000 +1   5.59200000 +1  19.15100000 +1                    -0.5188
    H(     3 LEU  24)  10.04000000 +1   5.40500000 +1  19.57200000 +1                     0.1090
    N(     4 ASP  25)   9.08100000 +1   3.59500000 +1  19.71600000 +1                    -0.4910
    C(     5 ASP  25)   7.89300000 +1   2.76600000 +1  19.57800000 +1                    -0.0307
    C(     6 ASP  25)   7.70800000 +0   1.88300000 +0  20.81000000 +0                     0.3465
    O(     7 ASP  25)   8.44900000 +1   0.95600000 +1  21.12200000 +1                    -0.4321
    C(     8 ASP  25)   7.97500000 +1   1.90500000 +1  18.33900000 +1                    -0.4663
    C(     9 ASP  25)   6.66900000 +1   1.15400000 +1  18.28400000 +1                     0.7179
    O(    10 ASP  25)   5.64600000 +1   1.70700000 +1  18.79700000 +1                    -0.7657
    O(    11 ASP  25)   6.69700000 +1   0.02300000 +1  17.72800000 +1                    -0.6565
    H(    12 ASP  25)   7.03100000 +1   3.43800000 +1  19.54700000 +1                     0.1841
    H(    13 ASP  25)   8.81500000 +1   1.20200000 +1  18.39200000 +1                     0.1979
    H(    14 ASP  25)   8.10000000 +1   2.50700000 +1  17.43400000 +1                     0.1919
    H(    15 ASP  25)   9.95700000 +1   3.14300000 +1  19.95300000 +1                     0.2791
    H(    16 ASP  25)   6.98200000 +1   2.29500000 +1  21.52500000 +1                     0.1043


What I'm especially interested in is the "+0" and "+1" flags, which 
sometimes are required but are quite inconvenient to find for single 
atoms in a large file, it's also very error prone. The parenthesis after 
the atom type can be omitted, also the very last column (0.4527, ...)
Would it be possible to write a PyMOL plugin, where single atoms could 
be added to a selection (using point-and-click) and when saving to the 
MOPAC file, the selected atoms would be written with the "+0" flags?
Any hints on what part of the API to look at are very appreciated.

Best regards
Martin