pymol-users Mailing List for PyMOL Molecular Graphics System

Hello everyone,

I have a comment concerning Ray trace mode 1. I wanted to display a protein DNA complex with only the protein outlined and to do that the only way I found was to change the cartoon transparency of the DNA to 0.1. The problem is that the outline completely overrides the transparency setting : I always see the outline on top of the DNA structure. Is there a way to modify the outline drawing to make it compatible with transparency settings ?

Thank you,

Marc

Thank You Andreas !!

With some modification the axes.py, it worked as I wanted.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


2010/9/30 Andreas Förster <doc...@gm...>

> When I type 'axes' into the search window at the PyMOL wiki, I get the
> following ONE hit:
>
> http://pymolwiki.org/index.php/Axes
>
> Try it!  It might just be what you're looking for.
>
>
> Andreas
>
>
>
>
> On 30/09/2010 10:28, Chandan Choudhury wrote:
>
>> Dear PyMOL users,
>> Is it possible to view the axes (x, y and z), of a pdb file using pymol?
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>>
>
> --
>        Andreas Förster, Research Associate
>        Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>            http://www.msf.bio.ic.ac.uk
>

When I type 'axes' into the search window at the PyMOL wiki, I get the 
following ONE hit:

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

Try it!  It might just be what you're looking for.


Andreas



On 30/09/2010 10:28, Chandan Choudhury wrote:
> Dear PyMOL users,
> Is it possible to view the axes (x, y and z), of a pdb file using pymol?
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>


-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Dear PyMOL users,
Is it possible to view the axes (x, y and z), of a pdb file using pymol?

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA

Hi Chandan,

Just use:

hide lines

If you then 'show spheres' you'll only have the arrangement. You can then
use 'set sphere_scale,0.3' to scale down the sphere radii to 30%.

And don't forget to check out the manual  ;)

Hope it helps,

Tsjerk

On Sep 30, 2010 7:00 AM, "Chandan Choudhury" <ii...@gm...> wrote:


Hello all !!

Is it possible to hide bonds in pymol. I want to visualize only the atoms'
arrangement, not how is it connected.

Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA

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Hello all !!

Is it possible to hide bonds in pymol. I want to visualize only the atoms'
arrangement, not how is it connected.

Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA

 My two cents on this issue.

I run PyMOL 1.3 on a PackardBell EasyNote TJ62 laptop, which has an ATI
Radeon HD 4570, with no glitches at all.
BUT, I use Gentoo Linux with the free xf86-video-ati driver, v6.13.1. My
version of xorg-server is 1.7.7, MESA is at 7.8.2 and libdrm is at
2.4.21. With Gentoo Linux you compile everything form source and the
system is rock solid.

When PyMOL 1.3 launches on my laptop (using it right now) I see this
message:
===

 PyMOL(TM) Molecular Graphics System, Version 1.3.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.
 
    Created by Warren L. DeLano, Ph.D.
 
    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.
 
    If PyMOL is helpful in your work or study, then please volunteer
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.
 
    More information can be found at "http://www.pymol.org".
 
    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.
 
 Hit ESC anytime to toggle between text and graphics.
 
 Detected 2 CPU cores.  Enabled multithreaded rendering.
===

No mention whatsoever to the ATI warning. However, I used to see the
warning when I was the suffering user of ATI's official drivers for Linux.

So, to everyone running Linux with an ATI card, just get rid of the
official ATI drivers and use the free xf86-video-ati driver instead. It
works much better and you don't get any OpenGL performance penalty.

Ramiro Tellez Sanz
Dept. Physical Chemistry
University of Almeria
Spain

El 29/09/10 20:14, Jason Vertrees escribió:
> Hi Adam,
>
> Thanks for expressing your concerns.
>
> This message,
>
>>     Note: Radeon HD cards tend not to run PyMOL well.
>>     Use nVidia or Intel instead, if OpenGL glitches occur.
>>     Attempting to compensate for known issues...
> has been in PyMOL for a long time.  It's just a fact that NVidia cards
> have been less buggy and have better Linux drivers than ATI and Intel.
>  The heterogeneity in (buggy) hardware makes development difficult and
> expensive.  And, we're not the only ones running into this either: the
> CCP4 list recently discussed this, and I've also been talking to John
> Stone, the main VMD developer, who also faces such issues.
>
>
>> So the new Macs only come with Radeon video cards... there are no other
>> choices with a Mac. This means the MacPros no are no longer a good platform
>> for running PyMOL? I just tossed $3K down the drain?
> The new MacPros should be more than capable of running PyMOL.  In
> fact, the above warning is more for low-end cards which are buggier,
> not the high-end ones found in MacPros.  Your $3k wasn't thrown away,
> you're just ahead of the curve.  I'm sure more people will buy
> MacPros, forcing me to follow suit.  Also, if Apple hasn't already, I
> hope they'll release a list of NVidia cards which will run on their
> new MacPros, just like they have a list of Radeon cards for the
> NVidia-based MacPros.
>
>
>> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
>> tried to render just the top half and it still crashes.
> PyMOL is known to crash when trying to render large structures.  This
> is a legacy issue with the internal memory management, not your Radeon
> card.  3L5Q is a very large PDB (79,452 atoms w/o hydrogens).  I agree
> wholeheartedly that PyMOL should be able to render this without
> crashing.  Even my machine (early 2010 Dual Quad-core MacPro w/16GB
> RAM) cannot even "set surface_quality, 1" on that structure without
> crashing.
>
>
>> What are the OpenGL glitches that occur, are they documented somewhere?
> The glitches we talk about are those like:
>   * blank windows or windows not opening/closing properly (Intel GM945)
>   * sticks not coloring properly (Intel945, some ATI cards, some VMs);
> they're all blue when they should be mutlicolored
>   * partial geometry being rendered;
>
>
>> What does PyMOL do to compensate?
> We detect the video cards and add extra openGL calls (usually glFlush
> or glFinish) or reorder openGL calls to workaround known problems.
>
>
>> I checked the PyMOL web site and under the supported operating systems and
>> hardware there is no mention of the lack of Radeon support/poor Radeon
>> performance. Maybe that should be added because I wouldn't have bought this
>> new Mac if I would have known this. Is there anything I can do to make this
>> new machine work?
> We cannot list all possible systems on which PyMOL won't run.  We do
> try to provide a list of machines on which it will run.  Aside from
> not being able to ray trace a protein that's almost big enough to see
> with the naked eye, do you see any other performance issues or
> glitches or artifacts?  Could it be that PyMOL is in fact running okay
> on your machine but the memory-bug combined with the Radeon warning
> caught you off guard?  If PyMOL produces other bugs on your system due
> to the Radeon card or not, please email me a bug report or better yet
> visit http://pymol.org/contact (choose "Bug Reporting") and file it
> there so it's automatically tracked internally.
>
>
>> I see a 64-bit version is on the horizon, will this address Radeon
>> performance or should I go back to my old MacPro with it's nVidia 7300 video
>> cards?
> We wanted to release a 64-bit version for a while, but the Tcl/Tk
> toolkit was not ready.  I think it's still in alpha/beta.  64-bit
> MacPyMOL will be released when we're sure that works.
>
> Cheers,
>
> -- Jason
>

Hi Adam,

Thanks for expressing your concerns.

This message,

>     Note: Radeon HD cards tend not to run PyMOL well.
>     Use nVidia or Intel instead, if OpenGL glitches occur.
>     Attempting to compensate for known issues...

has been in PyMOL for a long time.  It's just a fact that NVidia cards
have been less buggy and have better Linux drivers than ATI and Intel.
 The heterogeneity in (buggy) hardware makes development difficult and
expensive.  And, we're not the only ones running into this either: the
CCP4 list recently discussed this, and I've also been talking to John
Stone, the main VMD developer, who also faces such issues.


> So the new Macs only come with Radeon video cards... there are no other
> choices with a Mac. This means the MacPros no are no longer a good platform
> for running PyMOL? I just tossed $3K down the drain?

The new MacPros should be more than capable of running PyMOL.  In
fact, the above warning is more for low-end cards which are buggier,
not the high-end ones found in MacPros.  Your $3k wasn't thrown away,
you're just ahead of the curve.  I'm sure more people will buy
MacPros, forcing me to follow suit.  Also, if Apple hasn't already, I
hope they'll release a list of NVidia cards which will run on their
new MacPros, just like they have a list of Radeon cards for the
NVidia-based MacPros.


> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
> tried to render just the top half and it still crashes.

PyMOL is known to crash when trying to render large structures.  This
is a legacy issue with the internal memory management, not your Radeon
card.  3L5Q is a very large PDB (79,452 atoms w/o hydrogens).  I agree
wholeheartedly that PyMOL should be able to render this without
crashing.  Even my machine (early 2010 Dual Quad-core MacPro w/16GB
RAM) cannot even "set surface_quality, 1" on that structure without
crashing.


> What are the OpenGL glitches that occur, are they documented somewhere?

The glitches we talk about are those like:
  * blank windows or windows not opening/closing properly (Intel GM945)
  * sticks not coloring properly (Intel945, some ATI cards, some VMs);
they're all blue when they should be mutlicolored
  * partial geometry being rendered;


> What does PyMOL do to compensate?

We detect the video cards and add extra openGL calls (usually glFlush
or glFinish) or reorder openGL calls to workaround known problems.


> I checked the PyMOL web site and under the supported operating systems and
> hardware there is no mention of the lack of Radeon support/poor Radeon
> performance. Maybe that should be added because I wouldn't have bought this
> new Mac if I would have known this. Is there anything I can do to make this
> new machine work?

We cannot list all possible systems on which PyMOL won't run.  We do
try to provide a list of machines on which it will run.  Aside from
not being able to ray trace a protein that's almost big enough to see
with the naked eye, do you see any other performance issues or
glitches or artifacts?  Could it be that PyMOL is in fact running okay
on your machine but the memory-bug combined with the Radeon warning
caught you off guard?  If PyMOL produces other bugs on your system due
to the Radeon card or not, please email me a bug report or better yet
visit http://pymol.org/contact (choose "Bug Reporting") and file it
there so it's automatically tracked internally.


> I see a 64-bit version is on the horizon, will this address Radeon
> performance or should I go back to my old MacPro with it's nVidia 7300 video
> cards?

We wanted to release a 64-bit version for a while, but the Tcl/Tk
toolkit was not ready.  I think it's still in alpha/beta.  64-bit
MacPyMOL will be released when we're sure that works.

Cheers,

-- Jason

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

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

Dear Jason,

I strongly support Adam's suggestion that the PyMOL website and the Wiki
display a clear warning to people planning on using PyMOL with ATI/AMD
graphics card. I have had numerous issues with ATI graphics cards + PyMOL
over the years and nVidia is unquestionably the better choice when it comes
to running professional OpenGL intensive software (like PyMOL and Blender)
on Linux or Mac OS.

Best regards,
Shiven



On Wed, Sep 29, 2010 at 11:07 AM, H. Adam Steinberg <ad...@st...>wrote:

> Hi All,
>
> I bought a new MacPro and now get this message when I open PyMOL:
>
>     Note: Radeon HD cards tend not to run PyMOL well.
>     Use nVidia or Intel instead, if OpenGL glitches occur.
>     Attempting to compensate for known issues...
>
> So the new Macs only come with Radeon video cards... there are no other
> choices with a Mac. This means the MacPros no are no longer a good platform
> for running PyMOL? I just tossed $3K down the drain?
>
> I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I
> tried to render just the top half and it still crashes.
>
> What are the OpenGL glitches that occur, are they documented somewhere?
> What does PyMOL do to compensate?
>
> I checked the PyMOL web site and under the supported operating systems and
> hardware there is no mention of the lack of Radeon support/poor Radeon
> performance. Maybe that should be added because I wouldn't have bought this
> new Mac if I would have known this. Is there anything I can do to make this
> new machine work?
>
> I see a 64-bit version is on the horizon, will this address Radeon
> performance or should I go back to my old MacPro with it's nVidia 7300 video
> cards?
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> 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 bought a new MacPro and now get this message when I open PyMOL:

    Note: Radeon HD cards tend not to run PyMOL well.
    Use nVidia or Intel instead, if OpenGL glitches occur.
    Attempting to compensate for known issues... 

So the new Macs only come with Radeon video cards... there are no other choices with a Mac. This means the MacPros no are no longer a good platform for running PyMOL? I just tossed $3K down the drain?

I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I tried to render just the top half and it still crashes.

What are the OpenGL glitches that occur, are they documented somewhere?
What does PyMOL do to compensate?

I checked the PyMOL web site and under the supported operating systems and hardware there is no mention of the lack of Radeon support/poor Radeon performance. Maybe that should be added because I wouldn't have bought this new Mac if I would have known this. Is there anything I can do to make this new machine work?

I see a 64-bit version is on the horizon, will this address Radeon performance or should I go back to my old MacPro with it's nVidia 7300 video cards? 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

Thank you!

Vitaly

----- Original Message -----
From: Judith Murray-Rust <jud...@ca...>
Date: Monday, September 27, 2010 4:48 am
Subject: RE: [PyMOL] Custom grid dimensions
To: Vitaly Vostrikov <vv...@ua...>

> 
> Seems to depend on the aspect ratio of the viewport (try dragging 
> it wider). But agree it is not sufficiently customizable.
> 
> J
> ------------------------------
> Dr Judith Murray-Rust
> Structural Biology Laboratory
> Cancer Research UK.
> > -----Original Message-----
> > From: Vitaly Vostrikov [mailto:vv...@ua...]
> > Sent: 26 September 2010 18:22
> > To: pym...@li...
> > Subject: [PyMOL] Custom grid dimensions
> > 
> > Hello,
> > 
> > Is there an option to change the grid dimensions for the grid_mode
> > setting? Suppose I load three objects: Pymol generates a 2x2 grid 
> for> them, while I would prefer to place them side by side in a 3x1 
> one. It
> > is possible to work around this by setting one of the objects in a
> > grid_slot, 0, but that leaves a lot of blank space.
> > 
> > Thank you,
> > Vitaly
> > 
> > ------------------------------------------------------------------
> -----
> > -------
> > Start uncovering the many advantages of virtual appliances
> > and start using them to simplify application deployment and
> > accelerate your shift to cloud computing.
> > http://p.sf.net/sfu/novell-sfdev2dev
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-
> us...@li...
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> 

 First of all, I would like to express my gratitude to both Tsjerk and
Thomas. If
only the rest of the world were like you!!

The script works very well indeed. Thanks!
I would like to make my own humble contribution, though, so that other
people
can benefit from the impressive work by Thomas and Tsjerk.

As a result of my docking studies I get a lot of candidate poses for my
ligands.
But, if you want to use the ring_angle.py program to measure
the angle between an aromatic ring in your pose and a protein residue,
you have
to manually edit the pose pdb. Why? Because all of the carbons
in the pose will probably be labeled just "C", as it was my case, but
all atoms
labeled as "C"'s are removed from the arguments in the ring_angle.py
program,
and you get either an error or an incorrect result. Here is step by step
what
you should do:

1) Load the pose.pdb in a text editor, the simpler the better. I use
KDE, so I
loaded it in KWrite.
2) Find the C atoms belonging to the aromatic ring. This can be
puzzling, though
3) Label them as CG, CD1, CE1, CZ, CE2 and CD2 in the pdb file (clockwise,
starting from CG which should rest pointing down on the paper).
4) Save the modified pose.pdb
5) Load the protein and the pose in pymol.
6) Select, atom by atom, the aromatic ring from the pose in pymol and
name the
selection (for instance pose-ring).
7) Load the ring_angle.py program
8) Finally, run the command "ring_angle chain X and resi Y, pose-ring). Be
careful that, depending on the relative position of both rings, the correct
answer may be the return value or its difference with 180º.

If you don't select the aromatic ring in the pose, but instead you issue the
command on the whole pose, the result is not correct.

I can provide a demo file if anyone is interested.
Hope this helps.

Ramiro Tellez Sanz
Dept. Physical Chemistry
University of Almeria
Spain

Hello,

Is there an option to change the grid dimensions for the grid_mode setting? Suppose I load three objects: Pymol generates a 2x2 grid for them, while I would prefer to place them side by side in a 3x1 one. It is possible to work around this by setting one of the objects in a grid_slot, 0, but that leaves a lot of blank space.

Thank you,
Vitaly

Dear Thomas,

at.hetatm works perfectly!  Thanks very much.

Best Regards,
  Zhijian Xu

Thomas Holder wrote:
> Hi Zhijian,
>
> it's the at.hetatm attribute.
>
> try this:
> print atoms.atom[0].__dict__
>
> Cheers,
>   Thomas
>
> On Sat, 2010-09-25 at 22:56 +0800, zjxu wrote:
>   
>> Dear everyone,
>>
>> I could print the atom properties in a script except the atom type:
>>   atoms = cmd.get_model("object")
>>   for at in atoms.atom:
>>     sele1 = model + " and i. " +  resi
>>     sele2="object and resi %s and name %s"% (at.resi, at.name)
>>       #print sele1, sele2
>>     dst=cmd.distance("tmp", sele1, sele2)
>>     #print at.chain, at.resn, at.resi, at.name, at.index, "%8.3f"%dst
>>     print model, resi, at.type, at.chain, at.resn, at.resi, at.name, 
>> "%8.3f"%dst
>> everything is OK if I delete at.tpye. 
>>  From the error in the pymol, I could see that the attibute type does 
>> not exist.
>> so how to print the atom tyep (the first column in the PDB, that is ATOM 
>> or HETATM)?
>>
>> On http://www.pymolwiki.org/index.php/Label, type is  one  of  the 
>> properties of the object: *type* /(ATOM,HETATM)/, the type of atom
>>
>> Thanks very much in advance
>>
>> Best regards,
>> Zhijian Xu
>>
>> Shanghai Institute of Materia Medica, China
>>     
>
>
>
>   

Hi Zhijian,

it's the at.hetatm attribute.

try this:
print atoms.atom[0].__dict__

Cheers,
  Thomas

On Sat, 2010-09-25 at 22:56 +0800, zjxu wrote:
> Dear everyone,
> 
> I could print the atom properties in a script except the atom type:
>   atoms = cmd.get_model("object")
>   for at in atoms.atom:
>     sele1 = model + " and i. " +  resi
>     sele2="object and resi %s and name %s"% (at.resi, at.name)
>       #print sele1, sele2
>     dst=cmd.distance("tmp", sele1, sele2)
>     #print at.chain, at.resn, at.resi, at.name, at.index, "%8.3f"%dst
>     print model, resi, at.type, at.chain, at.resn, at.resi, at.name, 
> "%8.3f"%dst
> everything is OK if I delete at.tpye. 
>  From the error in the pymol, I could see that the attibute type does 
> not exist.
> so how to print the atom tyep (the first column in the PDB, that is ATOM 
> or HETATM)?
> 
> On http://www.pymolwiki.org/index.php/Label, type is  one  of  the 
> properties of the object: *type* /(ATOM,HETATM)/, the type of atom
> 
> Thanks very much in advance
> 
> Best regards,
> Zhijian Xu
> 
> Shanghai Institute of Materia Medica, China

Hello,

I am running a remote desktop on my windows machine to work on my
office linux machine. When I launch pymol, it fails with the following
message:

freeglut (pymol):  ERROR:  Internal error <FBConfig with necessary
capabilities not found> in function fgOpenWindow
X Error of failed request:  BadWindow (invalid Window parameter)
  Major opcode of failed request:  4 (X_DestroyWindow)
  Resource id in failed request:  0x0
  Serial number of failed request:  27
  Current serial number in output stream:  30
 PyMOL: abrupt program termination.

Any help ? Most other graphics application work just fine.

-- 
Thank you and Regards,

Vivek Ranjan

Dear everyone,

I could print the atom properties in a script except the atom type:
  atoms = cmd.get_model("object")
  for at in atoms.atom:
    sele1 = model + " and i. " +  resi
    sele2="object and resi %s and name %s"% (at.resi, at.name)
      #print sele1, sele2
    dst=cmd.distance("tmp", sele1, sele2)
    #print at.chain, at.resn, at.resi, at.name, at.index, "%8.3f"%dst
    print model, resi, at.type, at.chain, at.resn, at.resi, at.name, 
"%8.3f"%dst
everything is OK if I delete at.tpye. 
 From the error in the pymol, I could see that the attibute type does 
not exist.
so how to print the atom tyep (the first column in the PDB, that is ATOM 
or HETATM)?

On http://www.pymolwiki.org/index.php/Label, type is  one  of  the 
properties of the object: *type* /(ATOM,HETATM)/, the type of atom

Thanks very much in advance

Best regards,
Zhijian Xu

Shanghai Institute of Materia Medica, China

Hi Sebastian,

If 'lig' is a defined object or selection, try

  show surface, poly within 5 of lig

Your selection could also be:

  show surface, (not org) and (org around 5)

which show the surface for all atoms that are not organic (so, polymer
or solvent) and those atoms within 5 of org.  I still prefer the first
selection.

Cheers,

-- Jason



On Fri, Sep 24, 2010 at 10:46 AM, Sebastian Kruggel
<kr...@ch...> wrote:
> dear pymol users,
>
> i installed the VASCo plugin to display surface properties
> (thanks for the hint) and it does a very good job! I just
> wanted to display only parts of my generated surface
> <prot.pdb_00_np> which are near to my ligand <lig> with
> something like
>
>  > hide surface, prot.pdb_00_np and not lig around 5
>
> which does not work at all. if i try hide everything, the
> surface indeed disappears - but than my selection does not
> work...
> has anybody an idea?
>
> thanks in advance,
> sebastian
>
>
>
> --
> Sebastian Kruggel
> Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel:   +49 (0)40 42838-3626 (-3484)
> mail:  kr...@ch...
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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> _______________________________________________
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>



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

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

dear pymol users,

i installed the VASCo plugin to display surface properties 
(thanks for the hint) and it does a very good job! I just 
wanted to display only parts of my generated surface 
<prot.pdb_00_np> which are near to my ligand <lig> with 
something like

 > hide surface, prot.pdb_00_np and not lig around 5

which does not work at all. if i try hide everything, the 
surface indeed disappears - but than my selection does not 
work...
has anybody an idea?

thanks in advance,
sebastian



-- 
Sebastian Kruggel
Institut für Pharmazie
Bundesstr. 45 | Raum 112 (406)
D 20146 Hamburg

Tel:   +49 (0)40 42838-3626 (-3484)
mail:  kr...@ch...
http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html

Hi Thomas and David,

Thanks for bringing this to my attention.  PyMOL was indeed trying to
fit to a degenerate case.  I fixed the bug: PyMOL will now print:
   ExecutiveAlign: No alignment found.
and leave your objects untouched.

This fix is mixed in with some other development code, so I'll extract
it and check it in soon.

Cheers,

-- Jason


On Thu, Sep 23, 2010 at 3:05 AM, Thomas Holder
<sp...@us...> wrote:
> Hi David,
>
> this is bug, indeed. I also hit this some time ago but didn't report it
> so far. The actual problem is that the cmd.super('1acb', '426d') fails
> completely and only aligns a single atom, resulting in a Null-matrix
> that collapses all of 1acb into a single point. The RMSD of 2.8 that you
> get in your last call is just an artefact that arises from aligning the
> correct protein to the collapsed one. Just run your example with GUI and
> you see what happens.
>
> fetch 1acb
> fetch 426d
> copy 1acb_2, 1acb
> super 1acb, 426d
> super 1acb, 1acb_2, object=aln
> zoom aln
>
> I think the super command should check if the resulting matrix is
> orthonormal or at least not a Null-matrix.
>
> Cheers,
>  Thomas
>
> On Wed, 2010-09-22 at 18:28 -0400, David Hall wrote:
>> In preparing my test for the odd request that I just sent, I came
>> across what seems to be a bug in super.  It has to do with this weird
>> nucleic acid thing I was talking about.
>>
>> Here's the script this time:
>> from pymol import cmd
>>
>> cmd.fetch('1acb', async=0)
>> cmd.fetch('1acb', '1acb_2', async=0)
>> cmd.fetch('426d', async=0)
>>
>>
>> print "1acb_2"; print cmd.super('1acb', '1acb_2')[0]
>> print "426d"; print cmd.super('1acb', '426d')[0]
>> print "1acb_2_again"; print cmd.super('1acb', '1acb_2')[0]
>>
>> ~> ~/src/pymol_trunk_20100922/pymol -qrkc script2.py
>> PyMOL>run script2.py,main
>> 1acb_2
>> 0.0
>> 426d
>> 0.0
>> 1acb_2_again
>> 2.80655193329
>>
>> super should give an rms between 1acb and 1acb_2 of 0.0, which it does
>> at first.  But once you super your protein to a nucleic acid that has
>> a calcium ion, when you run exactly the same command, you all of a
>> sudden get 2.8.  Very weird...
>>
>> Note, this does not happen if you use 100d, which is a nucleic acid
>> without a calcium ion, does not happen if you use a pdb file with a
>> calcium ion, and does happen with 1d56, which is another nucleic acid
>> with a calcium ion I just pulled out.
>>
>> In pymol 1.2, it also behaved incorrectly:
>> ~> pymol -qrkc script2.py
>> PyMOL>run script2.py,main
>> 1acb_2
>> 0.0
>> 426d
>> nan
>> 1acb_2_again
>> nan
>>
>>
>> -David
>
> --
> Thomas Holder
> Group of Steffen Schmidt
> Department of Biochemistry
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> 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

Hi Renuka,

Please keep all PyMOL-related correspondence on the mailing list. That way,
other people can find the answers by reading the mailing list or searching
the web.

Your task is now getting a little more complicated. I think you'll probably
want to define some Python functions and use them. It's useful to know that
using the distance command with mode=2 will show polar contacts. Also,
distance objects with names starting with an underscore won't show up in the
GUI.


I'd do something like this:

1. Define some functions in a Python file that you can use via "run" (or
perhaps in your .pymolrc). [see
http://www.pymolwiki.org/index.php/Python_Integration and
http://www.pymolwiki.org/index.php/Script_Tutorial]. You'll need to pass the
name of your protein to these functions.

import os
from pymol import cmd

def loadclust(filename,protname):
    cmd.load(filename)
    dir,fname = os.path.split(filename)
    # PyMOL automatically names the object by the filename
    fname,extension = os.path.splitext(fname)
    # cluster_4 --> 4
    custernum = fname.split('_')[1]
    # hidden from GUI display because it starts with _
    polarname = '_polar_'+clusternum
    cmd.dist(polarname,fname,protname,mode=2)
cmd.extend('loadclust',loadclust)
def delclust(filename):
    dir,fname = os.path.split(filename)
    # PyMOL automatically names the object by the filename
    fname,extension = os.path.splitext(fname)
    # cluster_4 --> 4
    custernum = fname.split('_')[1]
    # hidden from GUI display because it starts with _
    polarname = '_polar_'+clusternum
    cmd.delete(fname)
    cmd.delete(polarname)
cmd.extend('delclust',delclust)

2. Then you should be able to use a similar procedure to
before. Remember that you now need to delete things and pass the name of
your protein to the functions so that polar contacts can be displayed
correctly:

for i in glob.glob("Model_1/cluster_*.sdf"): loadclust(i,myprotein)

<analyze things>

for i in glob.glob("Model_1/cluster_*.sdf"): delclust(i,myprotein)

for i in glob.glob("Model_2/cluster_*.sdf"): loadclust(i,myprotein)

Unfortunately, I don't have any SD files on hand, so I haven't tested these!
Some modification may be necessary. You should also check out the script
that Jason linked.

Cheers,

-Michael

On Wed, Sep 22, 2010 at 11:52 AM, Renuka Robert <ren...@ym...>wrote:

> Dear Michael
> Thanks for your detailed reply. This is what exactly i needed. Now i want
> to find the hydrogen bonding between each cluster files and the protein. So
> i do the following step
>
> cd /home/user
>
> import glob
>
>
>  then I load the Model_1 files with
>
>
>  for i in glob.glob("Model_1/cluster_*.sdf"): cmd.load(i)
>
>
>  Now hydrogen bond should be displayed between protein and
> Model_1/cluster_*.sdf. Polar contacts in different colors would be more
> appreciated.
>
>
>  Could you please attach your script in the above command, so that all the
> cluster_*.sdf is loaded and its polar contacts is displayed in one press.
>
>
>  Thanks in advance
>
> Renuka.
>
>
> --- On *Wed, 22/9/10, Michael Lerner <mgl...@gm...<mglerner%2Bs...@gm...>
> >* wrote:
>
>
> From: Michael Lerner <mgl...@gm...<mglerner%2Bs...@gm...>
> >
> Subject: Re: [PyMOL] Deleting and Loading multiple SDF files
> To: "Renuka Robert" <ren...@ym...>
> Cc: PyM...@li...
> Date: Wednesday, 22 September, 2010, 1:46 PM
>
>
> Hi Renuka,
>
> If I understand correctly, this is what you want to do:
>
> 1. Load up all of the cluster*.sdf files in Model_1.
> 2. Analyze them
> 3. Delete them
> 4. Load up all of the cluster*.sdf files in Model_2.
> 5. Analyze them
> 6. Delete them
> etc.
>
> If that's right, I think the easiest thing is just to change to the
> directory that contains your Model_N subdirectories. In your example, that
> would be:
>
> cd /home/user
> import glob
>
> then load the Model_1 files with
>
> for i in glob.glob("Model_1/cluster_*.sdf"): cmd.load(i)
>
> then analyze them. It sounds like you're analyzing them by hand; if you're
> analyzing them by running some scripts, we can probably help to automate
> that process as well.
>
> After analyzing them, (and saving your results!), you'll want to delete the
> current batch of cluster files and load the new ones:
>
> delete cluster_*
> for i in glob.glob("Model_2/cluster_*.sdf"): cmd.load(i)
>
> Note that you only have to type "import glob" once.
>
> Hope that helps,
>
> -Michael
>
> On Wed, Sep 22, 2010 at 9:12 AM, Renuka Robert <ren...@ym...<http://mc/compose?to=...@ym...>
> > wrote:
>
>  Dear Pymol users
>
>
>  I have to do TWO jobs simultaneously in PYMOL.
>
>
>  JOB 1: Load multiple *sdf files
>
>
>  I have set of ligand files in *.sdf format as follows:
>
>
>  /home/user/Model_1/cluster_1.sdf
>
> /home/user/Model_1/cluster_2.sdf
>
> /home/user/Model_1/cluster_3.sdf
>
>
>  /home/user/Model_2/cluster_1.sdf
>
> /home/user/Model_2/cluster_2.sdf
>
> /home/user/Model_2/cluster_3.sdf
>
>
>  /home/user/Model_3/cluster_1.sdf
>
> /home/user/Model_3/cluster_2.sdf
>
> /home/user/Model_3/cluster_3.sdf
>
>
>  I've got an answer from one of the PYMOL user as:
>
>
>  PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  But this command works only in the present working directory. For the
> next try I have to change my directory every time. Like:
>
>
>  cd /home/user/Model_1/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  cd /home/user/Model_2/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  cd /home/user/Model_3/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  Could you please tell me how to load these multiple *.sdf files in one
> command without changing the directory?
>
>
>  JOB2: Delete multiple *.sdf files
>
>
>  I have to analyze cluster_*.sdf files of several 100 directories.
>
>
> So when I load cluster_*.sdf files from directory Model_2, the already
> loaded cluster:*.sdf files from Model_1 should be deleted.
>
> Like wise when I load cluster_*.sdf files from directory Model_3, the
> already loaded cluster:*.sdf files from Model_2 should be deleted.
>
>
> I am not good in programming. Could anybody help me in scripting to sort
> out this problem?
>
>
>  Thanks in advance.
>
> Regards
>
> Renuka
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
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> )
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> 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)
>
>
>


-- 
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)

Hi,

On Wed, 22 Sep 2010 23:29:14 -0400 Jason Vertrees
<jas...@sc...> wrote:

> Hi Mark,
> 
> We used to be able to call this to get the viewport size.  But,
> somewhere along the line Warren removed this.  I'll see if I can add
> it back in, or find out why he removed it.

As mentioned in this email:

http://www.mail-archive.com/pym...@li.../msg05888.html

this works for me:

width,height = cmd.get_session()['main'][0:2]

I note that a more recent e-mail:
http://www.mail-archive.com/pym...@li.../msg07563.html

suggests that it doesn't work.  In the latter case, printing
cmd.get_session().keys() showed the absence of the 'main' key.  I couldn't
say why it was absent then and present now (I build PyMOL for Linux from the
SVN sources).

Cheers,
Rob


-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

On Thu, 2010-09-23 at 09:54 -0400, Jason Vertrees wrote:
> Hi Ramiro,
> 
> Another option is to fit (in a least-squares sense) a plane to each of
> your rings and then calculate the angle between the fitted planes'
> normals.

that's what the recently posted ring_angle.py script does.

Cheers,
  Thomas

Hi Ramiro,

Another option is to fit (in a least-squares sense) a plane to each of
your rings and then calculate the angle between the fitted planes'
normals.  This would help if your rings are not perfectly planar: it
would spread the deviation among all atoms in the ring not just the
ones you selected for the crossproduct.  Cameron Mura created an
excellent example of this in our PLoS article's supplementary
information, posted on the PyMOLWiki
http://www.pymolwiki.org/index.php/PLoS#Case_6:_Higher-order_structures.28.E2.89.A5_intermediate.2Fadvanced.29

The article is all about biomolecular graphics.

Cheers,

-- Jason

On Thu, Sep 23, 2010 at 4:53 AM, Ramiro Téllez Sanz <urc...@gm...> wrote:
>
>
> Hi everyone and thanks for reading this!
>
> I am interested in measuring the angle between aromatic ring planes.
> Is there any easy way/script to do it?
>
> One way that came to my mind is creating a pseudoatom representing the
> centroid for each ring (I already know how to do that), then drawing two
> lines perpendicularly to the planes from both centroids, and finally
> measuring the angle between the lines. Will that be possible? How could
> this be done?
>
> Is there any other way? I'm completely clueless. Any help will be
> greatly appreciated.
>
> Thanks in advance,
>
> Ramiro Tellez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> 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

Hi Ramiro,

> * How do I adjust the code with my selected rings? Do I need to include
> both residues in the same selection in pymol, then rename the selection,
> and then include the chosen selection name in the code where you write
> "selection"?

you need two selections of two residues, in my example the part 'A/37/CG
+CD1+CE1+CZ+CE2+CD2' is the selection on chain A, residue 37 and ring
atoms.

> * How do I run the code after I adjust it with my "selection"? I have
> never run a python program from within pymol. What should I do?

I put the code (including Tsjerk's additions!) to a file, see attached.
You have to run it with pymol (File > Run...) and then call the
ring_angle command.

Example to get angle between aromatic residues 37 and 41 in chain A:
ring_angle chain A and resi 37, chain A and resi 41

Cheers,
  Thomas