pymol-users Mailing List for PyMOL Molecular Graphics System

I have find distance_states.py scripts on  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/  ;

However,  The scripts no working when the selector 2 is a multi selections like /MOD*///132/ON ,

which command of pymol will return a list of selection like /MOD*///132/ON ?

Anyone have ideas?






在2016年12月22 15时59分, "XP Chen"<chx...@16...>写道:


Hi, everyone.

I have many ligand docking results which stored as multi model pdbs. I want to generate the distance between every frame of ligand  and a residure in protein. How to script it ?

My idea is
first: cmd.split_states()
then: cmd.distance()
finally: cmd.delete()  delete all the states generated

Also, I want to retain the splite states (pdb) that the distance is the most short, However the mine idea hardly deal it.

Anyone have ideas? or any suggestion of other command? I am a beginner of pymol scripts and not skilled in python..

                                                                                                                         Chen.

Dear pymol developers,

I am sorry to bother you, but I am just wondering how the cavities is
defined when I use the cavity mode of surface representation. Are there any
references?

Thank you very much and happy holiday,
Chen

Hi, everyone.

I have many ligand docking results which stored as multi model pdbs. I want to generate the distance between every frame of ligand  and a residure in protein. How to script it ?

My idea is
first: cmd.split_states()
then: cmd.distance()
finally: cmd.delete()  delete all the states generated

Also, I want to retain the splite states (pdb) that the distance is the most short, However the mine idea hardly deal it.

Anyone have ideas? or any suggestion of other command? I am a beginner of pymol scripts and not skilled in python..

                                                                                                                         Chen.

Yes, you should be able to use PyMOL "File" -> "Edit pymolrc" and add
the command there:

feedback disable, opengl, warnings

It creates a file named .pymolrc (note the initial dot) in your home
directory (C:\Users\<username> by default on Win 7/8/10). Then the
command should be executed on startup.

- Piotr

On Mon, Dec 19, 2016 at 11:20 AM, Thomas Laughlin
<tho...@gm...> wrote:
> Yes, but the work around works for a single session.
> Is there a start-up script to add it to?
>
>
> Graphics look normal.
>
> Thomas G. Laughlin III
> PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present
> BS Biochemistry | Univ. of Missouri-Columbia | 2014
> tho...@gm...
>
> On Mon, Dec 19, 2016 at 7:55 AM, Piotr Rotkiewicz
> <pio...@sc...> wrote:
>>
>> Hello Tom,
>>
>> Have you tried this workaround to suppress the OpenGL warnings?
>>
>> https://sourceforge.net/p/pymol/mailman/message/32035245/
>>
>> PyMOL>feedback disable, opengl, warnings
>>
>> Are there any rendering issues besides the warnings flooding the
>> console? Does the graphics look normal?
>>
>> Thanks!
>> Piotr
>>
>>
>>
>>
>>
>> On Sun, Dec 18, 2016 at 3:28 PM, Thomas Laughlin
>> <tho...@gm...> wrote:
>> > Hello,
>> >
>> > I installed unofficial PyMOL 1.8.5.0 using  Anaconda2 on a windows 10
>> > machine possessing a Nvidia Quadro K620.
>> >
>> > In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL
>> > error" is repetitively printed which makes its nearly impossible to see
>> > other output or the help.
>> >
>> > I've installed unofficial PyMOL on other machines without dedicated
>> > graphics
>> > cards and never observed this.
>> > I saw a previous posted about this from 2014, but it doesn't list a
>> > solution.
>> >
>> > Any help is appreciated.
>> >
>> > Best,
>> >
>> > -Tom
>> >
>> >
>> > Thomas G. Laughlin III
>> > PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present
>> > BS Biochemistry | Univ. of Missouri-Columbia | 2014
>> > tho...@gm...
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> > _______________________________________________
>> > PyMOL-users mailing list (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>
>

Yes, but the work around works for a single session.
Is there a start-up script to add it to?


Graphics look normal.

Thomas G. Laughlin III
PhD MCB (BBSB, Student) | *Univ. of California-Berkeley* | Present
BS Biochemistry | *Univ. of Missouri-Columbia* | 2014
tho...@gm...

On Mon, Dec 19, 2016 at 7:55 AM, Piotr Rotkiewicz <
pio...@sc...> wrote:

> Hello Tom,
>
> Have you tried this workaround to suppress the OpenGL warnings?
>
> https://sourceforge.net/p/pymol/mailman/message/32035245/
>
> PyMOL>feedback disable, opengl, warnings
>
> Are there any rendering issues besides the warnings flooding the
> console? Does the graphics look normal?
>
> Thanks!
> Piotr
>
>
>
>
>
> On Sun, Dec 18, 2016 at 3:28 PM, Thomas Laughlin
> <tho...@gm...> wrote:
> > Hello,
> >
> > I installed unofficial PyMOL 1.8.5.0 using  Anaconda2 on a windows 10
> > machine possessing a Nvidia Quadro K620.
> >
> > In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL
> > error" is repetitively printed which makes its nearly impossible to see
> > other output or the help.
> >
> > I've installed unofficial PyMOL on other machines without dedicated
> graphics
> > cards and never observed this.
> > I saw a previous posted about this from 2014, but it doesn't list a
> > solution.
> >
> > Any help is appreciated.
> >
> > Best,
> >
> > -Tom
> >
> >
> > Thomas G. Laughlin III
> > PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present
> > BS Biochemistry | Univ. of Missouri-Columbia | 2014
> > tho...@gm...
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>

Hello Tom,

Have you tried this workaround to suppress the OpenGL warnings?

https://sourceforge.net/p/pymol/mailman/message/32035245/

PyMOL>feedback disable, opengl, warnings

Are there any rendering issues besides the warnings flooding the
console? Does the graphics look normal?

Thanks!
Piotr





On Sun, Dec 18, 2016 at 3:28 PM, Thomas Laughlin
<tho...@gm...> wrote:
> Hello,
>
> I installed unofficial PyMOL 1.8.5.0 using  Anaconda2 on a windows 10
> machine possessing a Nvidia Quadro K620.
>
> In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL
> error" is repetitively printed which makes its nearly impossible to see
> other output or the help.
>
> I've installed unofficial PyMOL on other machines without dedicated graphics
> cards and never observed this.
> I saw a previous posted about this from 2014, but it doesn't list a
> solution.
>
> Any help is appreciated.
>
> Best,
>
> -Tom
>
>
> Thomas G. Laughlin III
> PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present
> BS Biochemistry | Univ. of Missouri-Columbia | 2014
> tho...@gm...
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hello,

I installed unofficial PyMOL 1.8.5.0 using  Anaconda2 on a windows 10
machine possessing a Nvidia Quadro K620.

In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL
error" is repetitively printed which makes its nearly impossible to see
other output or the help.

I've installed unofficial PyMOL on other machines without dedicated
graphics cards and never observed this.
I saw a previous posted about this from 2014, but it doesn't list a
solution.

Any help is appreciated.

Best,

-Tom


Thomas G. Laughlin III
PhD MCB (BBSB, Student) | *Univ. of California-Berkeley* | Present
BS Biochemistry | *Univ. of Missouri-Columbia* | 2014
tho...@gm...

Hi Jiri,

Try this on the PyMOL command line:

# example structures (use your own here)
fetch 1ake, s1, async=0
fetch 4ake, s2, async=0

# import the "angle_between_domains" command
run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/orientation.py

# align on chain A
align s1 & chain A, s2 & chain A

# measure rotation and displacement of chain B
angle_between_domains s1 & chain B, s2 & chain B, method=cealign

For 1ake and 4ake, this reports:
 Angle: 21.70 deg, Displacement: 56.08 angstrom

See also:
https://www.mail-archive.com/pym...@li.../msg10995.html
https://www.mail-archive.com/pym...@li.../msg13015.html

Hope that helps.

Cheers,
  Thomas

On 15 Dec 2016, at 07:02, chemocev marker <jir...@GM...> wrote:

> Hi Pymol user
> I have a heterodimer protein and I wanted to compare it with homologous structures. The chain B of both the structures can be align with align command and in doing so, the chain A is misaligned and which can be only align by the cealign command. The sequence similarity between chain A is very low but the both chains have similar fold. I am interested to know, how much degree the subunits move or rotate when we aligned the chain A with cealign command.
> best
> Jiri

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Pymol user
I have a heterodimer protein and I wanted to compare it with homologous
structures. The chain B of both the structures can be align with align
command and in doing so, the chain A is misaligned and which can be only
align by the cealign command. The sequence similarity between chain A is
very low but the both chains have similar fold. I am interested to know,
how much degree the subunits move or rotate when we aligned the chain A
with cealign command.
best
Jiri

Dear Tsjerk:

Thanks a lot for such prompt reply.

It works very well.

Cheers.

Albert


On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote:
> Hi Albert,
>
> You can do:
>
> show cell
>
> Cheers,
>
> Tsjerk
>

Hi Albert,

You can do:

show cell

Cheers,

Tsjerk

On Dec 7, 2016 8:44 PM, "Albert" <mai...@gm...> wrote:

> Hello:
>
> I am visualizing a MD simulation system in PyMOL. It contains the PBC
> information. I am just wondering how can we show the PBC box in PyMOL?
> As far as I know the PBC box can be shown in VMD using the following
> command line:
>
>  >pbc box
>
> Is there any similar command line in PyMOL?
>
> Thank you very much.
>
> Albert
>
>
> ------------------------------------------------------------
> ------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello:

I am visualizing a MD simulation system in PyMOL. It contains the PBC 
information. I am just wondering how can we show the PBC box in PyMOL? 
As far as I know the PBC box can be shown in VMD using the following 
command line:

 >pbc box

Is there any similar command line in PyMOL?

Thank you very much.

Albert

Hi,

I am assuming it is because, when you pass the arguments on the 
cmd.dihedral() command, the "obj" is being read as a string, instead of 
the variable obj. I think your problem will be solved if you use 
something like, for your first example:
"/"+obj+"///655/CA"
Note the quotation marks placement. This is not the cleanest solution 
but should help.

Rui

Le 07/12/2016 07:09, Val Yu a écrit :
> Hi,
>
> I'm trying to use this script to get a specific dihedral angle from 
> all the objects and write into a file:
>
> PyMOL>f = open('dih.txt','w')
> PyMOL>for obj in cmd.get_object_list():\
> PyMOL>    dih = 
> cmd.dihedral('dih','/obj///655/CA','/obj///655/CB','/obj///655/CG','/obj///655/CD1')\
> PyMOL>    f.write(str(dih))
>
> The software shows following complains:
> Selector-Error: Invalid selection name "obj".
> ( ( ( % obj ) & i; 655 & n; CA ) )<--
> Selector-Error: Invalid selection name "obj".
> ( ( ( % obj ) & i; 655 & n; CB ) )<--
> Selector-Error: Invalid selection name "obj".
> ( ( ( % obj ) & i; 655 & n; CG ) )<--
> Selector-Error: Invalid selection name "obj".
> ( ( ( % obj ) & i; 655 & n; CD1 ) )<--
> ...
>
> What's wrong with my script?
>
> -- 
> Val Yu
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
>
>
> _______________________________________________
> 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,

I'm trying to use this script to get a specific dihedral angle from all the
objects and write into a file:

PyMOL>f = open('dih.txt','w')
PyMOL>for obj in cmd.get_object_list():\
PyMOL>    dih =
cmd.dihedral('dih','/obj///655/CA','/obj///655/CB','/obj///655/CG','/obj///655/CD1')\
PyMOL>    f.write(str(dih))

The software shows following complains:
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CA ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CB ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CG ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CD1 ) )<--
...

What's wrong with my script?

-- 
Val Yu

Hi Jason,

Middle mouse button always worked fine for me with MacPyMOL, using any kind of "normal" mouse (two buttons + wheel as middle button). I haven't tried a magic mouse, but also never received bug reports that those wouldn't work with MacPyMOL.

Could it be that any third party tool interferes here (like BetterTouchTool)?

A PyMOL script or plugin could also possibly redefine mouse actions (like https://pymolwiki.org/index.php/Mouse_modes ). You can suppress loading of plugins and pymolrc scripts with the -k flag (launch from Terminal as /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -k).

It's true that a trackpad doesn't fully replace a 3 button mouse. ALT+click mimics the middle click, but it looks like SHIFT+ALT+drag doesn't work.

The mouse action codes are not documented anywhere. But you could have a look at the cButMode names, which are a bit more meaningful:
https://sf.net/p/pymol/code/HEAD/tree/trunk/pymol/layer1/ButMode.cpp#l501

Cheers,
  Thomas

On 05 Dec 2016, at 18:39, Jason D. Kahn <jd...@um...> wrote:

> Hi --
> 
> I use Mac Pymol 1.8.4 / Mac OS Sierra, but this issue has been present forever. I usually cannot get the middle "M" commands to work, either with an old button mouse, a Magic mouse, or a laptop trackpad. I have tried Better TouchTool without success. In 3-button editing mode, the middle button is supposed to Move or MovO, but it just rotates instead. This makes any sort of docking much more difficult.
> 
> Also, is there a guide to what all the Mouse Mode commands actually do? MvAZ? MvSZ? PkTB? DrgM?
> 
> -- 
> Jason D. Kahn
> Dept. of Chemistry and Biochemistry
> University of Maryland
> College Park

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

----- Forwarded Message -----
From: "ABANTIKA PAL" <aba...@ii...>
To: pym...@li...
Sent: Tuesday, December 6, 2016 11:15:31 AM
Subject: Error while installing Pymol

Hi,
 
I have downloaded open source project PyMOL from SourceForge: http://sourceforge.net/projects/pymol/. I am using CentOS 7. I have performed following two installation steps:
python setup.py build install --home=~
~/bin/pymol

I have also installed the required softwares by 

# CentOS
yum install subversion gcc gcc-c++ kernel-devel python-devel tkinter python-pmw glew-devel \
  freeglut-devel libpng-devel freetype-devel libxml2-devel


Now, when I am trying to execute the pymol, following errors are coming

libGL error: unable to load driver: i965_dri.so
libGL error: driver pointer missing
libGL error: failed to load driver: i965
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
X Error of failed request:  GLXBadContext
  Major opcode of failed request:  153 (GLX)
  Minor opcode of failed request:  6 (X_GLXIsDirect)
  Serial number of failed request:  35
  Current serial number in output stream:  34
 PyMOL: abrupt program termination.

Please help me out.

Hi --

I use Mac Pymol 1.8.4 / Mac OS Sierra, but this issue has been present
forever. I usually cannot get the middle "M" commands to work, either with
an old button mouse, a Magic mouse, or a laptop trackpad. I have tried
Better TouchTool without success. In 3-button editing mode, the middle
button is supposed to Move or MovO, but it just rotates instead. This makes
any sort of docking much more difficult.

Also, is there a guide to what all the Mouse Mode commands actually do?
MvAZ? MvSZ? PkTB? DrgM?

-- 
Jason D. Kahn
Dept. of Chemistry and Biochemistry
University of Maryland
College Park

Since version 1.8.2, PyMOL auto-detects CA-only models, so no ribbon_trace_atoms or cartoon_trace_atoms needed anymore.

A nice tool that can assign secondary structure with CA trace only is SST:
http://lcb.infotech.monash.edu.au/sstweb2/

PSICO has an SST wrapper, so you can run it directly in PyMOL:

run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py
fetch 3b5d, async=0
sst
show cartoon

Hope that helps.

Cheers,
  Thomas

On 02 Dec 2016, at 08:24, Spencer Bliven <spe...@gm...> wrote:

> There is a cartoon variant too, although everything will look like a loop
> 
> set cartoon_trace_atoms, on
> show cartoon, polymer
> 
> On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao <Yux...@ut...> wrote:
> Hi Mohsen,
> 
> The PDB file of 3B5D only contains CA atoms, so most rendering like cartoon fails. You could try to visualize it by "set ribbon_trace_atoms, 1" and then show it as ribbon.
> 
> Yuxing
> 
> -----Original Message-----
> From: pym...@li... [mailto:pym...@li...]
> Sent: Tuesday, October 25, 2016 4:50 PM
> To: pym...@li...
> Subject: PyMOL-users Digest, Vol 125, Issue 14
> 
> Send PyMOL-users mailing list submissions to
>         pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>         pym...@li...
> 
> You can reach the person managing the list at
>         pym...@li...
> 
> When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..."
> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +0000
> From: Mohsen Chitsaz <moh...@fl...>
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pym...@li..."
>         <pym...@li...>
> Message-ID:
>         <SG2...@SG...>
> 
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi everyone,
> 
> Can someone please assist me opening this pdb file? I am trying to open EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it opens up as many little cross signs seem to be corresponding to CA atoms. When I try to preset it pretty or any other preset options, it disappears. The command "show cartoon" is not doing anything on it.
> 
> Cheers
> Mohsen
> 
> ________________________________
> 
> UT Southwestern
> 
> Medical Center
> 
> The future of medicine, today.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

There is a cartoon variant too, although everything will look like a loop

set cartoon_trace_atoms, on
show cartoon, polymer

On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao <
Yux...@ut...> wrote:

> Hi Mohsen,
>
> The PDB file of 3B5D only contains CA atoms, so most rendering like
> cartoon fails. You could try to visualize it by "set ribbon_trace_atoms, 1"
> and then show it as ribbon.
>
> Yuxing
>
> -----Original Message-----
> From: pym...@li... [mailto:
> pym...@li...]
> Sent: Tuesday, October 25, 2016 4:50 PM
> To: pym...@li...
> Subject: PyMOL-users Digest, Vol 125, Issue 14
>
> Send PyMOL-users mailing list submissions to
>         pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>         pym...@li...
>
> You can reach the person managing the list at
>         pym...@li...
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of PyMOL-users digest..."
>
> ------------------------------
>
> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +0000
> From: Mohsen Chitsaz <moh...@fl...>
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pym...@li..."
>         <pym...@li...>
> Message-ID:
>         <SG2PR03MB15688F28895FD8BF7A322112D5A80@SG2PR03MB1568.
> apcprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi everyone,
>
> Can someone please assist me opening this pdb file? I am trying to open
> EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation,
> but it opens up as many little cross signs seem to be corresponding to CA
> atoms. When I try to preset it pretty or any other preset options, it
> disappears. The command "show cartoon" is not doing anything on it.
>
> Cheers
> Mohsen
>
> -------------- next part --------------
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> ********************************************
>
> ________________________________
>
> UT Southwestern
>
>
> Medical Center
>
>
>
> The future of medicine, today.
>
>
>
> ------------------------------------------------------------
> ------------------
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
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> Learn the new .NET and ASP.NET CLI. Get your free copy!
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> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Tsjerk,

thanks for your reply!

this was also my first guess. However it isn't a formatting issue:

In [5]: print(cmd.get_coords("1xyz")[0,0])

41.0

Also fetched structures look "teared" in cartoon representation,
supposedly because of the wrong coordinates.

Calling the internal function from the _cmd.so C-lib also returns the
wrong coords:

>>> pymol._cmd.get_coords(cmd._COb, "1xyz")

array([[ 41., 25., 36.], [ 40., 25., 35.], [ 39., 24., 35.], ..., [ 11.,
26., 67.], [ 4., 32., 95.], [ 22., 45., 49.]], dtype=float32)

The error occurs both with local loaded pdb files and fetched pdb files.
(I initially supposed it had something to do with the fetch function of
the psicio plugin, which overloads the original fetch command)

So there must be something wrong with the loading of the pdb, when using
IPython...


regards

Leonhard


On 01.12.2016 16:35, Tsjerk Wassenaar wrote:
> Hi Leonhard,
>
> I would guess it's the formatting setting of numpy in IPython. You can
> see what one float really is:
>
> print(cmd.get_coords("1xyz")[0,0])
>
> Cheers,
>
> Tsjerk
>
>

Hi Leonhard,

I would guess it's the formatting setting of numpy in IPython. You can see
what one float really is:

print(cmd.get_coords("1xyz")[0,0])

Cheers,

Tsjerk

On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger <Leo...@ur...
> wrote:

> I guess formatting didn't work out as i expected. So once again and
> hopefully formatted:
>
>
> Hi!
>
> I stumbled upon some odd behavior when starting PyMol in an interactive
> IPython Session.
>
> PyMol can be launched from interactive IPython like this:
>
> In [1]: import pymol
> In [2]: from pymol import cmd
> In [3]: pymol.finish_launching()
> In [4]: cmd.fetch("1xyz")
>
> So far, everything is normal.
> However, when I want to get the coordinates of the structure the following
> happens:
>
> In [5]: cmd.get_coords("1xyz")
> Out[5]:
> array([[ 41., 25., 36.],
> [ 40., 25., 35.],
> [ 39., 24., 35.], ...,
> [ 11., 26., 67.],
> [ 4., 32., 95.],
> [ 22., 45., 49.]], dtype=float32)
>
> Even though the datatype is float32 apparently the decimals got lost
> somehow.
> The coordinates of the first atom should be: 41.511  25.152  36.876
>
> Repeating the above in a normal interactive Python Session everything
> works just fine:
>
> >>> import pymol
> >>> from pymol import cmd
> >>> pymol.finish_launching()
> >>> cmd.fetch("1xyz")
> >>> cmd.get_coords("1xyz")
> array([[ 41.51100159, 25.15200043, 36.87599945],
> [ 40.9070015 , 25.55500031, 35.56299973],
> [ 39.68399811, 24.70700073, 35.10599899], ...,
> [ 11.88700008, 26.97699928, 67.03900146],
> [ 4.45699978, 32.77299881, 95.16600037],
> [ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
>
> As I use IPython only for debugging of PyMol scripts/plugins this is not a
> very big problem.
> Still I'm interested in what causes this strange behavior. Is it a
> problem/bug in IPython or in PyMol?
> Maybe someone has more insights here and can give clarity!
>
> Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
>
> Thanks!
>
> regards
> Leonhard
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Dear Mohsen,

when I Google "pymol coordinates atom", the top hit is this:

https://pymolwiki.org/index.php/Get_Coordinates_I

Worth a try.

All best.


Andreas



On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz <
moh...@fl...> wrote:

> Hi all,
>
>
>
> Can anyone please help me in how to get coordinates of a selected atom or
> residue?
>
>
>
> Thank you
>
>
>
> Mohsen
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hej,

try this command and specify the atom selection:

cmd.get_atom_coords('atom selection')

see also:
https://pymolwiki.org/index.php/Get_Coordinates_I

Cheers,

Andreas

On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz <
moh...@fl...> wrote:

> Hi all,
>
>
>
> Can anyone please help me in how to get coordinates of a selected atom or
> residue?
>
>
>
> Thank you
>
>
>
> Mohsen
>
> ------------------------------------------------------------
> ------------------
>
> _______________________________________________
> 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,

Can anyone please help me in how to get coordinates of a selected atom or residue?

Thank you

Mohsen

I guess formatting didn't work out as i expected. So once again and
hopefully formatted:

Hi!

I stumbled upon some odd behavior when starting PyMol in an interactive
IPython Session.

PyMol can be launched from interactive IPython like this:

In [1]: import pymol
In [2]: from pymol import cmd
In [3]: pymol.finish_launching()
In [4]: cmd.fetch("1xyz")

So far, everything is normal.
However, when I want to get the coordinates of the structure the
following happens:

In [5]: cmd.get_coords("1xyz")
Out[5]:
array([[ 41., 25., 36.],
[ 40., 25., 35.],
[ 39., 24., 35.], ...,
[ 11., 26., 67.],
[ 4., 32., 95.],
[ 22., 45., 49.]], dtype=float32)

Even though the datatype is float32 apparently the decimals got lost
somehow.
The coordinates of the first atom should be: 41.511  25.152  36.876

Repeating the above in a normal interactive Python Session everything
works just fine:

>>> import pymol
>>> from pymol import cmd
>>> pymol.finish_launching()
>>> cmd.fetch("1xyz")
>>> cmd.get_coords("1xyz")
array([[ 41.51100159, 25.15200043, 36.87599945],
[ 40.9070015 , 25.55500031, 35.56299973],
[ 39.68399811, 24.70700073, 35.10599899], ...,
[ 11.88700008, 26.97699928, 67.03900146],
[ 4.45699978, 32.77299881, 95.16600037],
[ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)

As I use IPython only for debugging of PyMol scripts/plugins this is not
a very big problem.
Still I'm interested in what causes this strange behavior. Is it a
problem/bug in IPython or in PyMol?
Maybe someone has more insights here and can give clarity!

Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0

Thanks!

regards
Leonhard