pymol-users Mailing List for PyMOL Molecular Graphics System

Dear all,

I am trying to open a large trajectory file from a NAMD MD simulation on 
a Windows machine running Pymol 1.7.2..
In order to do this, I tried two things (both with defer_builds_mode 3):

  - Opening the .dcd file using load_traj, I was able to load most of it 
(400 frames); however, if I try to load the entire file (500 frames/1.1 
GB), Pymol crashes with a Runtime error once it gets to about 2GB RAM usage;
  - Converting the file to a PDB (and removing the solvent to save 
space), I can load around 1500 frames (1.1 GB); however, when I try to 
load a larger file (1.4 GB), Pymol crashes instantly with no message.

A few notes: the machine has 8GB RAM and an integrated graphics card.

Is there anything I can do?

Thanks,

Rui

PDB entry 3B5D is a low resolution (3.8 Å) structure that contains only C alpha coordinates (chain trace, no side chains) in the original pdb file. There are servers that will generate full backbone and side chain coordinates, e.g. SABBAC (http://bioserv.rpbs.univ-paris-diderot.fr/services/SABBAC/), however, be aware that low resolution structures do not get more precise by modelling in parts that were not resolved in the experimental structure .

Annemarie Honegger


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

That's lovely, David.

Thanks,
Albert

On 10/26/2016 11:56 AM, David Hall wrote:
> https://pymolwiki.org/index.php/Read_Pdbstr
>
> -David
>
> On Oct 26, 2016, at 3:55 AM, Albert Solernou <a.s...@LE...
> <mailto:a.s...@LE...>> wrote:
>
>> Dear All,
>> I was wondering if there was a way to load a PDB file stored in memory
>> instead of disk, i. e., a memory file, defined through StringIO or
>> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could
>> handle an open file instead of a file?
>>
>> Thanks,
>> Albert
>>
>>
>> --
>> ---------------------------------
>>   Dr Albert Solernou
>>   EPSRC Research Fellow,
>>   Department of Physics and Astronomy,
>>   University of Leeds
>>   Tel: +44 (0)1133 431451
>>
>> ------------------------------------------------------------------------------
>> The Command Line: Reinvented for Modern Developers
>> Did the resurgence of CLI tooling catch you by surprise?
>> Reconnect with the command line and become more productive.
>> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy!
>> http://sdm.link/telerik
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...
>> <mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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

-David

> On Oct 26, 2016, at 3:55 AM, Albert Solernou <a.s...@LE...> wrote:
> 
> Dear All,
> I was wondering if there was a way to load a PDB file stored in memory 
> instead of disk, i. e., a memory file, defined through StringIO or 
> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could 
> handle an open file instead of a file?
> 
> Thanks,
> Albert
> 
> 
> -- 
> ---------------------------------
>   Dr Albert Solernou
>   EPSRC Research Fellow,
>   Department of Physics and Astronomy,
>   University of Leeds
>   Tel: +44 (0)1133 431451
> 
> ------------------------------------------------------------------------------
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
> Reconnect with the command line and become more productive. 
> Learn the new .NET and ASP.NET CLI. Get your free copy!
> http://sdm.link/telerik
> _______________________________________________
> 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 Jordan,
I still don't figure out how to do that with "load_object". What is the 
"type" for a file handler? Would be "object" the file handler itself?

Albert

On 10/26/2016 10:58 AM, Jordan Willis wrote:
> Probably could use load_object instead.
>
>
>    def load_object(type,object,name,state=0,finish=1,discrete=0,
>                          quiet=1,zoom=-1,_self=cmd):
>         '''
> DESCRIPTION
>
>     "load_object" is a general developer function for loading Python objects
>     into PyMOL.
>> On Oct 26, 2016, at 1:55 AM, Albert Solernou <a.s...@le...
>> <mailto:a.s...@le...>> wrote:
>>
>> Dear All,
>> I was wondering if there was a way to load a PDB file stored in memory
>> instead of disk, i. e., a memory file, defined through StringIO or
>> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could
>> handle an open file instead of a file?
>>
>> Thanks,
>> Albert
>>
>>
>> --
>> ---------------------------------
>>   Dr Albert Solernou
>>   EPSRC Research Fellow,
>>   Department of Physics and Astronomy,
>>   University of Leeds
>>   Tel: +44 (0)1133 431451
>>
>> ------------------------------------------------------------------------------
>> The Command Line: Reinvented for Modern Developers
>> Did the resurgence of CLI tooling catch you by surprise?
>> Reconnect with the command line and become more productive.
>> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy!
>> http://sdm.link/telerik
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

Probably could use load_object instead.


   def load_object(type,object,name,state=0,finish=1,discrete=0,
                         quiet=1,zoom=-1,_self=cmd):
        '''
DESCRIPTION

    "load_object" is a general developer function for loading Python objects
    into PyMOL.
> On Oct 26, 2016, at 1:55 AM, Albert Solernou <a.s...@le...> wrote:
> 
> Dear All,
> I was wondering if there was a way to load a PDB file stored in memory 
> instead of disk, i. e., a memory file, defined through StringIO or 
> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could 
> handle an open file instead of a file?
> 
> Thanks,
> Albert
> 
> 
> -- 
> ---------------------------------
>   Dr Albert Solernou
>   EPSRC Research Fellow,
>   Department of Physics and Astronomy,
>   University of Leeds
>   Tel: +44 (0)1133 431451
> 
> ------------------------------------------------------------------------------
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
> Reconnect with the command line and become more productive. 
> Learn the new .NET and ASP.NET CLI. Get your free copy!
> http://sdm.link/telerik
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Dear All,
I was wondering if there was a way to load a PDB file stored in memory 
instead of disk, i. e., a memory file, defined through StringIO or 
tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could 
handle an open file instead of a file?

Thanks,
Albert


-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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

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------------------------------

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

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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

Hi Spencer,

Thanks a lot for that very useful information.

Regards,
Subha

On Tue, Oct 25, 2016 at 4:48 AM, Spencer Bliven <spe...@gm...>
wrote:

> First off, when the documentation includes square brackets in the command
> it indicates optional arguments. You don't include them in the command
> itself. In this case, pair_fit takes alternating selections from obj1 and
> obj 2. It also requires that the number of atoms in each selection be
> equal. I usually use CA atoms.
>
> From you example it seems like you want to align two structures in chunks
> of 254 residues, but in a permuted order. I would do it as follows. I'm
> going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and
> resi 1-255 and name CA").
>
> pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA,
> /obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA,
> /obj2///511-765/CA, /obj1///766-1020/CA
>
> Note that if you have any missing residues you might get an error 'Atom
> counts between selection sets don't match'. In this case you should make
> sure that the obj2 selections have the same number of atoms as the obj1
> selection.
>
> -Spencer
>
> On Fri, Oct 21, 2016 at 12:10 AM Subha K <sub...@gm...> wrote:
>
>> Hi there,
>>
>> Could somebody please help me with the correct syntax for pair fit?
>>
>> I tried this, but this doesn't work.
>>
>> pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi
>> 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi
>> 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]]
>>
>> Thanks,
>> Subha
>> ------------------------------------------------------------
>> ------------------
>> 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...
>
>

First off, when the documentation includes square brackets in the command
it indicates optional arguments. You don't include them in the command
itself. In this case, pair_fit takes alternating selections from obj1 and
obj 2. It also requires that the number of atoms in each selection be
equal. I usually use CA atoms.

>From you example it seems like you want to align two structures in chunks
of 254 residues, but in a permuted order. I would do it as follows. I'm
going to use the shorter "/obj1///1-255/CA" syntax to stand for "obj1 and
resi 1-255 and name CA").

pair_fit /obj2///256-510/CA, /obj1///1-255/CA, /obj2///1-255/CA,
/obj1///256-510/CA, /obj2///766-1020/CA, /obj1///511-765/CA,
/obj2///511-765/CA, /obj1///766-1020/CA

Note that if you have any missing residues you might get an error 'Atom
counts between selection sets don't match'. In this case you should make
sure that the obj2 selections have the same number of atoms as the obj1
selection.

-Spencer

On Fri, Oct 21, 2016 at 12:10 AM Subha K <sub...@gm...> wrote:

> Hi there,
>
> Could somebody please help me with the correct syntax for pair fit?
>
> I tried this, but this doesn't work.
>
> pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi
> 1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi
> 511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]]
>
> Thanks,
> Subha
>
> ------------------------------------------------------------------------------
> 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...

Hi there,

Could somebody please help me with the correct syntax for pair fit?

I tried this, but this doesn't work.

pairfit (obj2 and resi 256-510), (onj1 and resi 1-255), [(obj2 and resi
1-255), (obj1 and resi 256-510), [(obj2 and resi 766-1020), (obj1 and resi
511-765), [(obj2 and resi 511-765), (obj1 and resi 766-1020)]]]

Thanks,
Subha

Hi Gabriel,

Thanks for that suggestion. You are correct, the file is missing, but I
don't understand why my previous shutil.copy command is not working.

Thanks,
Subha

On Thu, Oct 20, 2016 at 11:38 AM, Gabriel Marques <
gab...@sc...> wrote:

> Is there an error output? I could see it not working if File10 is not
> located in the present working directory. If you are running the script by
> using the load command in pymol you can type pwd or cmd.pwd() on the input
> line to see the present working directory. The best bet to fix the problem
> is to prefix the absolute path to the directory with the pdb files. Like so:
>
> cmd.load(‘/home/me/pdbs/‘ + X + ‘.pdb’, x)
>
> Alternatively you can use the cd (change directory) command to move
> pymol’s pwd to the directory containing the pdbs, then you can run the load
> myscript.py command.
>
> Regards,
> Gabriel Marques
>
>
> > On Oct 20, 2016, at 1:06 PM, Subha K <sub...@gm...> wrote:
> >
> > Hi there,
> >
> > If the base name of my file is stored in a variable, how can I load the
> file using the variable?
> >
> > Eg., My filename is "File10.pdb"
> > and I have, X = File10
> >
> > I tried loading it using,
> > cmd.load ( X+".pdb", X), but it doesn't seem to work.
> >
> > Sorry for posting a very basic question.
> >
> > Thanks,
> > Subha
> >
> > ------------------------------------------------------------
> ------------------
> > 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...
>
>

Is there an error output? I could see it not working if File10 is not located in the present working directory. If you are running the script by using the load command in pymol you can type pwd or cmd.pwd() on the input line to see the present working directory. The best bet to fix the problem is to prefix the absolute path to the directory with the pdb files. Like so:

cmd.load(‘/home/me/pdbs/‘ + X + ‘.pdb’, x)

Alternatively you can use the cd (change directory) command to move pymol’s pwd to the directory containing the pdbs, then you can run the load myscript.py command.

Regards,
Gabriel Marques


> On Oct 20, 2016, at 1:06 PM, Subha K <sub...@gm...> wrote:
> 
> Hi there,
> 
> If the base name of my file is stored in a variable, how can I load the file using the variable?
> 
> Eg., My filename is "File10.pdb"
> and I have, X = File10
> 
> I tried loading it using,
> cmd.load ( X+".pdb", X), but it doesn't seem to work.
> 
> Sorry for posting a very basic question.
> 
> Thanks,
> Subha
> 
> ------------------------------------------------------------------------------
> 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...

Hi there,

If the base name of my file is stored in a variable, how can I load the
file using the variable?

Eg., My filename is "File10.pdb"
and I have, X = File10

I tried loading it using,
cmd.load ( X+".pdb", X), but it doesn't seem to work.

Sorry for posting a very basic question.

Thanks,
Subha

Dear Thomas,

Yes, confirmed fixed in rev 4163.  Thank you.

Best,
Quyen

On Tue, Oct 18, 2016 at 5:41 AM, Thomas Holder <
tho...@sc...> wrote:

> Hi Quyen,
>
> This should be fixed in svn rev 4163.
>
> Cheers,
>   Thomas
>
> On 18 Oct 2016, at 01:05, QT <rdi...@gm...> wrote:
>
> > Dear all,
> >
> > I'm having a compile error that I've never had before on the current svn
> revision 4162.  Compile broke on file CifDataValueFormatter.cpp
> >
> > g++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE
> -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS
> -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4
> -Ilayer5 -Imodules/cealign/src -Ibuild/generated
> -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
> -I/home/quyen/lib64/python2.7/site-packages/numpy/core/include
> -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2
> -I/usr/include/python2.7 -c layer3/CifDataValueFormatter.cpp -o
> build/temp.linux-x86_64-2.7/layer3/CifDataValueFormatter.o
> -Wno-write-strings -Wno-unused-function -Wno-char-subscripts -ffast-math
> -funroll-loops -fcommon -O3
> > In file included from layer3/CifDataValueFormatter.cpp:8:0:
> > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids
> initialization of member 'm_i'
> > layer3/CifDataValueFormatter.h:20:13: error: making 'm_i' static
> > layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids in-class
> initialization of non-const static member 'm_i'
> >
> > g++ version 4.5.1
> >
> > Do you have any advise on how to get past this blocker?
> >
> > Best,
> > Quyen
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Rename the script from .py to .pml

Regards,
Gabriel Marques
PyMOL

> On Oct 19, 2016, at 4:39 PM, #YEO JINGJIE# <JYEO1@e.ntu.edu.sg> wrote:
> 
> Dear Users,
> 
> I am trying to implement a script which uses a mix of pymol and python scripting. I enclosed the main portion within the 'python' and 'python end' commands. This runs perfectly fine in Pymol GUI mode, however when I tried it with 'pymol -cg my_script.py', it generates an error:
> 
> Traceback (most recent call last):
>  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 338, in parse
>    parsing.run_file(path,self.pymol_names,self.pymol_names)
>  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 452, in run_file
>    execfile(file,global_ns,local_ns)
>  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 447, in execfile
>    b.execfile(filename, global_ns, local_ns)
>  File "bondH.py", line 122
>    python end
>             ^
> SyntaxError: invalid syntax
> 
> How do I overcome this problem?
> 
> Best Regards,
> Jingjie
> **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.
> 
> ------------------------------------------------------------------------------
> 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...

Dear Users,

I am trying to implement a script which uses a mix of pymol and python scripting. I enclosed the main portion within the 'python' and 'python end' commands. This runs perfectly fine in Pymol GUI mode, however when I tried it with 'pymol -cg my_script.py', it generates an error:

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 338, in parse
    parsing.run_file(path,self.pymol_names,self.pymol_names)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 452, in run_file
    execfile(file,global_ns,local_ns)
  File "/usr/lib/python2.7/dist-packages/pymol/parsing.py", line 447, in execfile
    b.execfile(filename, global_ns, local_ns)
  File "bondH.py", line 122
    python end
             ^
SyntaxError: invalid syntax

How do I overcome this problem?

Best Regards,
Jingjie
**Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.

Thanks Gabriel and David for the useful suggestion.

Best Regards,
Subha

On Wed, Oct 19, 2016 at 12:11 PM, David Hall <li...@co...> wrote:

> I think the answer is to just use save, not that save_transformed function.
>
> -David
>
> On Oct 19, 2016, at 1:47 PM, Subha K <sub...@gm...> wrote:
>
> Hi there,
>
> I am trying to save the transformed coordinates of an object after
> performing an alignment. I came across the save_transformed.py [
> https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but,
> this seems to give a completely different coordinate of the object and not
> the one that is aligned.
>
> Is there any other way of saving the coordinates of an object after
> performing an alignment?
>
> Thanks,
> Subha
>
> ------------------------------------------------------------
> ------------------
> 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...
>
>

Hi Johan and Casper,

You can create a menu above the mouse mode panel by writing a wizard. There is no API documentation for wizards, so you have to learn from existing wizards as examples.

You can create an external menu or panel with Tkinter and/or Pmw. See for example eMovie as an example for a button panel, or BNI Tools for a multi-level menu.

Cheers,
  Thomas

On 10 Oct 2016, at 11:47, Schneiders J, Johan <j.s...@st...> wrote:

> Dear Pymol community, 
> We are students at the Hanze University of Applied Sciences, the Netherlands.
> Together with our teachers, Tsjerk Wassenaar and Jasper Bosman, we are working on integrating
> the leap motion sensor (hand gesture sensor) into Pymol for moving, and altering the display of, molecules in Pymol.
> 
> We want to create a menu within the GUI of Pymol that will be operated by hand gestures (the amount of extended fingers)
> and display what gestures you can make to manipulate the program.
> 
> Is there a built in way to add/create a menu within Pymol? We have looked on the Pymol wiki, tried googling 
> (keywords: 'pymol edit mouse viewing menu', 'Pymol external GUI', 'pymol adding GUI', 'pymol viewing menu', and so on...), 
> read some of the source code and searched the Pymol user mailing list archive,
> but haven't found a suitable solution.
> 
> In short:
> How do we go about adding an internal menu above the 'mouse mode' menu or adding
> an external window that will run alongside Pymol representing a menu, 
> and adding in our own attributes?
> 
> Thanks in advance,
> 
> Casper Peters and Johan Shcneiders.
> 
> P.S.
> Here are our e-mail addresses for contacting us:
> Casper Peters: c.c...@st...
> Johan Schneiders: j.s...@st...

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I think the answer is to just use save, not that save_transformed function.

-David

> On Oct 19, 2016, at 1:47 PM, Subha K <sub...@gm...> wrote:
> 
> Hi there,
> 
> I am trying to save the transformed coordinates of an object after performing an alignment. I came across the save_transformed.py [https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this seems to give a completely different coordinate of the object and not the one that is aligned.
> 
> Is there any other way of saving the coordinates of an object after performing an alignment?
> 
> Thanks,
> Subha
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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Subha K,

You can just call cmd.save or save on the object name as so:

fetch 1oky 1t46, async=0
align 1oky, 1t46
save /tmp/1oky_transformed.pdb, 1oky

PyMOL will write out the transformed coordinates of 1oky into the pdb file. The structure of the alignment command is such that pymol transforms the first object onto the second.

align mobile, target

mobile will have it’s coordinates changed, target will be unchanged.

Regards,
Gabriel Marques
PyMOL


> On Oct 19, 2016, at 1:47 PM, Subha K <sub...@gm...> wrote:
> 
> Hi there,
> 
> I am trying to save the transformed coordinates of an object after performing an alignment. I came across the save_transformed.py [https://pymolwiki.org/index.php/Modeling_and_Editing_Structures <" rel="nofollow">https://pymolwiki.org/index.php/Modeling_and_Editing_Structures>], but, this seems to give a completely different coordinate of the object and not the one that is aligned.
> 
> Is there any other way of saving the coordinates of an object after performing an alignment?
> 
> Thanks,
> Subha
> ------------------------------------------------------------------------------
> 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...

Hi there,

I am trying to save the transformed coordinates of an object after
performing an alignment. I came across the save_transformed.py [
https://pymolwiki.org/index.php/Modeling_and_Editing_Structures], but, this
seems to give a completely different coordinate of the object and not the
one that is aligned.

Is there any other way of saving the coordinates of an object after
performing an alignment?

Thanks,
Subha

Oh yeah, thanks a lot Gabriel Marques.

I figured out the rms_cur part too.

On Tue, Oct 18, 2016 at 12:23 PM, Gabriel Marques <
gab...@sc...> wrote:

> Looks like you’re missing a space in the string ‘and resn UNK’, it should
> be: i + ‘ and resn UNK’
>
> Regards,
> Gabriel Marques
>
> On Oct 18, 2016, at 1:57 PM, Subha K <sub...@gm...> wrote:
>
> Hi There,
>
> I am trying to calculate the rmsd of all ligands loaded in the pymol with
> reference to a reference ligand using a script. My current script looks
> like this,
>
>
> myobjects = cmd.get_object_list()
> print myobjects
> cmd.select('sele', "F60_target_14 and resn UNK")
> cmd.create('obj01', 'sele')
> for i in myobjects:
>     i = i.strip()
>     cmd.sele('sele', i +'and resn UNK')
>     cmd.create ('obj02', 'sele')
>     cmd.rms_cur ('obj02', 'obj01')
>     cmd.delete ('obj02')
>
>
> obj01 will be my reference and I want to use rms_cur to all objects loaded.
> The problems here are,
> (1) My obj02 selection part is not working properly. I know I am not
> calling the myobject list in the correct way. Could somebody help me fix
> this?
> (2) I want to write the rmsd values to a file. How can I do it?
>
> Thanks for the help.
>
> Regards,
> Subha
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org <http://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...
>
>
>

Looks like you’re missing a space in the string ‘and resn UNK’, it should be: i + ‘ and resn UNK’

Regards,
Gabriel Marques

> On Oct 18, 2016, at 1:57 PM, Subha K <sub...@gm...> wrote:
> 
> Hi There,
> 
> I am trying to calculate the rmsd of all ligands loaded in the pymol with reference to a reference ligand using a script. My current script looks like this,
> 
> 
> myobjects = cmd.get_object_list()
> print myobjects
> cmd.select('sele', "F60_target_14 and resn UNK")
> cmd.create('obj01', 'sele')
> for i in myobjects:
>     i = i.strip()
>     cmd.sele('sele', i +'and resn UNK')
>     cmd.create ('obj02', 'sele')
>     cmd.rms_cur ('obj02', 'obj01')
>     cmd.delete ('obj02')
> 
> 
> obj01 will be my reference and I want to use rms_cur to all objects loaded.
> The problems here are, 
> (1) My obj02 selection part is not working properly. I know I am not calling the myobject list in the correct way. Could somebody help me fix this?
> (2) I want to write the rmsd values to a file. How can I do it?
> 
> Thanks for the help.
> 
> Regards,
> Subha
> 
> 
> ------------------------------------------------------------------------------
> 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...