pymol-users Mailing List for PyMOL Molecular Graphics System

Hi all,
I have difficulty using Python scripts in PyMOL. I cannot install PyMOL in a way that is compatible to Python. I initially installed Python 3.5.2, and then PyMOL 1.7.4. But PyMOL doesn't recognise a Python script file that I have created in NotePad++. I have put the file in PyMOL active directory, and run this command in PyMOL command line "run script.py".
Can someone please help me with this?
Cheers
Mohsen

Greetings,
PyMOL 1.8.2.3 fixes an annoying picking bug, where picking atoms with the mouse can select the wrong atoms. If you use Incentive PyMOL 1.8.x, we recommend to upgrade. Builds are available as usual from http://pymol.org/download
Cheers,
- The PyMOL Team at Schrödinger
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Lukas,
All operators:
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l455
Operator types (e.g. number of arguments) and priority (order of operation):
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l365
Hope that helps.
Cheers,
 Thomas
On 19 Jul 2016, at 05:52, Lukáš Pravda <xp...@nc...> wrote:
> Dear PyMOL users,
> 
> I am trying to add support for pymol-like selection algebra into one of your software tools. Therefore, I was wondering, if there is any formal description of the language available in for example as context-free grammar. I was trying to find something in the source code rather unsuccessfully.
> 
> All the best
> 
> Lukas Pravda
> 
> CEITEC | Central European Institute of Technology
> http://webchem.ncbr.muni.cz/
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thank you for your responses guys.
CAVER is another possible PyMOL plugin http://www.caver.cz
Thanks Emilio. I have installed CAVER and I'm looking into it now - will
let you know if this works well for me.
Also thank you to Andreas and Doug. I'll be sure to check your suggestions
out! It doesn't necessarily need to be in PyMol, but more important that it
can iteratively check multiple pdbs and output all the results together. I
think at least one of your suggestions will allow this.
Daniel
On Wed, Jul 20, 2016 at 3:22 PM, Emilio Xavier Esposito <
emi...@gm...> wrote:
> Hi Daniel
> CAVER is another possible PyMOL plugin http://www.caver.cz
>
> From the CAVER website, "CAVER provides rapid, accurate and fully
> automated calculation of tunnels and channels in static and dynamic
> structures. The molecules amendable to analysis of CAVER include
> proteins, nucleic acids, or inorganic materials."
>
> Emilio
>
> On Tue, Jul 19, 2016 at 6:57 PM, Andreas Warnecke
> <4nd...@gm...> wrote:
> > I haven't used it before, but I there is a PyMOL plugin called KVfinder
> that
> > detects cavities. Potentially this offers an approach for you.
> >
> > On Jul 20, 2016 12:05 AM, "Daniel James" <dan...@gm...>
> wrote:
> >>
> >> Hi all,
> >>
> >> I haven't used this list before but can't find an answer to my question
> >> elsewhere. I am selecting the antibody binding site automatically to
> >> calculate the surface area of the binding sites.
> >>
> >> However, some of the binding sites have holes/cavities in the surface -
> I
> >> would like to be able to detect if a surface has a hole in it on PyMol
> (to
> >> make a note that it needs to be looked at manually).
> >>
> >> I create an object of the antigen binding site, show surface and then
> use
> >> get_area to get SASA.
> >>
> >> Any help will be appreciated.
> >>
> >> Thanks,
> >> Daniel
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> >> traffic
> >> patterns at an interface-level. Reveals which users, apps, and protocols
> >> are
> >> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> >> J-Flow, sFlow and other flows. Make informed decisions using capacity
> >> planning
> >> reports.http://sdm.link/zohodev2dev
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> ------------------------------------------------------------------------------
> > What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> > patterns at an interface-level. Reveals which users, apps, and protocols
> are
> > consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> > J-Flow, sFlow and other flows. Make informed decisions using capacity
> > planning
> > reports.http://sdm.link/zohodev2dev
> > _______________________________________________
> > 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 Daniel
CAVER is another possible PyMOL plugin http://www.caver.cz
>From the CAVER website, "CAVER provides rapid, accurate and fully
automated calculation of tunnels and channels in static and dynamic
structures. The molecules amendable to analysis of CAVER include
proteins, nucleic acids, or inorganic materials."
Emilio
On Tue, Jul 19, 2016 at 6:57 PM, Andreas Warnecke
<4nd...@gm...> wrote:
> I haven't used it before, but I there is a PyMOL plugin called KVfinder that
> detects cavities. Potentially this offers an approach for you.
>
> On Jul 20, 2016 12:05 AM, "Daniel James" <dan...@gm...> wrote:
>>
>> Hi all,
>>
>> I haven't used this list before but can't find an answer to my question
>> elsewhere. I am selecting the antibody binding site automatically to
>> calculate the surface area of the binding sites.
>>
>> However, some of the binding sites have holes/cavities in the surface - I
>> would like to be able to detect if a surface has a hole in it on PyMol (to
>> make a note that it needs to be looked at manually).
>>
>> I create an object of the antigen binding site, show surface and then use
>> get_area to get SASA.
>>
>> Any help will be appreciated.
>>
>> Thanks,
>> Daniel
>>
>>
>> ------------------------------------------------------------------------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>> are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning
>> reports.http://sdm.link/zohodev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
> _______________________________________________
> 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 Daniel,
If you don't HAVE to use Pymol, something like fPocket, HOLE or 
PocketDepth from this list might do what you want:
http://www.vls3d.com/links/bioinformatics/binding-pockets
You might find this list interesting too:
http://www.vls3d.com/links/bioinformatics/peptides-antibodies-epitopes
cheers,
Doug
Quoting Andreas Warnecke <4nd...@gm...> on Wed, 20 Jul 
2016 00:57:39 +0200:
> I haven't used it before, but I there is a PyMOL plugin called KVfinder
> that detects cavities. Potentially this offers an approach for you.
> On Jul 20, 2016 12:05 AM, "Daniel James" <dan...@gm...> wrote:
>
>> Hi all,
>>
>> I haven't used this list before but can't find an answer to my question
>> elsewhere. I am selecting the antibody binding site automatically to
>> calculate the surface area of the binding sites.
>>
>> However, some of the binding sites have holes/cavities in the surface - I
>> would like to be able to detect if a surface has a hole in it on PyMol (to
>> make a note that it needs to be looked at manually).
>>
>> I create an object of the antigen binding site, show surface and then use
>> get_area to get SASA.
>>
>> Any help will be appreciated.
>>
>> Thanks,
>> Daniel
>>
>>
>> ------------------------------------------------------------------------------
>> What NetFlow Analyzer can do for you? Monitors network bandwidth and
>> traffic
>> patterns at an interface-level. Reveals which users, apps, and protocols
>> are
>> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
>> J-Flow, sFlow and other flows. Make informed decisions using capacity
>> planning
>> reports.http://sdm.link/zohodev2dev
>> _______________________________________________
>> 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. Douglas R. Houston
Senior Lecturer in Computational Biochemistry
Institute of Quantitative Biology, Biochemistry and Biotechnology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

I haven't used it before, but I there is a PyMOL plugin called KVfinder
that detects cavities. Potentially this offers an approach for you.
On Jul 20, 2016 12:05 AM, "Daniel James" <dan...@gm...> wrote:
> Hi all,
>
> I haven't used this list before but can't find an answer to my question
> elsewhere. I am selecting the antibody binding site automatically to
> calculate the surface area of the binding sites.
>
> However, some of the binding sites have holes/cavities in the surface - I
> would like to be able to detect if a surface has a hole in it on PyMol (to
> make a note that it needs to be looked at manually).
>
> I create an object of the antigen binding site, show surface and then use
> get_area to get SASA.
>
> Any help will be appreciated.
>
> Thanks,
> Daniel
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
> _______________________________________________
> 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 haven't used this list before but can't find an answer to my question
elsewhere. I am selecting the antibody binding site automatically to
calculate the surface area of the binding sites.
However, some of the binding sites have holes/cavities in the surface - I
would like to be able to detect if a surface has a hole in it on PyMol (to
make a note that it needs to be looked at manually).
I create an object of the antigen binding site, show surface and then use
get_area to get SASA.
Any help will be appreciated.
Thanks,
Daniel

Dear PyMOL users, 
 
I am trying to add support for pymol-like selection algebra into one of your
software tools. Therefore, I was wondering, if there is any formal
description of the language available in for example as context-free
grammar. I was trying to find something in the source code rather
unsuccessfully.
 
All the best
 
Lukas Pravda
 
CEITEC | Central European Institute of Technology
http://webchem.ncbr.muni.cz/

Dear PyMol users!
Using present -> ligand sites context menu I would like to display
possible non-covalent contacts between ions embedded within the
protein.
First I tried to rename ATOM to HETATM record corresponds to ions
however pymol still don't recognize ions as ligand.
Will be very thankful for any suggestions!
James

Hi James,
The "super" method requires CA atoms in the selection because it aligns based on the backbone trace.
You should use "rms" or "rms_cur" to get a side chain RMSD.
Cheers,
 Thomas
On 12 Jul 2016, at 10:10, James Starlight <jms...@gm...> wrote:
> Dear pymol users!
> 
> I need to estimate how the side-chains dynamics are differs in MD
> compared to X-ray structure.
> 
> Assuming that I have 2 structures one from md and another from X-ray
> and I select Sidechains from the both as obj1 and obj02
> select xray &! n. n+ca+c+o
> select md &! n. n+ca+c+o
> 
> now trying to align both objects with any method I obtain error like
> 
> PyMOL>super obj01, obj02
> ExecutiveAlign: invalid selections for alignment.
> 
> How I can fix it?
> 
> James
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi James -
For the first part, you should use split_states and super or cealign, as in my response to one of your emails last month.
https://sourceforge.net/p/pymol/mailman/message/35156097/
Then, once you have aligned all the trajectory structures (let's say they're called traj_01 through traj_10), you can create new objects from each of the snapshots and the heme using the `or` operator in the selection passed to `create`.
create heme_traj_01, traj_01 or resn HEM
create heme_traj_02, traj_02 or resn HEM
etc.
Hope that helps.
Cheers,
Jared
For 1, you need to get your MD simulatio
On Jul 12, 2016, at 3:05 AM, James Starlight <jms...@gm...<mailto:jms...@gm...>> wrote:
Dear Pymol Users!
Here I desice to continue my topic regarding scripting in Pymol;
My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly
What I need from pymol to write some script, which will
1) align (superimpose) each MD snapshot againt reference
2) copy HEME residue from reference to each of the superimpsoed
snapshot within the same position.
Thanks so much for any suggestions regarding realization !
James
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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...

Dear pymol users!
I need to estimate how the side-chains dynamics are differs in MD
compared to X-ray structure.
Assuming that I have 2 structures one from md and another from X-ray
and I select Sidechains from the both as obj1 and obj02
select xray &! n. n+ca+c+o
select md &! n. n+ca+c+o
now trying to align both objects with any method I obtain error like
PyMOL>super obj01, obj02
 ExecutiveAlign: invalid selections for alignment.
How I can fix it?
James

Hi Mohsen,
So raytracing is indeed not available in the educational version. I find
this a bit strange, as I regarded the educational version the
least-changed-with-respect-to-the-original (say 0.99), which did have
raytracing available. Also, I like students to give me reports with pretty
pictures, and would argue that 'educational' should also allow some basic
raytracing.
Alternatives are:
- getting an academic license
- compile from source (or get from a repository)
- export the scene and ray trace in a different program.
Hope it helps,
Tsjerk
On Tue, Jul 12, 2016 at 10:16 AM, Mohsen Chitsaz <
moh...@fl...> wrote:
> Hi Pymol users,
>
>
>
> The "ray command" is not working in my Educational version of Pymol. It
> seems that educational version does not allow to use this command.
>
>
>
> Does anyone have a solution for this please?
>
>
>
> Your reply is very much appreciated.
>
>
>
> Cheers
>
> Mohsen
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning
> reports.http://sdm.link/zohodev2dev
> _______________________________________________
> 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.

Hi Mohsen,
What happens? What error do you get?
Best,
Tsjerk
On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" <moh...@fl...>
wrote:
Hi Pymol users,
The "ray command" is not working in my Educational version of Pymol. It
seems that educational version does not allow to use this command.
Does anyone have a solution for this please?
Your reply is very much appreciated.
Cheers
Mohsen
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning
reports.http://sdm.link/zohodev2dev
_______________________________________________
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 Pymol users,
The "ray command" is not working in my Educational version of Pymol. It seems that educational version does not allow to use this command.
Does anyone have a solution for this please?
Your reply is very much appreciated.
Cheers
Mohsen

Dear Pymol Users!
Here I desice to continue my topic regarding scripting in Pymol;
My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly
What I need from pymol to write some script, which will
1) align (superimpose) each MD snapshot againt reference
2) copy HEME residue from reference to each of the superimpsoed
snapshot within the same position.
Thanks so much for any suggestions regarding realization !
James

Problem solved, thanks to Folmer Fredslund, to whom I am obliged!
So, I will give you an idiot's guide on how to make PyMOL to produce movies, 
in Ubuntu:
* Download freemol-freemol.tar.gz from:
http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/freemol/?view=tar
* Copy freemol-freemol.tar.gz to a specific directory, eg /opt, typing:
sudo cp ~/Downloads/freemol-freemol.tar.gz /opt/.
* Unzip your file, typing:
cd /opt
sudo tar zxvf freemol-freemol.tar.gz
This is the tree of freemol directory:
.
├── bin
│ └── mpeg_encode.exe
├── include
├── lib
├── libpy
│ └── freemol
│ ├── apbs.py
│ ├── __init__.py
│ ├── mengine.py
│ └── mpeg_encode.py
├── licenses
│ └── mpeg_encode.txt
├── LICENSE.txt
├── README.txt
└── share
* Download freemol-mpeg_encode.tar.gz from:
www.bioinformatics.org/cgi-
bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/?view=tar
* Unzip your file:
sudo tar ztvf freemol-mpeg_encode.tar.gz 
* Define $FREEMOL directory. If this is /opt/freemol, type:
export FREEMOL=/opt/freemol
* Execute the following commands:
cd mpeg_encode
./configure
make
sudo make install
* If you have done it right, you have to see following two files:
/opt/freemol/bin/mpeg_encode.exe
/opt/freemol/licenses/mpeg_encode.txt
If you do not see them, the two files are probably at:
/bin/mpeg_encode.exe
/licenses/mpeg_encode.txt
In that case, just move them (sudo mv) to the appropriate directories.
* Type:
cd
cd bin/
pico pymol.sh
* Put this content into your script:
#!/bin/bash
FREEMOL=/opt/freemol
export FREEMOL
pymol
* Give execution rights to the script:
chmod 755 pymol.sh
* As ~/bin is in the $PATH, from now on, you should run pymol through this 
script, by typing anywhere:
pymol.sh
Finally, I suggest that all this could be included in the source code of 
pymol, in the following releases.
Best Regards,
Ioannis
-- 
Dr Ioannis Michalopoulos
Staff Research Scientist - Associate Professor Level
Centre of Systems Biology
Tel: +30 210 6597 127
Fax: +30 210 6597 545
Email: imi...@bi...
_________________________________________________
Biomedical Research Foundation, Academy of Athens
Soranou tou Efessiou 4, 115 27 Athens, Greece

Nope! I do not know what I am supposed to do with it (where to find it and how 
to compile it, if necessary)... Any idea, David?
BTW: The link to the Parallel Berkeley Encoder (mpeg_encode) is not working. 
Nevertheless, we can still get freemol from bioinformatics.org. I have the 
feeling that I only need mpeg_encode (and not APBS, PDB2PQR and mengine), 
right?
Ioannis
On Friday 08 of July 2016 09:16:40 David Hall wrote:
> Do you have the python code from freemol.org ?
> 
> -David
> 
> > On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos 
<imi...@bi...> wrote:
> >> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote:
> >> Dear Ioannis,
> >> 
> >>> On 2016年07月08日 09:04, Ioannis Michalopoulos wrote:
> >>> Dear PyMOL users,
> >>> 
> >>> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on
> >>> the
> >>> web. This produced the directory:
> >>> 
> >>> /opt/pymol-svn/
> >>> 
> >>> and a symbolic link to pymol executable:
> >>> 
> >>> /usr/bin/pymol -> /opt/pymol-svn/pymol*
> >>> 
> >>> PyMOL works fine. Nevertheless, when I try:
> >>> 
> >>> File > Save Movie As > MPEG...
> >>> 
> >>> I get the following error message:
> >>> 
> >>> MPEG encoder missing.
> >>> The FreeMOL add-ons may not be installed
> >>> 
> >>> I downloaded the source code for mpeg_encode
> >>> (freemol-mpeg_encode.tar.gz)
> >>> from:
> >>> 
> >>> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_
> >>> en
> >>> code/?view=tar
> >>> 
> >>> and I did the following:
> >>> 
> >>> tar zxvf freemol-mpeg_encode.tar.gz
> >>> cd mpeg_encode
> >>> ./configure
> >>> make
> >>> sudo make install
> >>> 
> >>> This created the following file:
> >>> 
> >>> /bin/mpeg_encode.exe
> >>> 
> >>> That means that mpeg_encode.exe is in the PATH (it runs from any
> >>> directory). mpeg_encode.exe seems to work. Unfortunately, when I try to
> >>> produce a movie in pymol, I get the same error message. What have I done
> >>> wrong?
> >> 
> >> I hope it is very simple.
> >> You need to include an environment variable $FREEEMOL pointing at the
> >> directory where
> >> freemol is installed
> >> 
> >> If you are using bash that would be
> >> export FREEMOL=/your/bath/to/freemol/
> >> where the mpeg_encode.exe file is in
> >> /your/bath/to/freemol/bin/mpeg_encode.exe
> >> 
> >> Hope this helps!
> > 
> > I created a directory:
> > 
> > /opt/freemol
> > 
> > with two subdirectories:
> > 
> > /opt/freemol/bin
> > /opt/freemol/licenses
> > 
> > which contain the files:
> > 
> > /opt/freemol/bin/mpeg_encode.exe
> > /opt/freemol/licenses/mpeg_encode.txt
> > 
> > I created the file:
> > 
> > pymol.sh
> > 
> > with this content:
> > 
> > #!/bin/bash
> > FREEMOL=/opt/freemol
> > export FREEMOL
> > pymol
> > 
> > I ran pymol.sh, but the problem remained the same. Any idea?
> > 
> > Ioannis
> > 
> >> Folmer
> >> 
> >>> Thank you in advance.
> >>> 
> >>> Best Regards,
> >>> 
> >>> Ioannis
-- 
Dr Ioannis Michalopoulos
Staff Research Scientist - Associate Professor Level
Centre of Systems Biology
Tel: +30 210 6597 127
Fax: +30 210 6597 545
Email: imi...@bi...
_________________________________________________
Biomedical Research Foundation, Academy of Athens
Soranou tou Efessiou 4, 115 27 Athens, Greece

Do you have the python code from freemol.org ?
-David
> On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos <imi...@bi...> wrote:
> 
>> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote:
>> Dear Ioannis,
>> 
>>> On 2016年07月08日 09:04, Ioannis Michalopoulos wrote:
>>> Dear PyMOL users,
>>> 
>>> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the
>>> web. This produced the directory:
>>> 
>>> /opt/pymol-svn/
>>> 
>>> and a symbolic link to pymol executable:
>>> 
>>> /usr/bin/pymol -> /opt/pymol-svn/pymol*
>>> 
>>> PyMOL works fine. Nevertheless, when I try:
>>> 
>>> File > Save Movie As > MPEG...
>>> 
>>> I get the following error message:
>>> 
>>> MPEG encoder missing.
>>> The FreeMOL add-ons may not be installed
>>> 
>>> I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
>>> from:
>>> 
>>> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_en
>>> code/?view=tar
>>> 
>>> and I did the following:
>>> 
>>> tar zxvf freemol-mpeg_encode.tar.gz
>>> cd mpeg_encode
>>> ./configure
>>> make
>>> sudo make install
>>> 
>>> This created the following file:
>>> 
>>> /bin/mpeg_encode.exe
>>> 
>>> That means that mpeg_encode.exe is in the PATH (it runs from any
>>> directory). mpeg_encode.exe seems to work. Unfortunately, when I try to
>>> produce a movie in pymol, I get the same error message. What have I done
>>> wrong?
>> 
>> I hope it is very simple.
>> You need to include an environment variable $FREEEMOL pointing at the
>> directory where
>> freemol is installed
>> 
>> If you are using bash that would be
>> export FREEMOL=/your/bath/to/freemol/
>> where the mpeg_encode.exe file is in
>> /your/bath/to/freemol/bin/mpeg_encode.exe
>> 
>> Hope this helps!
> 
> I created a directory:
> 
> /opt/freemol
> 
> with two subdirectories:
> 
> /opt/freemol/bin
> /opt/freemol/licenses
> 
> which contain the files:
> 
> /opt/freemol/bin/mpeg_encode.exe
> /opt/freemol/licenses/mpeg_encode.txt
> 
> I created the file:
> 
> pymol.sh
> 
> with this content:
> 
> #!/bin/bash
> FREEMOL=/opt/freemol
> export FREEMOL
> pymol
> 
> I ran pymol.sh, but the problem remained the same. Any idea?
> 
> Ioannis
> 
>> Folmer
>> 
>>> Thank you in advance.
>>> 
>>> Best Regards,
>>> 
>>> Ioannis
> 
> -- 
> Dr Ioannis Michalopoulos
> Staff Research Scientist - Associate Professor Level
> Centre of Systems Biology
> 
> Tel: +30 210 6597 127
> Fax: +30 210 6597 545
> Email: imi...@bi...
> _________________________________________________
> Biomedical Research Foundation, Academy of Athens
> Soranou tou Efessiou 4, 115 27 Athens, Greece
> 
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote:
> Dear Ioannis,
> 
> On 2016年07月08日 09:04, Ioannis Michalopoulos wrote:
> > Dear PyMOL users,
> > 
> > I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the
> > web. This produced the directory:
> > 
> > /opt/pymol-svn/
> > 
> > and a symbolic link to pymol executable:
> > 
> > /usr/bin/pymol -> /opt/pymol-svn/pymol*
> > 
> > PyMOL works fine. Nevertheless, when I try:
> > 
> > File > Save Movie As > MPEG...
> > 
> > I get the following error message:
> > 
> > MPEG encoder missing.
> > The FreeMOL add-ons may not be installed
> > 
> > I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
> > from:
> > 
> > http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_en
> > code/?view=tar
> > 
> > and I did the following:
> > 
> > tar zxvf freemol-mpeg_encode.tar.gz
> > cd mpeg_encode
> > ./configure
> > make
> > sudo make install
> > 
> > This created the following file:
> > 
> > /bin/mpeg_encode.exe
> > 
> > That means that mpeg_encode.exe is in the PATH (it runs from any
> > directory). mpeg_encode.exe seems to work. Unfortunately, when I try to
> > produce a movie in pymol, I get the same error message. What have I done
> > wrong?
> 
> I hope it is very simple.
> You need to include an environment variable $FREEEMOL pointing at the
> directory where
> freemol is installed
> 
> If you are using bash that would be
> export FREEMOL=/your/bath/to/freemol/
> where the mpeg_encode.exe file is in
> /your/bath/to/freemol/bin/mpeg_encode.exe
> 
> Hope this helps!
I created a directory:
/opt/freemol
with two subdirectories:
/opt/freemol/bin
/opt/freemol/licenses
which contain the files:
/opt/freemol/bin/mpeg_encode.exe
/opt/freemol/licenses/mpeg_encode.txt
I created the file:
pymol.sh
with this content:
#!/bin/bash
FREEMOL=/opt/freemol
export FREEMOL
pymol
I ran pymol.sh, but the problem remained the same. Any idea?
Ioannis
> Folmer
> 
> > Thank you in advance.
> > 
> > Best Regards,
> > 
> > Ioannis
-- 
Dr Ioannis Michalopoulos
Staff Research Scientist - Associate Professor Level
Centre of Systems Biology
Tel: +30 210 6597 127
Fax: +30 210 6597 545
Email: imi...@bi...
_________________________________________________
Biomedical Research Foundation, Academy of Athens
Soranou tou Efessiou 4, 115 27 Athens, Greece

Dear Ioannis,
On 2016年07月08日 09:04, Ioannis Michalopoulos wrote:
> Dear PyMOL users,
>
> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the web.
> This produced the directory:
>
> /opt/pymol-svn/
>
> and a symbolic link to pymol executable:
>
> /usr/bin/pymol -> /opt/pymol-svn/pymol*
>
> PyMOL works fine. Nevertheless, when I try:
>
> File > Save Movie As > MPEG...
>
> I get the following error message:
>
> MPEG encoder missing.
> The FreeMOL add-ons may not be installed
>
> I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
> from:
>
> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/?view=tar
>
> and I did the following:
>
> tar zxvf freemol-mpeg_encode.tar.gz
> cd mpeg_encode
> ./configure
> make
> sudo make install
>
> This created the following file:
>
> /bin/mpeg_encode.exe
>
> That means that mpeg_encode.exe is in the PATH (it runs from any directory).
> mpeg_encode.exe seems to work. Unfortunately, when I try to produce a movie in
> pymol, I get the same error message. What have I done wrong?
I hope it is very simple.
You need to include an environment variable $FREEEMOL pointing at the 
directory where
freemol is installed
If you are using bash that would be
export FREEMOL=/your/bath/to/freemol/
where the mpeg_encode.exe file is in 
/your/bath/to/freemol/bin/mpeg_encode.exe
Hope this helps!
Folmer
> Thank you in advance.
>
> Best Regards,
>
> Ioannis

Dear PyMOL users,
I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the web. 
This produced the directory:
/opt/pymol-svn/
and a symbolic link to pymol executable:
/usr/bin/pymol -> /opt/pymol-svn/pymol*
PyMOL works fine. Nevertheless, when I try:
File > Save Movie As > MPEG...
I get the following error message:
MPEG encoder missing.
The FreeMOL add-ons may not be installed
I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz) 
from:
http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/?view=tar
and I did the following:
tar zxvf freemol-mpeg_encode.tar.gz
cd mpeg_encode
./configure 
make
sudo make install
This created the following file:
/bin/mpeg_encode.exe
That means that mpeg_encode.exe is in the PATH (it runs from any directory). 
mpeg_encode.exe seems to work. Unfortunately, when I try to produce a movie in 
pymol, I get the same error message. What have I done wrong?
Thank you in advance.
Best Regards,
Ioannis
-- 
Dr Ioannis Michalopoulos
Staff Research Scientist - Associate Professor Level
Centre of Systems Biology
Tel: +30 210 6597 127
Fax: +30 210 6597 545
Email: imi...@bi...
_________________________________________________
Biomedical Research Foundation, Academy of Athens
Soranou tou Efessiou 4, 115 27 Athens, Greece

http://www.poissonboltzmann.org
psize.py and pdb2pqr.py are part of pdb2pqr
The others are part of apbs
> On Jul 6, 2016, at 5:15 AM, Yanni <y.g...@ma...> wrote:
> 
> Hello
> 
> I'm using pymol 1.7 on OS X 10.11.5.
> XQuartz version: 2.7.9
> python version: 2.7.12
> 
> When I launch the ABPS Tools 2.1, I get these errors:
> 
> Could not find default location for file: psize.py
> Could not find default location for file: apbs.exe
> Could not find default location for file: apbs-mpi.exe
> Could not find default location for file: apbs-mpi-openmpi.exe
> Could not find default location for file: apbs-mpi-lammpi.exe
> Could not find default location for file: pdb2pqr.py
> 
> I run a "find / -name psize.py " command but it can not locate the file.
> 
> Can somebody please help me? Where can I get 'psize.py' and the APBS 
> binary so I can
> specify them in the APBS plugin under "Program locations"?
> 
> Many thanks
> 
> 
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> 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'm using pymol 1.7 on OS X 10.11.5.
XQuartz version: 2.7.9
python version: 2.7.12
When I launch the ABPS Tools 2.1, I get these errors:
Could not find default location for file: psize.py
Could not find default location for file: apbs.exe
Could not find default location for file: apbs-mpi.exe
Could not find default location for file: apbs-mpi-openmpi.exe
Could not find default location for file: apbs-mpi-lammpi.exe
Could not find default location for file: pdb2pqr.py
I run a "find / -name psize.py " command but it can not locate the file.
Can somebody please help me? Where can I get 'psize.py' and the APBS 
binary so I can
specify them in the APBS plugin under "Program locations"?
Many thanks