pymol-users Mailing List for PyMOL Molecular Graphics System

Ah, thanks for the correction, Thomas.  I didn't realize the behavior was different between the command and Python function.  I guess I should have looked into it further and not just emailed from my phone!

Cheers,
Jared

On March 29, 2018 at 6:58:41 PM, Thomas Holder (tho...@sc...) wrote:

Hi Gary & Jared,  

PyMOL session files do not contain any graphics geometry. Export as COLLADA or VRML are the best options.  

The cmd.fetch() function is not asynchronous by default, only the fetch command is. This is controlled by the quiet=0 argument which is passed to all commands.  

Cheers,  
Thomas  


> On Mar 29, 2018, at 9:54 PM, Gary Oberbrunner <ga...@da...> wrote:  
>  
> Thanks for the idea Jared, but no, still nothing but atoms.  
>  
> On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson <jar...@co...> wrote:  
> Hi Gary -  
>  
> `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might execute before the structure is actually loaded. Try amending to:  
>  
> cmd.fetch(mol_id, async=0)  
>  
> Does that make a difference?  
>  
> Cheers,  
> Jared  
>  
>  
> On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (ga...@da...) wrote:  
>  
>> I'm running pymol "headless" in a script. After initializing pymol and calling finish_loading(), I do this:  
>> cmd.fetch(mol_id)  
>> cmd.show('spheres','all')  
>> session = cmd.get_session()  
>>  
>> ... but my session object only includes one object, the cObjectMolecule. I'm looking for it to include the graphics objects as well if that's possible. Any hints?  
>>  
>>  
>> --  
>> Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.  

--  
Thomas Holder  
PyMOL Principal Developer  
Schrödinger, Inc.  

Hi Gary & Jared,

PyMOL session files do not contain any graphics geometry. Export as COLLADA or VRML are the best options.

The cmd.fetch() function is not asynchronous by default, only the fetch command is. This is controlled by the quiet=0 argument which is passed to all commands.

Cheers,
  Thomas


> On Mar 29, 2018, at 9:54 PM, Gary Oberbrunner <ga...@da...> wrote:
> 
> Thanks for the idea Jared, but no, still nothing but atoms.
> 
> On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson <jar...@co...> wrote:
> Hi Gary - 
> 
> `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might execute before the structure is actually loaded.  Try amending to:
> 
> cmd.fetch(mol_id, async=0)
> 
> Does that make a difference?
> 
> Cheers,
> Jared
> 
> 
> On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (ga...@da...) wrote:
> 
>> I'm running pymol "headless" in a script. After initializing pymol and calling finish_loading(), I do this:
>>   cmd.fetch(mol_id)
>>   cmd.show('spheres','all')
>>   session = cmd.get_session()
>> 
>> ... but my session object only includes one object, the cObjectMolecule. I'm looking for it to include the graphics objects as well if that's possible. Any hints?
>> 
>> 
>> --
>> Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thanks for the idea Jared, but no, still nothing but atoms.

On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson <jar...@co...>
wrote:

> Hi Gary -
>
> `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might
> execute before the structure is actually loaded.  Try amending to:
>
> cmd.fetch(mol_id, async=0)
>
> Does that make a difference?
>
> Cheers,
> Jared
>
>
> On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (
> ga...@da...) wrote:
>
> I'm running pymol "headless" in a script. After initializing pymol and
> calling finish_loading(), I do this:
>   cmd.fetch(mol_id)
>   cmd.show('spheres','all')
>   session = cmd.get_session()
>
> ... but my session object only includes one object, the cObjectMolecule.
> I'm looking for it to include the graphics objects as well if that's
> possible. Any hints?
>
>
> --
> Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.
> ------------------------------------------------------------------------------
>
> Check out the vibrant tech community on one of the world's most
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>
>


-- 
Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.

Hi Gary - 

`cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might execute before the structure is actually loaded.  Try amending to:

cmd.fetch(mol_id, async=0)

Does that make a difference?

Cheers,
Jared


On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner (ga...@da...) wrote:

I'm running pymol "headless" in a script. After initializing pymol and calling finish_loading(), I do this:
  cmd.fetch(mol_id)
  cmd.show('spheres','all')
  session = cmd.get_session()

... but my session object only includes one object, the cObjectMolecule. I'm looking for it to include the graphics objects as well if that's possible. Any hints?


--
Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.
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 I'm running pymol "headless" in a script. After initializing pymol and
calling finish_loading(), I do this:
  cmd.fetch(mol_id)
  cmd.show('spheres','all')
  session = cmd.get_session()

... but my session object only includes one object, the cObjectMolecule.
I'm looking for it to include the graphics objects as well if that's
possible. Any hints?


-- 
Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.

Dear David,

We used the win_amd64.whl files for all 3 versions, taken from the link in
my first email. I would think, that those are compiled from the 64 Bit
binaries?
The issue also precedes the Fall Creators Update, we first experienced it
in July 2017.
Thank you for your suggestions.

Dear Vijay,

I am also using .bat file to install the dependencies and Pymol using pip,
see the .txt file attached.
Could you please share your script with me in order to test this further?

Best,
Florian

On Tue, Mar 27, 2018 at 12:31 AM, David Mathog <ma...@ca...> wrote:

> On 26-Mar-2018 06:26, Arsanis IT wrote:
>
>> This seems to happen only on Windows 10, as we tried it successfully with
>> the same files on a Windows 7 Pro 64 Bit machine.
>>
>> Any idea what the issue could be?
>>
>
>
> Was it by any chance a 32 bit PyMOL binary?  Could be this:
>
> https://support.microsoft.com/en-us/help/4054150/issues-when
> -windows-10-fall-creators-update-calls-createwindowex-for-s
>
> So it may not be a W7 vs. W10 thing, it could be a W10 version problem.
>
> Regards,
>
> David Mathog
> ma...@ca...
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
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> Archives: http://www.mail-archive.com/pym...@li...
>



-- 

*Florian Wende |** IT Support*
Arsanis Biosciences GmbH | Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria
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Hi Gary -

I’m admittedly not very familiar with Pymol2glmol, but the choice will depend on what kind of integration you want. If you’re looking for a static 3D representation that can be rotated around but not otherwise altered, COLLADA could be ok. I wrote the code for that exporter as part of a PyMOL Open Source Fellowship with an aim to help get PyMOL graphics into things like Apple iBooks (for which COLLADA was the required format for interactive models) and for 3D printing. For anything interactive, though, you're right that you’ll want to use one of the more sophisticated options.  In addition to GLmol, I would also check out JSmol and maybe Uglymol, depending on what your specific requirements might be.

Hope that helps.

Cheers,
Jared


On March 26, 2018 at 9:08:13 AM, Gary Oberbrunner (ga...@da...) wrote:

Hi; I'm interested in integrating open-source pymol into another package.  I'd like to get the graphics representation of the molecule(s); I've looked at the COLLADA exporter and Pymol2glmol. Pymol2gmol uses cmd.get_session() and parses the result; is that the best way to go?

thanks,

--
Gary Oberbrunner
------------------------------------------------------------------------------  
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On 26-Mar-2018 06:26, Arsanis IT wrote:
> This seems to happen only on Windows 10, as we tried it successfully 
> with
> the same files on a Windows 7 Pro 64 Bit machine.
> 
> Any idea what the issue could be?


Was it by any chance a 32 bit PyMOL binary?  Could be this:

https://support.microsoft.com/en-us/help/4054150/issues-when-windows-10-fall-creators-update-calls-createwindowex-for-s

So it may not be a W7 vs. W10 thing, it could be a W10 version problem.

Regards,

David Mathog
ma...@ca...

Hi all,

A colleague of mine has the same issue as mentioned in a previous email
from 7th March (see attachment), namely that Pymol seems to get stuck every
time on Windows 10 Pro 64 Bit.
To install Pymol we used the precompiled versions (1.8.2, 1.9.0 and 2.1.0)
provided here https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol using the
installation guide from this site:
http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/

This seems to happen only on Windows 10, as we tried it successfully with
the same files on a Windows 7 Pro 64 Bit machine.

Any idea what the issue could be?

Best regards,
Florian


-- 

*Florian Wende |** IT Support*
Arsanis Biosciences GmbH | Helmut-Qualtinger-Gasse 2, 1030 Vienna, Austria
<" rel="nofollow">https://maps.google.com/?q=Helmut-Qualtinger-Gasse+2,+1030+Vienna,+Austria&entry=gmail&source=g>
O: +43 1 7990 117 34 |  E: it...@ar...

Confidentiality Note: This information and any attachments is confidential
and only for use by the individual or entity to whom it has been sent. Any
unauthorized
dissemination, distribution or copying of this message is strictly
prohibited. If you are not the intended recipient please inform the
sender immediately by reply e-mail and delete this message from your
system. Thank you for your co-operation.

Hi; I'm interested in integrating open-source pymol into another package.
I'd like to get the graphics representation of the molecule(s); I've looked
at the COLLADA exporter and Pymol2glmol. Pymol2gmol uses cmd.get_session()
and parses the result; is that the best way to go?

thanks,

-- 
Gary Oberbrunner

Hi ,

I am trying to generate random sequences for a given region in order to run
Gromacs

This is the sequence of my protein

MEEKLKKTKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEI
MEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDA
GPETMTQRLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVD
SVFSQVCTHLDALK

I want to generate random sequences from two different regions

This is one of the region

TGDLLRSEVSSGSARGKKLSEI

This is another region

KATEPVIAFYEKRGIVRKVNAE


Would it be possible to do that and set up the model to run Gromacs?

Thanks

Mohammad

Thanks, I have all my answers !

Fabrice Carles - PhD student
Structural Bioinformatics & Chemoinformatics,
Institut de Chimie Organique et Analytique (ICOA)
University of Orleans - France



2018-03-16 13:41 GMT+01:00 Thomas Holder <tho...@sc...>:

> Hi Fabrice,
>
> Interesting observation. PyMOL reads "metalc" bonds from mmCIF files and
> represents them as "zero order" bonds. Apparently this breaks double bond
> detection in your given example. This is something we need to fix.
>
> Possible workarounds:
> 1) Load .pdb files instead of .cif files
> 2) Load .mmtf files, they have full bonding information, including bond
> orders
> 3) Load .cif files, but with connect_mode=4, which looks up all bond
> orders from the chemical components dictionary
>
> Relevant settings:
> https://pymolwiki.org/index.php/Fetch_type_default
> https://pymolwiki.org/index.php/Connect_mode
>
> Cheers,
>   Thomas
>
> > On Mar 15, 2018, at 5:55 PM, Fabrice Carles <car...@gm...>
> wrote:
> >
> > Dear pymol users,
> >
> > I would like to know if there is a way to change pymol2 settings in
> order to fit older version.
> >
> > My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same
> results.
> >
> > I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:
> >
> > cmd.fetch('1atp')
> > cmd.select('lig','organic')
> >
> > Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of
> ATP molecule but pymol2 does not.
> > Using the command below, I compare the differences between the two
> versions in sdf file format.
> >
> > cmd.save('atp.sdf',selection='lig')
> >
> > diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf
> > 2c2
> > <   PyMOL186          3D                             0
> > ---
> > >   PyMOL2.0          3D                             0
> > 18,19c18,19
> > <    11.1000    9.8800   -1.4300 O   0  5  0  0  0  0  0  0  0  0  0  0
> > <    13.9290    9.9200   -2.7000 O   0  5  0  0  0  0  0  0  0  0  0  0
> > ---
> > >    11.1000    9.8800   -1.4300 O   0  0  0  0  0  0  0  0  0  0  0  0
> > >    13.9290    9.9200   -2.7000 O   0  0  0  0  0  0  0  0  0  0  0  0
> > 24c24
> > <    15.7480    6.8350   -0.4270 O   0  5  0  0  0  0  0  0  0  0  0  0
> > ---
> > >    15.7480    6.8350   -0.4270 O   0  0  0  0  0  0  0  0  0  0  0  0
> > 38c38
> > <   1 18  2  0  0  0  0
> > ---
> > >   1 18  1  0  0  0  0
> > 41c41
> > <   2 19  2  0  0  0  0
> > ---
> > >   2 19  1  0  0  0  0
> > 47c47
> > <   3 24  2  0  0  0  0
> > ---
> > >   3 24  1  0  0  0  0
> >
> >
> >
> > How can I force pymol2 to write exactly the same sdf as before ?
> > Is there new defaults settings in pymol2 that I can override ?
> >
> > Thanks,
> >
> > Fabrice
> >
> > Fabrice Carles - PhD student
> > Structural Bioinformatics & Chemoinformatics,
> > Institut de Chimie Organique et Analytique (ICOA)
> >
> > University of Orleans - France
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Fabrice,

Interesting observation. PyMOL reads "metalc" bonds from mmCIF files and represents them as "zero order" bonds. Apparently this breaks double bond detection in your given example. This is something we need to fix.

Possible workarounds:
1) Load .pdb files instead of .cif files
2) Load .mmtf files, they have full bonding information, including bond orders
3) Load .cif files, but with connect_mode=4, which looks up all bond orders from the chemical components dictionary

Relevant settings:
https://pymolwiki.org/index.php/Fetch_type_default
https://pymolwiki.org/index.php/Connect_mode

Cheers,
  Thomas

> On Mar 15, 2018, at 5:55 PM, Fabrice Carles <car...@gm...> wrote:
> 
> Dear pymol users,
> 
> I would like to know if there is a way to change pymol2 settings in order to fit older version. 
> 
> My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same results. 
> 
> I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:
> 
> cmd.fetch('1atp')
> cmd.select('lig','organic')
> 
> Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of ATP molecule but pymol2 does not.
> Using the command below, I compare the differences between the two versions in sdf file format.
> 
> cmd.save('atp.sdf',selection='lig')
> 
> diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf 
> 2c2
> <   PyMOL186          3D                             0
> ---
> >   PyMOL2.0          3D                             0
> 18,19c18,19
> <    11.1000    9.8800   -1.4300 O   0  5  0  0  0  0  0  0  0  0  0  0
> <    13.9290    9.9200   -2.7000 O   0  5  0  0  0  0  0  0  0  0  0  0
> ---
> >    11.1000    9.8800   -1.4300 O   0  0  0  0  0  0  0  0  0  0  0  0
> >    13.9290    9.9200   -2.7000 O   0  0  0  0  0  0  0  0  0  0  0  0
> 24c24
> <    15.7480    6.8350   -0.4270 O   0  5  0  0  0  0  0  0  0  0  0  0
> ---
> >    15.7480    6.8350   -0.4270 O   0  0  0  0  0  0  0  0  0  0  0  0
> 38c38
> <   1 18  2  0  0  0  0
> ---
> >   1 18  1  0  0  0  0
> 41c41
> <   2 19  2  0  0  0  0
> ---
> >   2 19  1  0  0  0  0
> 47c47
> <   3 24  2  0  0  0  0
> ---
> >   3 24  1  0  0  0  0
> 
> 
> 
> How can I force pymol2 to write exactly the same sdf as before ? 
> Is there new defaults settings in pymol2 that I can override ?  
> 
> Thanks,
> 
> Fabrice
> 
> Fabrice Carles - PhD student
> Structural Bioinformatics & Chemoinformatics,
> Institut de Chimie Organique et Analytique (ICOA)
> 
> University of Orleans - France

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

It works!

Thanks,
Yang

On Thu, Mar 15, 2018 at 3:29 AM, Thomas Holder <
tho...@sc...> wrote:

> Hi Yang,
>
> With PyMOL 2.1, "finish_launching" should not be necessary to use the
> PyMOL API in jupyter notebook. PyMOL will now automatically start a backend
> process (without the GUI, like with "-c") in the main thread if you call
> any pymol.cmd function. Check out this screenshot:
>
> https://pymol.org/alpha/jupyter-notebook.png
>
> On the other hand, "finish_launching" will launch PyMOL in a new thread
> with an event loop, which will cause 100% CPU usage (at least with "-c").
>
> Cheers,
>   Thomas
>
> > On Mar 15, 2018, at 1:35 AM, Yang Su <su...@cr...> wrote:
> >
> > Dear List,
> >
> > I would like to use some of the pymol capabilities with my other python
> code in jupyter notebook. But after running
> >
> > import pymol
> > pymol.finish_launching(['pymol', '-qc'])
> >
> > CPU usage stays at 100% for the python process. After
> >
> > pymol.cmd.quit()
> >
> > CPU usage returns to normal.  I see the same pattern when I run those
> commands in an interactive python shell. Tried pymol 2.0/2.1 with both
> python 2.7 and 3.6 on mac (anaconda) and linux.
> >
> > Did I do anything wrong or is it a bug in pymol?
> >
> > Thanks,
> >
> > Yang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Dear pymol users,

I would like to know if there is a way to change pymol2 settings in order
to fit older version.

My problem is very simple. Pymol 2 and pymol 1.8 do not provide the same
results.

I download and select the ATP molecule in both pymol 1.8.6.0. and 2.0.7:

cmd.fetch('1atp')
cmd.select('lig','organic')

Pymol 1.8.6.0 detect three double bonds between phosphate and oxygen of ATP
molecule but pymol2 does not.
Using the command below, I compare the differences between the two versions
in sdf file format.

cmd.save('atp.sdf',selection='lig')

diff 1atp_pymol1.8.sdf 1atp_pymol2.sdf
2c2
<   PyMOL186          3D                             0
---
>   PyMOL2.0          3D                             0
18,19c18,19
<    11.1000    9.8800   -1.4300 O   0  5  0  0  0  0  0  0  0  0  0  0
<    13.9290    9.9200   -2.7000 O   0  5  0  0  0  0  0  0  0  0  0  0
---
>    11.1000    9.8800   -1.4300 O   0  0  0  0  0  0  0  0  0  0  0  0
>    13.9290    9.9200   -2.7000 O   0  0  0  0  0  0  0  0  0  0  0  0
24c24
<    15.7480    6.8350   -0.4270 O   0  5  0  0  0  0  0  0  0  0  0  0
---
>    15.7480    6.8350   -0.4270 O   0  0  0  0  0  0  0  0  0  0  0  0
38c38
<   1 18  2  0  0  0  0
---
>   1 18  1  0  0  0  0
41c41
<   2 19  2  0  0  0  0
---
>   2 19  1  0  0  0  0
47c47
<   3 24  2  0  0  0  0
---
>   3 24  1  0  0  0  0



How can I force pymol2 to write exactly the same sdf as before ?
Is there new defaults settings in pymol2 that I can override ?

Thanks,

Fabrice

Fabrice Carles - PhD student
Structural Bioinformatics & Chemoinformatics,
Institut de Chimie Organique et Analytique (ICOA)
University of Orleans - France

Hi Yang,

With PyMOL 2.1, "finish_launching" should not be necessary to use the PyMOL API in jupyter notebook. PyMOL will now automatically start a backend process (without the GUI, like with "-c") in the main thread if you call any pymol.cmd function. Check out this screenshot:

https://pymol.org/alpha/jupyter-notebook.png

On the other hand, "finish_launching" will launch PyMOL in a new thread with an event loop, which will cause 100% CPU usage (at least with "-c").

Cheers,
  Thomas

> On Mar 15, 2018, at 1:35 AM, Yang Su <su...@cr...> wrote:
> 
> Dear List,
> 
> I would like to use some of the pymol capabilities with my other python code in jupyter notebook. But after running
> 
> import pymol
> pymol.finish_launching(['pymol', '-qc'])
> 
> CPU usage stays at 100% for the python process. After
> 
> pymol.cmd.quit()
> 
> CPU usage returns to normal.  I see the same pattern when I run those commands in an interactive python shell. Tried pymol 2.0/2.1 with both python 2.7 and 3.6 on mac (anaconda) and linux.
> 
> Did I do anything wrong or is it a bug in pymol?
> 
> Thanks,
> 
> Yang

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear List,

I would like to use some of the pymol capabilities with my other python
code in jupyter notebook. But after running

import pymol
pymol.finish_launching(['pymol', '-qc'])

CPU usage stays at 100% for the python process. After

pymol.cmd.quit()

CPU usage returns to normal.  I see the same pattern when I run those
commands in an interactive python shell. Tried pymol 2.0/2.1 with both
python 2.7 and 3.6 on mac (anaconda) and linux.

Did I do anything wrong or is it a bug in pymol?

Thanks,

Yang

Greetings,

We are happy to announce the release of PyMOL 2.1. Download ready-to-use installers from https://pymol.org/ or update your 2.0 installation with "conda update -c schrodinger pymol".

We also have exciting news for those who prefer to compile PyMOL from source.  We’ve pushed the PyMOL 2.0 and 2.1 user interface updates to the open-source repository at sourceforge (rev 4187).

New features include (Incentive and Open-Source):
- new selection keywords "polymer.protein" and "polymer.nucleic"
- MMTF export
- plugins initialized by default (can be suppressed with -k)

Incentive PyMOL only:
- "auto_copy_images" support on all platforms
- SpaceNavigator support on all platforms (requires installation of additional
  drivers, see https://pymol.org/spacenavigator/ )
- colored errors and warnings in the feedback window
- Stereo 3D auto-detection on Linux

Find the complete release notes at:
https://pymol.org/d/media:new21 

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear everyone,



The following link has a script about calculating the radius of gyration for a protein: https://pymolwiki.org/index.php/Radius_of_gyration



Can someone explain the steps of the calculation? what are the rr and mm values? in the comments it just says (First part of the sum under the sqrt) for rr, and (Second part of the sum under the sqrt) for mm, but there is no indication what they are.


Also why in the sqrt is rr/(tmax - mm) isnt tmax the total mass of the protein? so what are you minusing from it?



Regards,

AC Research

Hi Martin,

Regarding "contribute with others who only have 1.3 available": If this is about exchanging session files, it should be fine to use a recent version of PyMOL and set the "pse_export_version" setting before saving files:

set pse_export_version, 1.3
save compatible-with-1-3.pse

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

Cheers,
  Thomas

> On Mar 8, 2018, at 11:45 PM, Martin Plochberger <mar...@un...> wrote:
> 
> Dear all,
> 
> I recently was asked to install Pymol 1.3 from source on MacOSX 10.13.
> 
> It had worked on 10.12 and after the update to 10.13 had stopped
> working.
> 
> The person needs that specific version to contribute with others who
> only have 1.3 available.
> 
> After my failed installation attempts we will probably try other
> options (installing it on a Linux machine etc.), but I am still
> wondering if it would be possible on MacOSX 10.13.
> 
> What I did:
> 
>   1. I downloaded the source code from sourceforge (https://sourceforge.n
>      et/projects/pymol/files/pymol/1.3r2/)
>   2. I installed the dependencies described in the README to the best of
>      my knowledge :)
>   3. I ran 'python setup.py build install
> 
> At 3. I then got the "build errors" below.
> 
> I am happy to provide more details on my installation steps if someone
> wants to get into it :).
> 
> My questions:
> 
> * Did you have success installing the 1.3 sourceforge version I linked
>   above? If yes, please be so kind and share your findings.
> * Are the below "build errors" only due to buggy code or does it look
>   like I am possibly missing a dependency?
> 
> Thanks in advance for any help you can give me and ... Cheers ;)
> 
> ======================= BUILD ERRORS START =======================
> python setup.py build install
> running build
> running build_py
> package init file 'modules/web/javascript/__init__.py' not found (or
> not 
> a regular file)
> package init file 'modules/web/javascript/__init__.py' not found (or
> not 
> a regular file)
> running build_ext
> building 'pymol._cmd' extension
> clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g 
> -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG 
> -D_PYMOL_FREETYPE -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3
> -Ilayer4 
> -Ilayer5 -I/usr/X11R6/include 
> -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include 
> -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include/GL 
> -I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-
> 1.3r2/ext/include/freetype2 
> -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/local/include 
> -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include 
> -I/usr/local/opt/tcl-tk/include 
> -I/usr/local/Cellar/python@2/2.7.14_2/Frameworks/Python.framework/Versi
> ons/2.7/include/python2.7 
> -c modules/cealign/src/ccealignmodule.cpp -o 
> build/temp.macosx-10.13-x86_64-2.7/modules/cealign/src/ccealignmodule.o
> In file included from modules/cealign/src/ccealignmodule.cpp:32:
> In file included from modules/cealign/src/ccealignmodule.H:36:
> In file included from modules/cealign/src/tnt/tnt.h:41:
> modules/cealign/src/tnt/tnt_array1d.h:238:15: warning: '&&' within '||'
>       [-Wlogical-op-parentheses]
>         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
>             ~~~~~~~~~^~~~~~~~~~~~ ~~
> modules/cealign/src/tnt/tnt_array1d.h:238:15: note: place parentheses 
> around the
>       '&&' expression to silence this warning
>         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
>                      ^
>             (                    )
> In file included from modules/cealign/src/ccealignmodule.cpp:32:
> In file included from modules/cealign/src/ccealignmodule.H:36:
> In file included from modules/cealign/src/tnt/tnt.h:48:
> modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: warning: '&&' 
> within '||'
>       [-Wlogical-op-parentheses]
>         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
>             ~~~~~~~~~^~~~~~~~~~~~ ~~
> modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: note: place 
> parentheses
>       around the '&&' expression to silence this warning
>         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
>                      ^
>             (                    )
> In file included from modules/cealign/src/ccealignmodule.cpp:32:
> In file included from modules/cealign/src/ccealignmodule.H:36:
> In file included from modules/cealign/src/tnt/tnt.h:55:
> modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:3: error: no
> matching
>       constructor for initialization of 'Array1D<int>'
>                 rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
>                 ^       ~~~~
> modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
> constructor 
> not
>       viable: no known conversion from 'const int *' to 'const int'
> for 
> 2nd
>       argument; dereference the argument with *
>                  Array1D(int n, const T &a);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
> constructor 
> not
>       viable: 2nd argument ('const int *') would lose const qualifier
>                  Array1D(int n,  T *a);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
> constructor 
> not
>       viable: requires single argument 'n', but 2 arguments were 
> provided
>         explicit Array1D(int n);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
> constructor 
> not
>       viable: requires single argument 'A', but 2 arguments were 
> provided
>     inline   Array1D(const Array1D &A);
>              ^
> modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate
> constructor 
> not
>       viable: requires 0 arguments, but 2 were provided
>                  Array1D();
>                  ^
> In file included from modules/cealign/src/ccealignmodule.cpp:32:
> In file included from modules/cealign/src/ccealignmodule.H:36:
> In file included from modules/cealign/src/tnt/tnt.h:55:
> modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no 
> matching
>       constructor for initialization of 'Array1D<int>'
>                 rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
>                                ^       ~~~~~
> modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
> constructor 
> not
>       viable: no known conversion from 'const int *' to 'const int'
> for 
> 2nd
>       argument; dereference the argument with *
>                  Array1D(int n, const T &a);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
> constructor 
> not
>       viable: 2nd argument ('const int *') would lose const qualifier
>                  Array1D(int n,  T *a);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
> constructor 
> not
>       viable: requires single argument 'n', but 2 arguments were 
> provided
>         explicit Array1D(int n);
>                  ^
> modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
> constructor 
> not
>       viable: requires single argument 'A', but 2 arguments were 
> provided
>     inline   Array1D(const Array1D &A);
>              ^
> modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate
> constructor 
> not
>       viable: requires 0 arguments, but 2 were provided
>                  Array1D();
>                  ^
> modules/cealign/src/ccealignmodule.cpp:588:5: warning: variable 'o' is
>       incremented both in the loop header and in the loop body
>       [-Wfor-loop-analysis]
>     o++;
>     ^
> modules/cealign/src/ccealignmodule.cpp:431:36: note: incremented here
>   for ( int o = 0; o < bufferSize; o++ ) {
>                                    ^
> 3 warnings and 2 errors generated.
> error: command 'clang' failed with exit status 1
> ======================= BUILD ERRORS END =======================
> 
> -- 
> Martin Plochberger
> ******************************
> Max F. Perutz Support GmbH
> Dr. Bohr-Gasse 9, Room: 4.220
> A-1030 Vienna
> ******************************
> Tel.: +43-1-4277-24041

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear all,

I recently was asked to install Pymol 1.3 from source on MacOSX 10.13.

It had worked on 10.12 and after the update to 10.13 had stopped
working.

The person needs that specific version to contribute with others who
only have 1.3 available.

After my failed installation attempts we will probably try other
options (installing it on a Linux machine etc.), but I am still
wondering if it would be possible on MacOSX 10.13.

What I did:

   1. I downloaded the source code from sourceforge (https://sourceforge.n
      et/projects/pymol/files/pymol/1.3r2/)
   2. I installed the dependencies described in the README to the best of
      my knowledge :)
   3. I ran 'python setup.py build install

At 3. I then got the "build errors" below.

I am happy to provide more details on my installation steps if someone
wants to get into it :).

My questions:

 * Did you have success installing the 1.3 sourceforge version I linked
   above? If yes, please be so kind and share your findings.
 * Are the below "build errors" only due to buggy code or does it look
   like I am possibly missing a dependency?

Thanks in advance for any help you can give me and ... Cheers ;)

======================= BUILD ERRORS START =======================
python setup.py build install
running build
running build_py
package init file 'modules/web/javascript/__init__.py' not found (or
not 
a regular file)
package init file 'modules/web/javascript/__init__.py' not found (or
not 
a regular file)
running build_ext
building 'pymol._cmd' extension
clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g 
-fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE -D_PYMOL_LIBPNG 
-D_PYMOL_FREETYPE -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3
-Ilayer4 
-Ilayer5 -I/usr/X11R6/include 
-I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include 
-I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-1.3r2/ext/include/GL 
-I/Users/4dm1n1str4t0r/Desktop/1_3_source/pymol-
1.3r2/ext/include/freetype2 
-Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/local/include 
-I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include 
-I/usr/local/opt/tcl-tk/include 
-I/usr/local/Cellar/python@2/2.7.14_2/Frameworks/Python.framework/Versi
ons/2.7/include/python2.7 
-c modules/cealign/src/ccealignmodule.cpp -o 
build/temp.macosx-10.13-x86_64-2.7/modules/cealign/src/ccealignmodule.o
In file included from modules/cealign/src/ccealignmodule.cpp:32:
In file included from modules/cealign/src/ccealignmodule.H:36:
In file included from modules/cealign/src/tnt/tnt.h:41:
modules/cealign/src/tnt/tnt_array1d.h:238:15: warning: '&&' within '||'
       [-Wlogical-op-parentheses]
         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
             ~~~~~~~~~^~~~~~~~~~~~ ~~
modules/cealign/src/tnt/tnt_array1d.h:238:15: note: place parentheses 
around the
       '&&' expression to silence this warning
         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
                      ^
             (                    )
In file included from modules/cealign/src/ccealignmodule.cpp:32:
In file included from modules/cealign/src/ccealignmodule.H:36:
In file included from modules/cealign/src/tnt/tnt.h:48:
modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: warning: '&&' 
within '||'
       [-Wlogical-op-parentheses]
         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
             ~~~~~~~~~^~~~~~~~~~~~ ~~
modules/cealign/src/tnt/tnt_fortran_array1d.h:224:15: note: place 
parentheses
       around the '&&' expression to silence this warning
         if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
                      ^
             (                    )
In file included from modules/cealign/src/ccealignmodule.cpp:32:
In file included from modules/cealign/src/ccealignmodule.H:36:
In file included from modules/cealign/src/tnt/tnt.h:55:
modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:3: error: no
matching
       constructor for initialization of 'Array1D<int>'
                 rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
                 ^       ~~~~
modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
constructor 
not
       viable: no known conversion from 'const int *' to 'const int'
for 
2nd
       argument; dereference the argument with *
                  Array1D(int n, const T &a);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
constructor 
not
       viable: 2nd argument ('const int *') would lose const qualifier
                  Array1D(int n,  T *a);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
constructor 
not
       viable: requires single argument 'n', but 2 arguments were 
provided
         explicit Array1D(int n);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
constructor 
not
       viable: requires single argument 'A', but 2 arguments were 
provided
     inline   Array1D(const Array1D &A);
              ^
modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate
constructor 
not
       viable: requires 0 arguments, but 2 were provided
                  Array1D();
                  ^
In file included from modules/cealign/src/ccealignmodule.cpp:32:
In file included from modules/cealign/src/ccealignmodule.H:36:
In file included from modules/cealign/src/tnt/tnt.h:55:
modules/cealign/src/tnt/tnt_sparse_matrix_csr.h:97:18: error: no 
matching
       constructor for initialization of 'Array1D<int>'
                 rowptr_(M, r), colind_(nz, c), dim1_(M), dim2_(N) {}
                                ^       ~~~~~
modules/cealign/src/tnt/tnt_array1d.h:63:11: note: candidate
constructor 
not
       viable: no known conversion from 'const int *' to 'const int'
for 
2nd
       argument; dereference the argument with *
                  Array1D(int n, const T &a);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:64:11: note: candidate
constructor 
not
       viable: 2nd argument ('const int *') would lose const qualifier
                  Array1D(int n,  T *a);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:62:11: note: candidate
constructor 
not
       viable: requires single argument 'n', but 2 arguments were 
provided
         explicit Array1D(int n);
                  ^
modules/cealign/src/tnt/tnt_array1d.h:65:14: note: candidate
constructor 
not
       viable: requires single argument 'A', but 2 arguments were 
provided
     inline   Array1D(const Array1D &A);
              ^
modules/cealign/src/tnt/tnt_array1d.h:61:11: note: candidate
constructor 
not
       viable: requires 0 arguments, but 2 were provided
                  Array1D();
                  ^
modules/cealign/src/ccealignmodule.cpp:588:5: warning: variable 'o' is
       incremented both in the loop header and in the loop body
       [-Wfor-loop-analysis]
     o++;
     ^
modules/cealign/src/ccealignmodule.cpp:431:36: note: incremented here
   for ( int o = 0; o < bufferSize; o++ ) {
                                    ^
3 warnings and 2 errors generated.
error: command 'clang' failed with exit status 1
======================= BUILD ERRORS END =======================

-- 
Martin Plochberger
******************************
Max F. Perutz Support GmbH
Dr. Bohr-Gasse 9, Room: 4.220
A-1030 Vienna
******************************
Tel.: +43-1-4277-24041

Hi Wolfram - The "level" parameter corresponds to sigma level.  

https://pymolwiki.org/index.php/Display_CCP4_Maps

Hope that helps.

Cheers,
Jared


On March 8, 2018 at 11:07:41 AM, wtempel (wt...@gm...) wrote:

Hello all,
even though I have some intuition about what the "level" parameter of the "isomesh" command may mean, I would like to know what unit I should use when I describe the contour level in figure caption, for example.
Thank you.
Wolfram
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Hello all,
even though I have some intuition about what the "level" parameter of the
"isomesh" command may mean, I would like to know what unit I should use
when I describe the contour level in figure caption, for example.
Thank you.
Wolfram

Hi Ulrike,

> - Is there a command, which would be: select all residues, which are right now shown as sticks ? Background : sometimes you analyze the protein a little bit more empirically, that means you highlight some residues in sticks e.g. at domain interfaces , then you undo this and take others. If there is not a command like this, it would be convenient to have it.

Yes you can select by representation:

select mysele, rep sticks

See "Style" selectors in the operator table:
https://pymolwiki.org/index.php/Selection_Algebra

> - the undo button (academic pymol version 2.0.5) is still not working (but I guess you know this, would be nice to have an undo in the academic licence)

Adding undo for styling etc. is on the roadmap!

The already existing undo button only covers editing operations (stuff you can do in the builder, like adding bonds or fragments).

> - Is there a command, which would give you all the image specific stettings. Background: sometimes you create a figure you save the .png,  but you don't click the log command for the .pse file. After some  month/years you want to generate a similar figure, and then it looks pretty similar but not identical. I guess it would be more complicated, to import the .png in pymol, and retrieve all "figure" options (like ray trace mode, antialias, dash width, transparency etc) . But still .. such a feature would be useful.

If you want to list all settings which have been changed (have a non-default value) you can use this script: https://pymolwiki.org/index.php/Save_settings

> - sometimes pymol (version 2.0.5) crashes, especially before ray-ing more complex sceneries (but I guess this is a common bug. Still, would be nice to have that fixed)

It's possible that you run out of memory when ray tracing a very complex scene. You could try lowering the "hash_max" setting, which trades computing time for memory usage: https://pymolwiki.org/index.php/Hash_max

If it's crashing for a different reason, we should fix it. It would be great if you can provide the exact steps which lead to a crash for you.

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello


I'm using the pymol ver. 2.0.7 in windows 10 64bit system


i have an error for running pymol.


pymol doesn't answer temporarily (around 10sec) after every action

(ex. click the residues, copy image to clipboard etc)


decisively,  In APBS tool,  if i click the button to show  the surface charge of protein,


Pymol doesn't answer entirely. And windows show the error message, python doesn't answer anymore.


To, solve this problem i tried to reinstall all the data in the system after removing all several times.


In the first time pymol answer normally, but after using few days, it show same error.


the other programs work well.



How can i fix this problem?