[PyMOL] molmol to pymol

2021-05-10 Thread Yanan He 
Hi All,

How can I convert MOLMOL format coordinates to PYMOL format? The reason for
me to do this is because I need to deposit my MOLMOL aligned NMR ensemble
to PDB, but it is  not recognized by PDB for the format difference.

Any help will be very helpful, thanks.

Yanan
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Re: [PyMOL] PyMOL 2.5 released

2021-05-10 Thread Jarrett Johnson 
Hi,

Open-source features are typically added on a rolling basis as they're
implemented (for example, support for curved helices have been in open
source since last October), so many of the features listed here (the
non-Incentive Only ones) should have already applied. If they aren't, feel
free to open a ticket on the open-source github repo. A PyMOL 2.5 github
tag and source release archive should also be uploaded within the next hour
or so.

Best,

Jarrett J

On Mon, May 10, 2021 at 1:59 PM Stephen P. Molnar 
wrote:

> very good.
>
> When will this migrate to github.com/schrodinger/pymol-open-source.git?
>
> On 05/10/2021 12:27 PM, Jarrett Johnson wrote:
>
> Greetings,
>
> We are happy to announce the release of PyMOL 2.5. Download ready-to-use
> bundles from https://pymol.org/ or update your installation with "conda
> install -c schrodinger pymol".
>
> New features include:
> - Multiple-level undo for PyMOL actions (Incentive Only)
> - Curved cartoon cylindrical helices
> - Customizable keyboard shortcut menu
> - Improved isosurface generation
> - Nucleotides from the PDB can now be extended in builder (Incentive Only)
> - Improved MAE import (Incentive Only)
> - ...and more. Please check our release notes.
>
> Python 2 support has been removed. Python 2 to 3 converter tools including
> 2to3 may be useful if you need to update python scripts.
>
> Find the complete release notes at:
> https://pymol.org/d/media:new25
>
> We welcome any feedback and bug reports.
>
> Cheers,
> - The PyMOL Team at Schr�dinger
>
> --
>
> *Jarrett Johnson*�| Senior Developer
> [image: Schrodinger Logo] 
>
>
>
>
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> Skype:  smolnar1
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Re: [PyMOL] PyMOL 2.5 released

2021-05-10 Thread Stephen P. Molnar 

very good.

When will this migrate to github.com/schrodinger/pymol-open-source.git?

On 05/10/2021 12:27 PM, Jarrett Johnson wrote:

Greetings,

We are happy to announce the release of PyMOL 2.5. Download 
ready-to-use bundles from https://pymol.org/ or update your 
installation with "conda install -c schrodinger pymol".


New features include:
- Multiple-level undo for PyMOL actions (Incentive Only)
- Curved cartoon cylindrical helices
- Customizable keyboard shortcut menu
- Improved isosurface generation
- Nucleotides from the PDB can now be extended in builder (Incentive Only)
- Improved MAE import (Incentive Only)
- ...and more. Please check our release notes.

Python 2 support has been removed. Python 2 to 3 converter tools 
including 2to3 may be useful if you need to update python scripts.


Find the complete release notes at:
https://pymol.org/d/media:new25

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schr�dinger

--

*Jarrett Johnson* | Senior Developer

Schrodinger Logo 





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Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

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[PyMOL] PyMOL 2.5 released

2021-05-10 Thread Jarrett Johnson 
Greetings,

We are happy to announce the release of PyMOL 2.5. Download ready-to-use
bundles from https://pymol.org/ or update your installation with "conda
install -c schrodinger pymol".

New features include:
- Multiple-level undo for PyMOL actions (Incentive Only)
- Curved cartoon cylindrical helices
- Customizable keyboard shortcut menu
- Improved isosurface generation
- Nucleotides from the PDB can now be extended in builder (Incentive Only)
- Improved MAE import (Incentive Only)
- ...and more. Please check our release notes.

Python 2 support has been removed. Python 2 to 3 converter tools including
2to3 may be useful if you need to update python scripts.

Find the complete release notes at:
https://pymol.org/d/media:new25

We welcome any feedback and bug reports.

Cheers,
- The PyMOL Team at Schrödinger

-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] 
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Re: [PyMOL] Cartoon_transparency

2021-05-10 Thread Criss Hartzell 
Transparency mode solves it. Thanks.

On Sat, May 8, 2021 at 2:41 PM Jarrett Johnson <
jarrett.john...@schrodinger.com> wrote:

> Hi Criss,
>
> It doesn't appear to be broken from what I see. Helices may not appear
> transparent to each other if you're using single-layer transparency by
> default. Setting `transparency_mode` to 3 should show transparent objects
> beneath each other.
>
> https://pymolwiki.org/index.php/Transparency_mode
>
> Best,
>
> Jarrett J
>
> On Sat, May 8, 2021 at 10:01 AM Criss Hartzell 
> wrote:
>
>> I am using PYMOL2.4.1 on windows.
>> I want to make two cartoon helices transparent in an object having 10
>> heleices. Before version 2.3, I would make a copy of the object, hide the
>> two transparent helices on the original object and show them on the copy
>> with transparency set to 0.5. After PYMOL2.3, cartoon-transparency is
>> supposed to work on the atom level, but when I try to apply cartoon
>> transparency to the two helices as a selection
>> (cartoon_transparency,0.5,sele), the helices change color but do not become
>> transparent. Am I doing something wrong?
>>
>> --
>> Criss Hartzell
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>
>
> --
>
> *Jarrett Johnson* | Senior Developer
> [image: Schrodinger Logo] 
>


-- 
Criss Hartzell
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