[PyMOL] smooth-ribbon

[Oganesyan, Vaheh]

Hey PyMOLers,

Would you know how to show smooth ribbon?
I can use cartoon_oval_length command to get almost what I want, however only 
for helices. Thanks in advance.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


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[PyMOL] real time minization in Pymol

[Albert]

Hello:

I just found a a very nice module of pymol, called "Molecular 
Sculpting". However, according to the description in Pymolwiki, it works 
like a real-time energy minimizer, except that it isn't minimizing the 
energy. Instead, its just trying to return local atomic geometries 
(bonds, angles, chirality, planarity) to the configuration the molecules 
possess when they were first loaded into PyMOL.

So I am just wondering does the developer have any planning to improve 
this nice too? For instance introducing forcefiled for this tool (eg: 
Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
in Pymol, maybe the developer can consider merge them together?

Thank you very much

Albert

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Re: [PyMOL] real time minization in Pymol

[Albert]

Yes, I also really love this function. However, for the sake of 
accuracy, I believe many users will also strongly demand for introducing 
forcefield for minimization..I am looking forward to see that 
"optimize" plugin would somehow merged into "Molecular Sculpting".At 
least, it is very easy and free to get access to Amber and GAFF forcefield.

Thanks again.

On 11/23/2015 05:07 PM, H. Adam Steinberg wrote:
> I would love to see this feature improved!
>
> Try it out if you have never used it. It works quite well. It is quite 
> processor intensive and it can take over your computer when it is running…. I 
> have also found when you uncheck it in the menu, it will still continue to 
> run and I end up force quitting to get it to stop.


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Re: [PyMOL] real time minization in Pymol

[H. Adam Steinberg]

I would love to see this feature improved!

Try it out if you have never used it. It works quite well. It is quite 
processor intensive and it can take over your computer when it is running…. I 
have also found when you uncheck it in the menu, it will still continue to run 
and I end up force quitting to get it to stop.

> On Nov 23, 2015, at 8:46 AM, Albert  wrote:
> 
> Hello:
> 
> I just found a a very nice module of pymol, called "Molecular 
> Sculpting". However, according to the description in Pymolwiki, it works 
> like a real-time energy minimizer, except that it isn't minimizing the 
> energy. Instead, its just trying to return local atomic geometries 
> (bonds, angles, chirality, planarity) to the configuration the molecules 
> possess when they were first loaded into PyMOL.
> 
> So I am just wondering does the developer have any planning to improve 
> this nice too? For instance introducing forcefiled for this tool (eg: 
> Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin 
> in Pymol, maybe the developer can consider merge them together?
> 
> Thank you very much
> 
> Albert
> 
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> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] smooth-ribbon

[Oganesyan, Vaheh]

Found:

hide everything
show cartoon
cartoon tube
set cartoon_tube_radius, (number)


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


-Original Message-
From: Oganesyan, Vaheh
Sent: Monday, November 23, 2015 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: smooth-ribbon

Hey PyMOLers,

Would you know how to show smooth ribbon?
I can use cartoon_oval_length command to get almost what I want, however only 
for helices. Thanks in advance.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.
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Re: [PyMOL] default fetch format

[Schubert, Carsten [JRDUS]]

You may want to form you own opinion and take a look at this thread and others 
in CCP4

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;8e513bea.1308

I hope the link works. There has been extensive and heated debate over the 
merits of mmCIF vs. PDB on the same BB. The wwPDB is pushing mmCIF, which was 
developed as an ARCHIVAL format, but in my opinion the community as a whole is 
rather reluctant to accept mmCIF as a WORKING format. The distinction between a 
working and archiving format is vital in this context. 
As far as I am concerned the PDB format as a working format is unmatched in its 
utility (try to concatenate 2 structures in both formats or prepare a file for 
MR and you see what I mean), but has drawbacks, some of which would be adapted 
by an extended PDB format.
So as long as the current programs support PDB, I really could care less what 
the wwPDB thinks; however if programs drop support for the PDB format, I'll be 
more than happy to look for alternatives... 

Cheers,

Carsten

-Original Message-
From: Albert [mailto:mailmd2...@gmail.com] 
Sent: Sunday, November 22, 2015 2:23 PM
To: Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] default fetch format

Hi Thomas:

thanks a lot for helpful advice.

May I ask is there any superior features of mmCIF format against PDB format?

regards

Albert

On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can 
> override the fetch command. Example which you could place in your ~/.pymolrc 
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
>  if 'type' not in kwargs:
>  kwargs['type'] = 'pdb'
>  return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of 
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,


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