date:20141010

Re: [PyMOL] Show all residues forming H-bonds

2014-10-10 Thread Markus Heller

Jared,

You da man!!

Sounds exactly like what i'm looking for!!  Unfortunately i won't be able to 
try until Tuesday :/

Thanks and cheers
Markus

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Scientist, NMR

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On Oct 10, 2014, at 4:15 PM, "Sampson, Jared" 
mailto:jared.samp...@nyumc.org>> wrote:

Actually, an even better option is Thomas’ polarpairs.py script: 
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle 
as well as distance.

Apologies for the multiple emails, but I hope that is closer to what you’re 
looking for.

Cheers,
Jared


On Oct 10, 2014, at 7:10 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:

Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the “acceptors” and “donors” selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 6:41 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hi Jared,

Thanks for the reply.

This is NOT what I’m looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don’t want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it’s clearer now what I’m after …

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI “action” menu A > find > polar contacts, you’ll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
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Re: [PyMOL] Show all residues forming H-bonds

2014-10-10 Thread Sampson, Jared

Actually, an even better option is Thomas’ polarpairs.py script: 
http://www.pymolwiki.org/index.php/Polarpairs, which considers the H-bond angle 
as well as distance.

Apologies for the multiple emails, but I hope that is closer to what you’re 
looking for.

Cheers,
Jared


On Oct 10, 2014, at 7:10 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:

Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the “acceptors” and “donors” selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 6:41 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hi Jared,

Thanks for the reply.

This is NOT what I’m looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don’t want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it’s clearer now what I’m after …

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI “action” menu A > find > polar contacts, you’ll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
--
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Re: [PyMOL] Show all residues forming H-bonds

2014-10-10 Thread Sampson, Jared

Hi Markus -

Ah, sorry, I misunderstood your request at first.

What about the “acceptors” and “donors” selectors?  
http://www.pymolwiki.org/index.php/Single-word_Selectors

e.g.
select hbond_residues, byres ((acceptors within 3.5 of donors) or (donors 
within 3.5 of acceptors))

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Oct 10, 2014, at 6:41 PM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:

Hi Jared,

Thanks for the reply.

This is NOT what I’m looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don’t want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it’s clearer now what I’m after …

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI “action” menu A > find > polar contacts, you’ll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
--
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Re: [PyMOL] Show all residues forming H-bonds

2014-10-10 Thread Markus Heller

Hi Jared,

Thanks for the reply.

This is NOT what I'm looking for.  As you stated, distance mode 2 yields the 
*distances* as dashes, but not the actual residues.  I don't want the dashes, 
but I want the residues (i.e. the donors and acceptors) in selectable objects.

I hope it's clearer now what I'm after ...

Cheers
M

From: Sampson, Jared [mailto:jared.samp...@nyumc.org]
Sent: Friday, October 10, 2014 3:33 PM
To: Markus Heller
Subject: Re: [PyMOL] Show all residues forming H-bonds

Hi Markus -

Under the GUI "action" menu A > find > polar contacts, you'll find several 
options which will create a new object with all the specified distances as 
dashes.

This is also available with `distance` command.  
http://www.pymolwiki.org/index.php/Distance

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/





On Oct 10, 2014, at 2:45 AM, Markus Heller 
mailto:mhel...@cdrd.ca>> wrote:


Hello list,

subject says it all.  The 2 options I came across search the www are:

http://sourceforge.net/p/pymol/mailman/message/7562444/http://sourceforge.net/p/pymol/mailman/message/7562444/

and DistancesRH 
(http://www.pymolwiki.org/index.php/DistancesRH)http://www.pymolwiki.org/index.php/DistancesRH

Is this current state-of-the-art, true-and-tried, or is there something more 
powerful hiding out there?

Thanks
Markus
--
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[PyMOL] Render dot surface

2014-10-10 Thread Colin Levy

Hi,

I am running the latest incentive version of MacPymol and have noticed that I 
am unable to render figures containing dot surfaces. If I setup the figure with 
show dots and then ray, my dot surface is not visible in the ray output. I 
tried increasing the dot radius incase it was simply too small but thus far no 
luck.

Anyone else experienced this? Any suggestions on a work around?

Many thanks,

Colin

Manchester
Protein
Structure
Facility

Dr. Colin W. Levy
MIB G034
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk
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Re: [PyMOL] Show all residues forming H-bonds

Re: [PyMOL] Show all residues forming H-bonds

Re: [PyMOL] Show all residues forming H-bonds

Re: [PyMOL] Show all residues forming H-bonds

[PyMOL] Render dot surface

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