Re: [PyMOL] [EXTERNAL] broken DNA cartoon

[Mooers, Blaine H.M. (HSC)]

The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms.
This is outside the bond length range that PyMOL accepts so the bond is absent 
when you display the model as line or stick model.
This is why the cartoon is missing or broken.
5FUR is a 8.5 Angstrom cryo EM structure.
Perhaps the associated paper explains this discrepancy. 

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: h. adam steinberg [h.adam.steinb...@gmail.com]
Sent: Friday, March 20, 2020 8:57 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] broken DNA cartoon

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken 
and mostly missing (it should span from left to right). Any ideas on how to get 
the cartoon to work?

Pymol version 2.3.4




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Re: [PyMOL] broken DNA cartoon

[Jared Sampson]

Hi Adam - 

That's a fun one.  It appears that most of these O3' atoms are not bonded to 
the P atom of the following nucleotide, which you can see if you show the DNA 
chains as sticks.  Creating a bond via `bond atom1, atom2` results in a normal 
cartoon.  Fortunately, the DNA chains are sequentially numbered, so you can do 
something like:

for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")

The offending bond lengths are much longer than a typical P–O bond, which is 
why PyMOL's default distance-based bonding doesn't pick it up.

Hope that helps.

Cheers,
Jared



From: h. adam steinberg 
Reply: h. adam steinberg 
Date: March 20, 2020 at 9:59:45 PM
To: pymol-users 
Subject:  [PyMOL] broken DNA cartoon  

Hi All,

When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken 
and mostly missing (it should span from left to right). Any ideas on how to get 
the cartoon to work?

Pymol version 2.3.4


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Re: [PyMOL] Selection of elements in object

[Marko Hyvonen]

  
  
Hello Henrik, 
  
  your syntax is not correct:
  select name_for_selection, selected_parts
  https://pymolwiki.org/index.php/Select
  
  eg. 
  select my_carbons, elem C & obj 
  will select atoms that are element C AND in obj and calls this
  selection my_carbons. 
  
  hth, Marko

On 20/03/2020 13:40, Henrik Gotfredsen
  wrote:


  
  Dear Pymol users


Would anyone be able to help with the correct syntax used
  for selecting specific elements within an object?


For example, I would like to be able to select only carbon
  or hydrogen. 


select elem c (works but selects all the carbons in my
  project)
select elem c, obj (this selects all atoms within 'obj' as
  selection 'elem_c')


Any suggestions are much appreciated :)


Many thanks!
Henrik 
  
  
  
  
  
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-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@cam.ac.uk
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk
 


  


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[PyMOL] Selection of elements in object

[Henrik Gotfredsen]

Dear Pymol users

Would anyone be able to help with the correct syntax used for selecting
specific elements within an object?

For example, I would like to be able to select only carbon or hydrogen.

select elem c (works but selects all the carbons in my project)
select elem c, obj (this selects all atoms within 'obj' as selection
'elem_c')

Any suggestions are much appreciated :)

Many thanks!
Henrik
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[PyMOL] Accessibility Conformance Report

[William Marcotte Jr]

My university is aking me to provide the following information:


Please include an Accessibility Conformance Report (ACR) for this solution as 
an 
attachment.
 The vendor should be able to provide an ACR that meets the following criteria:

  *   The ACR should be based on a Voluntary Product Accessibility Template® 
(VPAT®) version 2.1 or higher, provided by the Industry Technology Industry 
Council (ITIC).
  *   The ACR should include conformance to Web Content Accessibility 
Guidelines (WCAG) version 2.0 levels A and AA.

Please advise
Bill Marcotte

William R Marcotte Jr, PhD
Professor
Department of Genetics & Biochemistry
Clemson University
(864) 656-0119
(864) 328-4089
(864) 656-6879

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