Re: [PyMOL] fix cartoon backbone

[h. adam steinberg]

Thank you.

Interestingly…
These alter commands do work on the DNA in my original working .pse file, the 
file that contains all of the structures.
They do work on the “save molecule” as a cif file that I shared with you, if I 
open it into PyMOL by itself.
They also work if I open the chain F.cif into my original working .pse file. 
This will fix the new chain F but not the old chain F.

Something about saving the chain out as a cif file and bringing it back in 
alters something besides just the atom naming. 

> On Mar 22, 2019, at 1:43 PM, Thomas Holder  
> wrote:
> 
> Hi Adam,
> 
> The atom naming is nonstandard. If you fix that, the cartoon will be complete.
> 
> alter name P01, name="P"
> alter name O01, name="O5'"
> alter name O02, name="OP1"
> alter name O03, name="OP2"
> unbond name OP1, name O3'+O5'
> unbond name OP2, name O3'+O5'
> 
> PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately 
> the mmCIF spec doesn't make this straight forward). You could save to MMTF 
> instead, it stores all bonds.
> 
> Cheers,
>  Thomas
> 
> 
>> On Mar 22, 2019, at 5:42 PM, h. adam steinberg  
>> wrote:
>> 
>> Thank you, that certainly brought the chains together, but sill no completed 
>> cartoon even after a rebuild.
>> 
>> Attached is chain F, can you see anything wrong with this file that won’t 
>> let it display a complete chain? It must be with how I joined the missing 
>> atoms?
>> 
>> I also notice that every time I open this object in PyMOL I get odd bonding 
>> happening. Even when I unbond those odd connections and resave the file, it 
>> puts them right back in when I reopen the file.
>> 
>> I could simply fake the connection using photoshop, but I’m trying to learn 
>> to do it correctly! :) I appreciate your help!
>> 
>> 
>> 
>>> On Mar 22, 2019, at 11:31 AM, Jared Sampson  
>>> wrote:
>>> 
>>> Hi Adam -
>>> 
>>> The characters between the object names and the chain IDs are the segment 
>>> IDs.  You can remove them by setting them to the empty string using `alter`:
>>> 
>>> alter all, segi=""
>>> 
>>> Hope that helps.
>>> 
>>> Cheers,
>>> Jared
>>> 
>>> 
>>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg 
>>> (h.adam.steinb...@gmail.com) wrote:
>>> 
 
 
> On Mar 21, 2019, at 1:41 AM, Kevin Jude  wrote:
> 
> The DNA in 1CGP is made up of two annealed half sites, so there are four 
> chain assignments for the two strands. If you want to display it as 
> intact DNA, after adding the linking phosphate you can use the alter 
> command to make the chains continuous. HTH.
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg 
>  wrote:
> Hi All,
> 
> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. 
> After I fixed those two breaks (add in the correct atoms and join them) 
> how do I get the cartoon of the DNA to be complete? PyMOL still creates 
> the cartoon with the breaks.
> 
> Thanks!
> 
> Adam
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

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Re: [PyMOL] fix cartoon backbone

[Thomas Holder]

Hi Adam,

The atom naming is nonstandard. If you fix that, the cartoon will be complete.

alter name P01, name="P"
alter name O01, name="O5'"
alter name O02, name="OP1"
alter name O03, name="OP2"
unbond name OP1, name O3'+O5'
unbond name OP2, name O3'+O5'

PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately 
the mmCIF spec doesn't make this straight forward). You could save to MMTF 
instead, it stores all bonds.

Cheers,
  Thomas


> On Mar 22, 2019, at 5:42 PM, h. adam steinberg  
> wrote:
> 
> Thank you, that certainly brought the chains together, but sill no completed 
> cartoon even after a rebuild.
> 
> Attached is chain F, can you see anything wrong with this file that won’t let 
> it display a complete chain? It must be with how I joined the missing atoms?
> 
> I also notice that every time I open this object in PyMOL I get odd bonding 
> happening. Even when I unbond those odd connections and resave the file, it 
> puts them right back in when I reopen the file.
> 
> I could simply fake the connection using photoshop, but I’m trying to learn 
> to do it correctly! :) I appreciate your help!
> 
> 
> 
>> On Mar 22, 2019, at 11:31 AM, Jared Sampson  
>> wrote:
>> 
>> Hi Adam -
>> 
>> The characters between the object names and the chain IDs are the segment 
>> IDs.  You can remove them by setting them to the empty string using `alter`:
>> 
>> alter all, segi=""
>> 
>> Hope that helps.
>> 
>> Cheers,
>> Jared
>> 
>> 
>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg 
>> (h.adam.steinb...@gmail.com) wrote:
>> 
>>> 
>>> 
 On Mar 21, 2019, at 1:41 AM, Kevin Jude  wrote:
 
 The DNA in 1CGP is made up of two annealed half sites, so there are four 
 chain assignments for the two strands. If you want to display it as intact 
 DNA, after adding the linking phosphate you can use the alter command to 
 make the chains continuous. HTH.
 
 --
 Kevin Jude, PhD
 Structural Biology Research Specialist, Garcia Lab
 Howard Hughes Medical Institute
 Stanford University School of Medicine
 Beckman B177, 279 Campus Drive, Stanford CA 94305
 Phone: (650) 723-6431
 
 On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg 
  wrote:
 Hi All,
 
 I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. 
 After I fixed those two breaks (add in the correct atoms and join them) 
 how do I get the cartoon of the DNA to be complete? PyMOL still creates 
 the cartoon with the breaks.
 
 Thanks!
 
 Adam

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] fix cartoon backbone

[h. adam steinberg]

Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!

chain F.cif
Description: Binary data
On Mar 22, 2019, at 11:31 AM, Jared Sampson  wrote:Hi Adam -The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:alter all, segi=""Hope that helps.Cheers,JaredOn March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com) wrote:On Mar 21, 2019, at 1:41 AM, Kevin Jude  wrote:The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.--Kevin Jude, PhDStructural Biology Research Specialist, Garcia LabHoward Hughes Medical InstituteStanford University School of MedicineBeckman B177, 279 Campus Drive, Stanford CA 94305Phone: (650) 723-6431On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg  wrote:Hi All,I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.Thanks!Adam___PyMOL-users mailing listArchives: http://www.mail-archive.com/pymol-users@lists.sourceforge.netUnsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___
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Re: [PyMOL] fix cartoon backbone

[Jared Sampson]

Hi Adam -

The characters between the object names and the chain IDs are the segment IDs.  
You can remove them by setting them to the empty string using `alter`:

alter all, segi=""

Hope that helps.

Cheers,
Jared


On March 22, 2019 at 12:14:46 PM, h. adam steinberg 
(h.adam.steinb...@gmail.com) wrote:



On Mar 21, 2019, at 1:41 AM, Kevin Jude  wrote:

The DNA in 1CGP is made up of two annealed half sites, so there are four chain 
assignments for the two strands. If you want to display it as intact DNA, after 
adding the linking phosphate you can use the alter command to make the chains 
continuous. HTH.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg  
wrote:
Hi All,

I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I 
fixed those two breaks (add in the correct atoms and join them) how do I get 
the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the 
breaks.

Thanks!

Adam

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Re: [PyMOL] Pymol recolour B factors

[Robert Campbell]

Hi Mark,

In that data2bfactor.py script (which I wrote) you need to provide the 
molecular object name, not a file name.  In other words in your example you 
should load the 1d3z.pdb file as an object (defaults to 1d3z as object name).  
Then after using the run command to load the script into your pymol session 
then you can type:

data2b_res 1d3z, shift_to_b.txt

The other script you mention works the same way.  The pdb file needs to be 
loaded into PyMOL as a molecular object first.

Cheers,
Rob

On Fri, 2019-03-22 11:36  +,  Dr Mark Bostock  wrote:

> Hello,
> 
> I'm trying to recolour the B factors in a pymol file with chemical
> shift differences (from NMR data). There's a nice script here for
> this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
> (data2bfactor.py) and also a simpler one here 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffigshare.com%2Farticles%2FPymol_script_loadBfacts_py%2F1176991&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&sdata=jDmJ4NSc%2F%2BXy5IG%2BRCCsQOmqh1Xj9l4j6gTMEmJB6Zc%3D&reserved=0.
> 
> In both cases after loading the script with the run command, when I
> execute the script I get the following error
> 
> data2b_res 1d3z.pdb, shift_to_b.txt
> Selector-Error: Invalid selection name "1d3z.pdb".
> ( 1d3z.pdb )<--
> 
> The pdb file and list of new b-factor values are in the same
> directory and can be filled in with tab-completion. I've also tried
> using the full file path but get a similar error. I've tried with a
> couple of different pdb files as well so it's not just a problem with
> that particular pdb file.
> 
> I'd be grateful if anyone has any experience with this or suggestions
> as to what is going wrong.
> 
> Thanks in advance,
> 
> Mark
> 
> 
> 
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-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc


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[PyMOL] Pymol recolour B factors

[Dr Mark Bostock]

Hello,

I'm trying to recolour the B factors in a pymol file with chemical shift 
differences (from NMR data). There's a nice script here for this 
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ (data2bfactor.py) and 
also a simpler one here 
https://figshare.com/articles/Pymol_script_loadBfacts_py/1176991.


In both cases after loading the script with the run command, when I execute 
the script I get the following error


data2b_res 1d3z.pdb, shift_to_b.txt
Selector-Error: Invalid selection name "1d3z.pdb".
( 1d3z.pdb )<--

The pdb file and list of new b-factor values are in the same directory and 
can be filled in with tab-completion. I've also tried using the full file 
path but get a similar error. I've tried with a couple of different pdb 
files as well so it's not just a problem with that particular pdb file.


I'd be grateful if anyone has any experience with this or suggestions as to 
what is going wrong.


Thanks in advance,

Mark



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