pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello Dr. Xiang-Jun Lu,

Thanks a lot for your help. The model you have duplicated is exactly what I
am looking for (checked it with VMD). Unfortunately I do not have access to
DSSR-Pro. Is there any way that I can reproduce your procedure with
x3dna-dssr?
I need to create different numbers of duplicates (2,4,6,5,8) for different
systems and this will be very helpful.

Thanks in advance.

Best regards,
Amir

On Fri, Nov 12, 2021 at 10:33 AM Xiang-Jun Lu <3d...@gm...> wrote:

> Dear Blaine,
>
> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
> Bla...@ou...> wrote:
>
>> Hi Xiang-Jun Lu,
>>
>> Thanks for proving me wrong. Congratulations on your duplicated model!
>> Please share the commands that you used with DSSR to generate the
>> duplicated helix.
>>
>
> The duplicated model was generated with following DSSR Pro commands:
>
> ```
> x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
>
> x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
> x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
> -o=ref-conn.pdb
>
> x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
> -o=temp1.pdb
>
> x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
> x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb
>
> x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
> -o=duplicate-model.pdb
> ```
>
> It takes seconds to run. Moreover, by replacing `--seq=GG` with
> `--seq=GA10G` for example, one can easily get a linker with 10 adenines.
> The 'GG` is just a space-holder, and can be replaced with any other bases.
> The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
> want to know more about DSSR can watch the overview video
> http://docs.x3dna.org/dssr-overview/ (20m).
>
>
>> PyMOL does not generate the cartoon representation for the backbones of
>> your duplicate helix.
>> Do you know why?
>>
>
> I noticed the phenomenon but I really do not know why. I used 'as lines'
> in PyMOL to verify the duplicated model.
>
> Best regards,
>
> Xiang-Jun
>
> Best regards,
>>
>> Blaine
>>
>> Blaine Mooers, Ph.D.
>> Associate Professor
>> Department of Biochemistry and Molecular Biology, College of Medicine
>> Director of the Laboratory of Biomolecular Structure and Function
>> Academic Director, Biomolecular Structure Core, COBRE in Structural
>> Biology
>> Full Member, Cancer Biology Program, Stephenson Cancer Center
>> University of Oklahoma Health Sciences Center
>>
>> Mailing Address:
>> 975 NE 10th Street, BRC 466
>> Oklahoma City, OK 73104-5419
>> Office: 405-271-8300 Lab: 405-271-8312
>>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

Dear Blaine,

On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Xiang-Jun Lu,
>
> Thanks for proving me wrong. Congratulations on your duplicated model!
> Please share the commands that you used with DSSR to generate the
> duplicated helix.
>

The duplicated model was generated with following DSSR Pro commands:

```
x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair
-o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb'
-o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb'
-o=duplicate-model.pdb
```

It takes seconds to run. Moreover, by replacing `--seq=GG` with
`--seq=GA10G` for example, one can easily get a linker with 10 adenines.
The 'GG` is just a space-holder, and can be replaced with any other bases.
The linker sequence could be any bases: eg. A5T3G6, AAATTGG, etc. Users who
want to know more about DSSR can watch the overview video
http://docs.x3dna.org/dssr-overview/ (20m).


> PyMOL does not generate the cartoon representation for the backbones of
> your duplicate helix.
> Do you know why?
>

I noticed the phenomenon but I really do not know why. I used 'as lines' in
PyMOL to verify the duplicated model.

Best regards,

Xiang-Jun

Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Xiang-Jun Lu,

Thanks for proving me wrong. Congratulations on your duplicated model!
Please share the commands that you used with DSSR to generate the duplicated helix.

PyMOL does not generate the cartoon representation for the backbones of your duplicate helix. 
Do you know why?

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Xiang-Jun Lu [3d...@gm...]
Sent: Friday, November 12, 2021 8:05 AM
To: pym...@li...
Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Message: 1
Date: Thu, 11 Nov 2021 01:21:47 +0000
From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...<mailto:Bla...@ou...>>
To: amirhossein taghavi <tag...@gm...<mailto:tag...@gm...>>,
        "pym...@li...<mailto:pym...@li...>"
        <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
        system
Message-ID:
        <87D...@CO...<mailto:87D...@CO...>>
Content-Type: text/plain; charset="us-ascii"

Hi Amir,

No, not automatically. Your RNA is very distorted from
the standard A-form. I doubt any modeling program
can accurately extend such a distorted helix. Maybe
someone else will prove me wrong.


DSSR was used to create the attached 26-base-pair (bp) long RNA by duplicating the initial 13-bp model. I'm not sure whether this is the outcome Amir was hoping for.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...<mailto:xia...@x3...>
Web: http://x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=SCbMW3JwZkTKAxEfPB8w5TtSItCw4MMTIOr8sxCVEIE&e=>
Forum: http://forum.x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=R5l09hlMu8Qv8Uw7eKpaBtB-k1s-E1xX0jqFJ9b_oDg&e=>

 Your RNA does not have the expected
doughnut cross-section of the A-form when
viewed down the helical axis.

Your model has triclinic unit cell dimensions on the first line of the coordinate file.
Is it from a crystal structure? If it is, it might be stacked
end-on-end in the crystal lattice. You could generate its
symmetry mate and save its coordinates.
However, the cryst card in your file is corrupted, and
PyMOL cannot use it to generate symmetry mates.

You can align the terminal base pairs manually through a
series of commands. If you try by dragging one copy
relative to another, you will wind up pulling out all of your
hair. The commands and patience will keep you out  of the mad house.

load model_.pdb
orient
# align along the x-axis
copy model2, model_
translate [38,0,0], model2
rotate x, -45, model2

Issue a series of subsequent translate, rotate, and orient commands as needed.
Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
The angle between the terminal base pairs should be about 33 degrees.
With patience, you can do this in less than an hour.

However, I am not sure how relevant the duplicated structure will be given
the distortions in model_.pdb.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC> (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: amirhossein taghavi [tag...@gm...<mailto:tag...@gm...>]
Sent: Wednesday, November 10, 2021 5:03 PM
To: pym...@li...<mailto:pym...@li...>
Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to duplicate this system and then fuse the two molecules to create a 26 base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir



------------------------------

Message: 2
Date: Wed, 10 Nov 2021 21:44:21 -0500
From: amirhossein taghavi <tag...@gm...<mailto:tag...@gm...>>
To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...<mailto:Bla...@ou...>>
Cc: "pym...@li...<mailto:pym...@li...>"
        <pym...@li...<mailto:pym...@li...>>
Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
        system
Message-ID:
        <CAP4-oUjYJ-PbCdeoBsOJ3=cnEje_7vwhTWGVitxd=gK6...@ma...<mailto:gK6...@ma...>>
Content-Type: text/plain; charset="utf-8"

Hello Prof. Blaine,

Thanks a lot for the detailed explanation. The model is out of MD
simulations with the box information.
I will try the workflow you suggested.
I very much appreciate your help.

Best regards,
Amir

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

> Message: 1
> Date: Thu, 11 Nov 2021 01:21:47 +0000
> From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...>
> To: amirhossein taghavi <tag...@gm...>,
>         "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <
> 87D...@CO...>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Amir,
>
> No, not automatically. Your RNA is very distorted from
> the standard A-form. I doubt any modeling program
> can accurately extend such a distorted helix. Maybe
> someone else will prove me wrong.
>
>
DSSR was used to create the attached 26-base-pair (bp) long RNA by
duplicating the initial 13-bp model. I'm not sure whether this is the
outcome Amir was hoping for.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

 Your RNA does not have the expected
> doughnut cross-section of the A-form when
> viewed down the helical axis.
>
> Your model has triclinic unit cell dimensions on the first line of the
> coordinate file.
> Is it from a crystal structure? If it is, it might be stacked
> end-on-end in the crystal lattice. You could generate its
> symmetry mate and save its coordinates.
> However, the cryst card in your file is corrupted, and
> PyMOL cannot use it to generate symmetry mates.
>
> You can align the terminal base pairs manually through a
> series of commands. If you try by dragging one copy
> relative to another, you will wind up pulling out all of your
> hair. The commands and patience will keep you out  of the mad house.
>
> load model_.pdb
> orient
> # align along the x-axis
> copy model2, model_
> translate [38,0,0], model2
> rotate x, -45, model2
>
> Issue a series of subsequent translate, rotate, and orient commands as
> needed.
> Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
> The angle between the terminal base pairs should be about 33 degrees.
> With patience, you can do this in less than an hour.
>
> However, I am not sure how relevant the duplicated structure will be given
> the distortions in model_.pdb.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC>
> (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: amirhossein taghavi [tag...@gm...]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system
>
> Hello,
>
> I have an RNA duplex with 13 base-pairs (attached). Is it possible to
> duplicate this system and then fuse the two molecules to create a 26
> base-pair long system using the pymol.
>
> Thanks in advance.
>
> Cheers,
> Amir
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Nov 2021 21:44:21 -0500
> From: amirhossein taghavi <tag...@gm...>
> To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>
> Cc: "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <CAP4-oUjYJ-PbCdeoBsOJ3=cnEje_7vwhTWGVitxd=
> gK6...@ma...>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Prof. Blaine,
>
> Thanks a lot for the detailed explanation. The model is out of MD
> simulations with the box information.
> I will try the workflow you suggested.
> I very much appreciate your help.
>
> Best regards,
> Amir
>
>
>

Re: [PyMOL] [EXTERNAL] How to set spectrum color by default in Pymol

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

I second G.V.'s question. It touches upon a problem that I have been having.

The cartoon representation is shown when the 
structure is loaded from disk or fetched from the PDB.

The default cartoon representation overrides the settings in my pymolrc file.
I have the following in my .pymolrc file. I do not have a /.pymolrc-settings.py file or
any other .pymolrc* files.

hide cartoon
show sticks

I still get the cartoon representation when I fetch a structure or load a structure.

The user should be able to control how the structure appears when it is first loaded.

This behavior started occurring with PyMOL 2.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Gundala Viswanath [gun...@gm...]
Sent: Thursday, November 11, 2021 11:39 PM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] How to set spectrum color by default in Pymol

Hi,

Is there a way to do that?
I tried putting this line in .pymolrc, but it doesn't work.

spectrum b, red_yellow_green_cyan_blue, minimum=50, maximum=90

I attached the example PDB file, where the B-factor column is used for the coloring.
An this is the image:

[Screen Shot 2021-11-12 at 14.38.06.png]

G.V/

[PyMOL] How to set spectrum color by default in Pymol

[Gundala V. <gun...@gm...>]

Hi,

Is there a way to do that?
I tried putting this line in *.pymolrc*, but it doesn't work.

spectrum b, red_yellow_green_cyan_blue, minimum=50, maximum=90

I attached the example PDB file, where the B-factor column is used for the
coloring.
An this is the image:

[image: Screen Shot 2021-11-12 at 14.38.06.png]

G.V/

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello Prof. Blaine,

Thanks a lot for the detailed explanation. The model is out of MD
simulations with the box information.
I will try the workflow you suggested.
I very much appreciate your help.

Best regards,
Amir

On Wed, Nov 10, 2021 at 8:21 PM Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Amir,
>
> No, not automatically. Your RNA is very distorted from
> the standard A-form. I doubt any modeling program
> can accurately extend such a distorted helix. Maybe
> someone else will prove me wrong.
>
> Your RNA does not have the expected
> doughnut cross-section of the A-form when
> viewed down the helical axis.
>
> Your model has triclinic unit cell dimensions on the first line of the
> coordinate file.
> Is it from a crystal structure? If it is, it might be stacked
> end-on-end in the crystal lattice. You could generate its
> symmetry mate and save its coordinates.
> However, the cryst card in your file is corrupted, and
> PyMOL cannot use it to generate symmetry mates.
>
> You can align the terminal base pairs manually through a
> series of commands. If you try by dragging one copy
> relative to another, you will wind up pulling out all of your
> hair. The commands and patience will keep you out  of the mad house.
>
> load model_.pdb
> orient
> # align along the x-axis
> copy model2, model_
> translate [38,0,0], model2
> rotate x, -45, model2
>
> Issue a series of subsequent translate, rotate, and orient commands as
> needed.
> Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
> The angle between the terminal base pairs should be about 33 degrees.
> With patience, you can do this in less than an hour.
>
> However, I am not sure how relevant the duplicated structure will be given
> the distortions in model_.pdb.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
> Faculty page:
> https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
> BSC-OKC
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC>
> (LBSF):
> https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: amirhossein taghavi [tag...@gm...]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system
>
> Hello,
>
> I have an RNA duplex with 13 base-pairs (attached). Is it possible to
> duplicate this system and then fuse the two molecules to create a 26
> base-pair long system using the pymol.
>
> Thanks in advance.
>
> Cheers,
> Amir
>

Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Amir,

No, not automatically. Your RNA is very distorted from 
the standard A-form. I doubt any modeling program 
can accurately extend such a distorted helix. Maybe
someone else will prove me wrong.

Your RNA does not have the expected
doughnut cross-section of the A-form when 
viewed down the helical axis. 

Your model has triclinic unit cell dimensions on the first line of the coordinate file.
Is it from a crystal structure? If it is, it might be stacked 
end-on-end in the crystal lattice. You could generate its
symmetry mate and save its coordinates. 
However, the cryst card in your file is corrupted, and 
PyMOL cannot use it to generate symmetry mates.

You can align the terminal base pairs manually through a
series of commands. If you try by dragging one copy 
relative to another, you will wind up pulling out all of your
hair. The commands and patience will keep you out  of the mad house.

load model_.pdb
orient
# align along the x-axis
copy model2, model_
translate [38,0,0], model2
rotate x, -45, model2

Issue a series of subsequent translate, rotate, and orient commands as needed.
Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
The angle between the terminal base pairs should be about 33 degrees.
With patience, you can do this in less than an hour. 

However, I am not sure how relevant the duplicated structure will be given
the distortions in model_.pdb.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312

Websites:
Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: amirhossein taghavi [tag...@gm...]
Sent: Wednesday, November 10, 2021 5:03 PM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to duplicate this system and then fuse the two molecules to create a 26 base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir

[PyMOL] create a 26 bp RNA from a 13 bp system

[amirhossein t. <tag...@gm...>]

Hello,

I have an RNA duplex with 13 base-pairs (attached). Is it possible to
duplicate this system and then fuse the two molecules to create a 26
base-pair long system using the pymol.

Thanks in advance.

Cheers,
Amir

Re: [PyMOL] Getting angle between z axis and a molecules principal axis

[Jared S. <jar...@co...>]

Hi Yogesh -

You may be able to do something similar to the antibody elbow angle script
on the PyMOL Wiki (and PyMOL-scripts GitHub repo) using rotation matrices
aligning various subunits to determine the principal axis. Or if you
already have a way of calculating the principal axis, you can use Christoph
Gohlke’s transformations.py module (which is used by the elbow angle
script) to calculate the angle.

I’m away from my computer at the moment but those two scripts should be
fairly easily found using your favorite search engine.

Hope that helps.

Cheers,
Jared

On Tue, Nov 9, 2021 at 8:03 AM Yogesh Sharma <yog...@gm...> wrote:

> Hi I want to get angle between a molecules principal axis and systems z
> axis iteratively over 100ns trajectory. I am new to pymol. Can someone help
> me with scripting it out? Thank you for your time.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Getting angle between z axis and a molecules principal axis

[Yogesh S. <yog...@gm...>]

Hi I want to get angle between a molecules principal axis and systems z
axis iteratively over 100ns trajectory. I am new to pymol. Can someone help
me with scripting it out? Thank you for your time.

Re: [PyMOL] About contacting the PYMOL-creators

[Jarrett J. <jar...@sc...>]

Hello,

General questions about PyMOL and its features could be answered here by
the community as well. Alternatively we have kept track of such community
requests of new features on our open-source issue tracker (
https://github.com/schrodinger/pymol-open-source/issues ).

Best,
Jarrett J.

On Thu, Nov 4, 2021 at 4:31 AM superpowered via PyMOL-users <
pym...@li...> wrote:

> Hello,
> I wonder is there a way to contact the makers of Pymol for general
> question or to request certain program features?
>
> Regards,
> K. Zeghida.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] About contacting the PYMOL-creators

[superpowered <sup...@pr...>]

Hello,
I wonder is there a way to contact the makers of Pymol for general question or to request certain program features?

Regards,
K. Zeghida.

Re: [PyMOL] APBS with ions

[Thomas H. <th...@th...>]

Hi Kamil,

The "Selection" field uses "polymer & ..." by default, which excludes
ions. You can use a selection which includes ions instead, for example
"all", "not solvent", or something like "(polymer | name CAL) & ...".

Here an example that works for me:

fetch 1rx1
alter elem Ca, resn="CAL"
alter elem Ca, name="CAL"

In the APBS Electrostatics panel, use "(polymer | name CAL) & 1rx1" as
the selection and "--ff=CHARMM" as pdb2pqr command line option.

Hope that helps.

Cheers,
  Thomas

On Mon, Nov 1, 2021 at 9:21 PM Kamil Steczkiewicz
<kam...@gm...> wrote:
>
> Hi,
> How to include Ca/Zn ions when using APBS built into Pymol? I'm switching to CHARMM in command line options; CHARMM has CAL and ZN2 atoms already defined in the DAT file. But there's still no difference in electrostatics maps with and without ions in the structure. Also, the default 'prepared01' object lacks the ions.
> Thanks for any clues,
> Kamil
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to show electrostatic interactions in Pymol on the wanted residue

[Joel T. <joe...@ot...>]

Hi Gundala,

There are a number of ways but primarily PyMOL will do it automatically under Action>find>polar contacts (to any atoms). This finds both hydrogen bonds and electrostatic interactions. You can select the residue you want (Lysine) and do it that way.

Also you can simply measure the distance between the atoms (nitrogen and oxygens. You can also turn of the labels.

Hope that helps
J

From: Gundala Viswanath <gun...@gm...>
Sent: Sunday, 31 October 2021 3:14 AM
To: pymol-users <pym...@li...>
Subject: [PyMOL] How to show electrostatic interactions in Pymol on the wanted residue

Hi,

I have the following Pymol visual,
The green molecule is  the receptor and red/yellow is the ligand.
In the ligand I highlighted Lysine (K) residue as yellow.

[cid:image001.png@01D7CFFE.4B9AADB0]


What I want to do is to highlight and draw the electrostatic contact of the ligand especially with Lysine residue. Like this in Pymol:

[cid:image002.png@01D7CFFE.4B9AADB0]

How can I achieve that?
G.V

[PyMOL] How to show electrostatic interactions in Pymol on the wanted residue

[Gundala V. <gun...@gm...>]

Hi,

I have the following Pymol visual,
The green molecule is  the receptor and red/yellow is the ligand.
In the ligand I highlighted Lysine (K) residue as yellow.

[image: Screen Shot 2021-10-30 at 22.57.10.png]


What I want to do is to highlight and draw the electrostatic contact of the
ligand especially with Lysine residue. Like this in Pymol:

[image: Screen Shot 2021-10-30 at 22.43.49.png]

How can I achieve that?

G.V

Re: [PyMOL] help - password cracked

[Jarrett J. <jar...@sc...>]

Hello,

We're aware of this issue, and I believe all EP license holders may have
received this warning from Google. However, this can safely be ignored for
now. The password students and other users receive just provides access to
the PyMOL Educational Product license and nothing there stores any
sensitive information.

Hope this helps,

Jarrett J

On Fri, Oct 29, 2021 at 6:10 AM Jola Bodinková <jol...@gm...>
wrote:

> Hey everybody!
>
> I may have a problem, maybe it's nothing, but better to be sure. About
> a week ago, I got a notification from Google that my password to the pymol.org/ep
> link had been cracked. Since then I've been trying to find any information
> concerning this problem - mainly in the form of 'how to change the
> password' - but I wasn't very successful. I had no idea who to contact, so
> I came here for any advice as to how to solve this.
>
> Many thanks in advance!
>
> Best,
>
> Joli
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] help - password cracked

[Jola B. <jol...@gm...>]

Hey everybody!

I may have a problem, maybe it's nothing, but better to be sure. About
a week ago, I got a notification from Google that my password to the
pymol.org/ep
link had been cracked. Since then I've been trying to find any information
concerning this problem - mainly in the form of 'how to change the
password' - but I wasn't very successful. I had no idea who to contact, so
I came here for any advice as to how to solve this.

Many thanks in advance!

Best,

Joli

Re: [PyMOL] Labeling residues for publication

[Jarrett J. <jar...@sc...>]

Hi George,

This issue should've been addressed in PyMOL 2.5.1. I would consider
upgrading if you can.

Best,
Jarrett J

On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users <
pym...@li...> wrote:

> Hi everybody,
>
> I’d be grateful for any suggestions regarding the editing of labels.
>
> I’ve labeled a few residues and I’m trying to give them a better placing
> in the structure. I’m using mouse/2 button editing.  Clicking on control
> and then moving the labels works, but alas as soon as I release the control
> key pymol crashes.
>
> I’m using
> PyMOL(TM) 2.5.0 - Incentive Product
>
> Thanks in advance
>
> George
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

Re: [PyMOL] Labeling residues for publication

[Jarrett J. <jar...@sc...>]

Hi George,

Can you try downloading from the pymol.org website?

Best,

Jarrett J

On Thu, Oct 28, 2021 at 9:50 AM George Tzotzos <gtz...@me...> wrote:

> Thank you both for the suggestions.
>
> I tried to upgrade. I get “pymol” is already at the latest version
>
> All the best
>
> George
>
> On 28.10.2021, at 14:40, Jarrett Johnson <jar...@sc...>
> wrote:
>
> Hi George,
>
> This issue should've been addressed in PyMOL 2.5.1. I would consider
> upgrading if you can.
>
> Best,
> Jarrett J
>
> On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi everybody,
>>
>> I’d be grateful for any suggestions regarding the editing of labels.
>>
>> I’ve labeled a few residues and I’m trying to give them a better placing
>> in the structure. I’m using mouse/2 button editing.  Clicking on control
>> and then moving the labels works, but alas as soon as I release the control
>> key pymol crashes.
>>
>> I’m using
>> PyMOL(TM) 2.5.0 - Incentive Product
>>
>> Thanks in advance
>>
>> George
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
>
>

-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

Re: [PyMOL] Labeling residues for publication

[George T. <gtz...@me...>]

Thank you both for the suggestions.

I tried to upgrade. I get “pymol” is already at the latest version

All the best

George

> On 28.10.2021, at 14:40, Jarrett Johnson <jar...@sc...> wrote:
> 
> Hi George,
> 
> This issue should've been addressed in PyMOL 2.5.1. I would consider upgrading if you can.
> 
> Best,
> Jarrett J
> 
> On Thu, Oct 28, 2021 at 9:31 AM George Tzotzos via PyMOL-users <pym...@li... <mailto:pym...@li...>> wrote:
> Hi everybody,
> 
> I’d be grateful for any suggestions regarding the editing of labels.
> 
> I’ve labeled a few residues and I’m trying to give them a better placing in the structure. I’m using mouse/2 button editing.  Clicking on control and then moving the labels works, but alas as soon as I release the control key pymol crashes.
> 
> I’m using 
> PyMOL(TM) 2.5.0 - Incentive Product
> 
> Thanks in advance
> 
> George
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
> 
> -- 
> Jarrett Johnson | Senior Developer
>  <https://www.schrodinger.com/>

[PyMOL] Labeling residues for publication

[George T. <gtz...@me...>]

Hi everybody,

I’d be grateful for any suggestions regarding the editing of labels.

I’ve labeled a few residues and I’m trying to give them a better placing in the structure. I’m using mouse/2 button editing.  Clicking on control and then moving the labels works, but alas as soon as I release the control key pymol crashes.

I’m using 
PyMOL(TM) 2.5.0 - Incentive Product

Thanks in advance

George

Re: [PyMOL] [EXTERNAL] basic trouble viewing electron density maps

[criss.hartzell <cri...@gm...>]

That explains it! Thanks. I guess I need a tutorial on how to look at EM maps. 

Criss Hartzell


> On Oct 27, 2021, at 12:26 PM, Brown, Zuben <zb...@cu...> wrote:
> 
> 
> They are different types of maps.
> 
> 2F67 -- X-ray map
> 7B5C -- EM map
> 
> 7B5C is not a 2fofc map.
> 
> Best wishes,
> Zuben
> From: Criss Hartzell <cri...@gm...>
> Sent: Wednesday, October 27, 2021 2:51 PM
> To: Pymol User list <pym...@li...>
> Subject: [EXTERNAL] [PyMOL] basic trouble viewing electron density maps
>  
> I am having trouble viewing electron density maps. 
> Everything works fine if I use the protein 2F67. But with 7B5C, I am stumped.
> 
> fetch 7b5c, type=2fofc gives me an error: 
> Warning: failed to fetch from https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4
> 
>  Error-fetch: unable to load '7b5c'.
> If I go to EMDB and download the map file (EMD_12025) and load it manually:
> (set normalize_ccp4_maps, 0
> load H:/.../emd_12025.map, \emd_12025
> isomesh emd_12025_isomesh, emd_12025, 1.0)
> The screen is blank and changing levels, etc. does nothing.
> But it works in UCSF Chimera. What am I missing?
> Thanks.
> Criss
> 
> 

Re: [PyMOL] [EXTERNAL] basic trouble viewing electron density maps

[Brown, Z. <zb...@cu...>]

They are different types of maps.

2F67 -- X-ray map
7B5C -- EM map

7B5C is not a 2fofc map.

Best wishes,
Zuben
________________________________
From: Criss Hartzell <cri...@gm...>
Sent: Wednesday, October 27, 2021 2:51 PM
To: Pymol User list <pym...@li...>
Subject: [EXTERNAL] [PyMOL] basic trouble viewing electron density maps

I am having trouble viewing electron density maps.
Everything works fine if I use the protein 2F67. But with 7B5C, I am stumped.

fetch 7b5c, type=2fofc gives me an error:

Warning: failed to fetch from https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ebi.ac.uk_pdbe_coordinates_files_7b5c.ccp4&d=DwMFaQ&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=8AY7h2N3TQ7k7n9RDhxT46t0ViqfY3ViGGLPrQZPtGw&m=gjXm-pi8KE6bTBC8di1Ue68XZy2E2aRL9MnN2J1bJLc&s=MUITh2JiB3m_JBC4jNMoDm8CR051F-3qt8WIJbFOHD4&e=>
 Error-fetch: unable to load '7b5c'.

If I go to EMDB and download the map file (EMD_12025) and load it manually:

(set normalize_ccp4_maps, 0

load H:/.../emd_12025.map, \emd_12025

isomesh emd_12025_isomesh, emd_12025, 1.0)

The screen is blank and changing levels, etc. does nothing.

But it works in UCSF Chimera. What am I missing?

Thanks.

Criss

[PyMOL] basic trouble viewing electron density maps

[Criss H. <cri...@gm...>]

I am having trouble viewing electron density maps.
Everything works fine if I use the protein 2F67. But with 7B5C, I am
stumped.

fetch 7b5c, type=2fofc gives me an error:

Warning: failed to fetch from
https://www.ebi.ac.uk/pdbe/coordinates/files/7b5c.ccp4
 Error-fetch: unable to load '7b5c'.

If I go to EMDB and download the map file (EMD_12025) and load it manually:

(set normalize_ccp4_maps, 0

load H:/.../emd_12025.map, \emd_12025

isomesh emd_12025_isomesh, emd_12025, 1.0)

The screen is blank and changing levels, etc. does nothing.

But it works in UCSF Chimera. What am I missing?

Thanks.

Criss