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

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

2021-11-12 Thread Xiang-Jun Lu

On Fri, Nov 12, 2021 at 11:15 AM amirhossein taghavi <
taghavi.amirhoss...@gmail.com> wrote:

> Hi Xiang-Jun,
>
> Sorry to bother. I meant if I can do the same thing you have done with
> DSSR pro with free version of x3dna-dssr, as I am getting some error
> messages:
>

No, as made clear in my previous response to Blaine: "The duplicated model
was generated with following DSSR Pro commands:"

Best regards,

Xiang-Jun


> x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
> Processing file 'model.pdb'
> total number of nucleotides: 26
> [e] no matched residue for option --frame
>
> Thanks for your help.
>
> Best,
> Amir
>
>
> On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3dna...@gmail.com> wrote:
>
>> Hi Amir,
>>
>> Please have a look at the announcement "No more grant funding for
>> 3DNA/DSSR" (
>> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
>> on the 3DNA Forum. DSSR results are reproduced, period.
>>
>> Best wishes,
>>
>> Xiang-Jun
>>
>> --
>> Xiang-Jun Lu (Ph.D.)
>> Email: xiang...@x3dna.org
>> Web: http://x3dna.org/
>> Forum: http://forum.x3dna.org/
>>
>>
>> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
>> taghavi.amirhoss...@gmail.com> wrote:
>>
>>> 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 <3dna...@gmail.com> wrote:
>>>
 Dear Blaine,

 On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
 blaine-moo...@ouhsc.edu> 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/pymol-users@lists.sourceforge.net
 Unsubscribe:
 https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-12 Thread amirhossein taghavi

Hi Xiang-Jun,

Sorry to bother. I meant if I can do the same thing you have done with DSSR
pro with free version of x3dna-dssr, as I am getting some error messages:

x3dna-dssr -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb
Processing file 'model.pdb'
total number of nucleotides: 26
[e] no matched residue for option --frame

Thanks for your help.

Best,
Amir


On Fri, Nov 12, 2021 at 11:00 AM Xiang-Jun Lu <3dna...@gmail.com> wrote:

> Hi Amir,
>
> Please have a look at the announcement "No more grant funding for
> 3DNA/DSSR" (
> http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
> on the 3DNA Forum. DSSR results are reproduced, period.
>
> Best wishes,
>
> Xiang-Jun
>
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xiang...@x3dna.org
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
>
>
> On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
> taghavi.amirhoss...@gmail.com> wrote:
>
>> 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 <3dna...@gmail.com> wrote:
>>
>>> Dear Blaine,
>>>
>>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>>> blaine-moo...@ouhsc.edu> 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/pymol-users@lists.sourceforge.net
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-12 Thread Xiang-Jun Lu

Hi Amir,

Please have a look at the announcement "No more grant funding for
3DNA/DSSR" (
http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/)
on the 3DNA Forum. DSSR results are reproduced, period.

Best wishes,

Xiang-Jun

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


On Fri, Nov 12, 2021 at 10:51 AM amirhossein taghavi <
taghavi.amirhoss...@gmail.com> wrote:

> 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 <3dna...@gmail.com> wrote:
>
>> Dear Blaine,
>>
>> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
>> blaine-moo...@ouhsc.edu> 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/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-12 Thread amirhossein taghavi

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 <3dna...@gmail.com> wrote:

> Dear Blaine,
>
> On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
> blaine-moo...@ouhsc.edu> 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/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-12 Thread Xiang-Jun Lu

Dear Blaine,

On Fri, Nov 12, 2021 at 10:14 AM Mooers, Blaine H.M. (HSC) <
blaine-moo...@ouhsc.edu> 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
>
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-12 Thread Mooers, Blaine H.M. (HSC)

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 [3dna...@gmail.com]
Sent: Friday, November 12, 2021 8:05 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

Message: 1
Date: Thu, 11 Nov 2021 01:21:47 +
From: "Mooers, Blaine H.M.  (HSC)" 
mailto:blaine-moo...@ouhsc.edu>>
To: amirhossein taghavi 
mailto:taghavi.amirhoss...@gmail.com>>,

"pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>"

mailto:pymol-users@lists.sourceforge.net>>
Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
system
Message-ID:

<87dcc6c40b22804192b6892e6429ec5f019d5e3...@countach.hsc.net.ou.edu<mailto:87dcc6c40b22804192b6892e6429ec5f019d5e3...@countach.hsc.net.ou.edu>>
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: xiang...@x3dna.org<mailto:xiang...@x3dna.org>
Web: 
http://x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__x3dna.org_=DwMFaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4=SCbMW3JwZkTKAxEfPB8w5TtSItCw4MMTIOr8sxCVEIE=>
Forum: 
http://forum.x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.x3dna.org_=DwMFaQ=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4=R5l09hlMu8Qv8Uw7eKpaBtB-k1s-E1xX0jqFJ9b_oDg=>

 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://

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

2021-11-10 Thread amirhossein taghavi

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) <
blaine-moo...@ouhsc.edu> 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
> 
> (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 [taghavi.amirhoss...@gmail.com]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pymol-users@lists.sourceforge.net
> 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
>
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Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

2021-11-10 Thread Mooers, Blaine H.M. (HSC)

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 [taghavi.amirhoss...@gmail.com]
Sent: Wednesday, November 10, 2021 5:03 PM
To: pymol-users@lists.sourceforge.net
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


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

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

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

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

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

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

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

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

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