try this.
Matrix Copy - PyMOLWiki<https://pymolwiki.org/index.php/Matrix_Copy>
Matrix Copy - PyMOLWiki<https://pymolwiki.org/index.php/Matrix_Copy>
Matrix_copy copies the object matrix from one object to another.. This command
is often used after a protein structure alignment to bring other related
objects into the same frame of reference.
pymolwiki.org
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Today's Topics:
1. Re: CCP4 maps not aligning to my PDB file (Tamas Hegedus)
2. Re: CCP4 maps not aligning to my PDB file
(shubhashish chakraborty)
3. Re: CCP4 maps not aligning to my PDB file (Tamas Hegedus)
----------------------------------------------------------------------
Message: 1
Date: Mon, 12 Apr 2021 09:11:37 +0200
From: Tamas Hegedus <biohege...@gmail.com>
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CCP4 maps not aligning to my PDB file
Message-ID: <7c7d2677-0e52-164b-cea6-d5ed6690b...@gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hi,
PyMOL seems not to primarily target working with densities.
I suggest to use Chimera if you work with cryo EM maps.
E.g. you can use it to fit your struct into the density map.
If you decide to use Chimera, be careful, a first step of frustration
could be caused by the extension of the density file. Yes, the extension
- .mrc or .map; depending on the extension the map is aligned to the
origo or not (or something like that).
Bests,
Tamas
On 4/12/21 8:34 AM, shubhashish chakraborty wrote:
> Hello,
> I am not able to align my pdb file with its respective electron
> density map generated by CCP4i. Kindly?let me know what is going wrong.
> An image is attached for better reference.
>
> Thank you
> Shubhashish Chakraborty
> PhD Research Scholar (SRF)
> Varma Lab
> Structural and Molecular biology Lab
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
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Message: 2
Date: Mon, 12 Apr 2021 12:55:16 +0530
From: shubhashish chakraborty <cshubhash...@gmail.com>
To: Tamas Hegedus <biohege...@gmail.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CCP4 maps not aligning to my PDB file
Message-ID:
<caeyonzzof8r17jnbf_9+b4tytbcethoozxabs5x6n4l8ghp...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
Thank you for a reply.
I am not working with cryo-EM but it's an X-ray diffraction map.
A similar kind of problem I am facing in chimera, so what could be done?
Thank you
Shubhashish Chakraborty
PhD Research Scholar (SRF)
Varma Lab
Structural and Molecular biology Lab
Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
Khargar, Navi Mumbai
On Mon, Apr 12, 2021 at 12:42 PM Tamas Hegedus <biohege...@gmail.com> wrote:
> Hi,
>
> PyMOL seems not to primarily target working with densities.
>
> I suggest to use Chimera if you work with cryo EM maps.
> E.g. you can use it to fit your struct into the density map.
> If you decide to use Chimera, be careful, a first step of frustration
> could be caused by the extension of the density file. Yes, the extension -
> .mrc or .map; depending on the extension the map is aligned to the origo or
> not (or something like that).
>
> Bests,
> Tamas
>
> On 4/12/21 8:34 AM, shubhashish chakraborty wrote:
>
> Hello,
> I am not able to align my pdb file with its respective electron density
> map generated by CCP4i. Kindly let me know what is going wrong.
> An image is attached for better reference.
>
> Thank you
>
> Shubhashish Chakraborty
> PhD Research Scholar (SRF)
> Varma Lab
> Structural and Molecular biology Lab
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=04%7C01%7Cqic8%40pitt.edu%7Cf9a347cfbbee4a43277708d8fd849f93%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637538093362773384%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MQy0dow0CfxHb6tl%2FPlYFhOti26cfcsWPgnQXaicsF8%3D&reserved=0
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Message: 3
Date: Mon, 12 Apr 2021 09:28:25 +0200
From: Tamas Hegedus <biohege...@gmail.com>
To: shubhashish chakraborty <cshubhash...@gmail.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CCP4 maps not aligning to my PDB file
Message-ID: <5d3f2262-699d-b569-71d0-ee7ef2312...@gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
pls. google
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cgl.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Ffitmaps%2Ffitmaps.html&data=04%7C01%7Cqic8%40pitt.edu%7Cf9a347cfbbee4a43277708d8fd849f93%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637538093362773384%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=vRmk6Er8CMRxI8saFy65%2FVjHjwdyzzqpOkkmgVLAXeg%3D&reserved=0
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On 4/12/21 9:25 AM, shubhashish chakraborty wrote:
> Hi,
> Thank you for a reply.
> I am not working with cryo-EM but it's an X-ray diffraction map.
> A similar kind of problem I am facing in chimera, so what could be done?
>
> Thank you
>
> Shubhashish Chakraborty
> PhD Research Scholar (SRF)
> Varma Lab
> Structural and Molecular biology Lab
> Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)
> Khargar, Navi Mumbai
>
>
>
>
> On Mon, Apr 12, 2021 at 12:42 PM Tamas Hegedus <biohege...@gmail.com
> <mailto:biohege...@gmail.com>> wrote:
>
> Hi,
>
> PyMOL seems not to primarily target working with densities.
>
> I suggest to use Chimera if you work with cryo EM maps.
> E.g. you can use it to fit your struct into the density map.
> If you decide to use Chimera, be careful, a first step of
> frustration could be caused by the extension of the density file.
> Yes, the extension - .mrc or .map; depending on the extension the
> map is aligned to the origo or not (or something like that).
>
> Bests,
> Tamas
>
> On 4/12/21 8:34 AM, shubhashish chakraborty wrote:
>> Hello,
>> I am not able to align my pdb file with its respective electron
>> density map generated by CCP4i. Kindly?let me know what is going
>> wrong.
>> An image is attached for better reference.
>>
>> Thank you
>> Shubhashish Chakraborty
>> PhD Research Scholar (SRF)
>> Varma Lab
>> Structural and Molecular biology Lab
>> Advanced Centre for Treatment, Research and Education in Cancer
>> (ACTREC)
>> Khargar, Navi Mumbai
>>
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>>
>> Archives:https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=04%7C01%7Cqic8%40pitt.edu%7Cf9a347cfbbee4a43277708d8fd849f93%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637538093362773384%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MQy0dow0CfxHb6tl%2FPlYFhOti26cfcsWPgnQXaicsF8%3D&reserved=0
>>
>> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=04%7C01%7Cqic8%40pitt.edu%7Cf9a347cfbbee4a43277708d8fd849f93%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637538093362773384%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MQy0dow0CfxHb6tl%2FPlYFhOti26cfcsWPgnQXaicsF8%3D&reserved=0>
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