Re: [PyMOL] CCP4 maps not aligning to my PDB file

2021-04-12 Thread Chen, Qiang 
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 
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
> Archives: 
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Message: 2
Date: Mon, 12 Apr 2021 12:55:16 +0530
From: shubhashish chakraborty 
To: Tamas Hegedus 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CCP4 maps not aligning to my PDB file
Message-ID:

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  wrote:

> Hi,
>
> PyMOL seems not to primarily target working with densities.
>
> I suggest to use Chimera if you work with cryo EM maps.
>

Re: [PyMOL] CCP4 maps not aligning to my PDB file

2021-04-12 Thread Roger Rowlett 
One way of displaying CCP4-generated maps in Pymol is described on this web
page:

https://sites.google.com/colgate.edu/xrd-protocols/home/visualization-of-protein-models

One way of generating CCP4 maps suitable for use in Pymol is described on
this page:

https://sites.google.com/colgate.edu/xrd-protocols/home/model-building-and-validation

Roger Rowlett


On Mon, Apr 12, 2021, 2:35 AM shubhashish chakraborty <
cshubhash...@gmail.com> 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: 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] CCP4 maps not aligning to my PDB file

2021-04-12 Thread Tamas Hegedus 

pls. google

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html
https://www.cgl.ucsf.edu/chimera/data/tutorials/emfit09/emfit.html

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 > 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




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Re: [PyMOL] CCP4 maps not aligning to my PDB file

2021-04-12 Thread shubhashish chakraborty 
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  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: 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] CCP4 maps not aligning to my PDB file

2021-04-12 Thread Tamas Hegedus 

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




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