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

[Tamas H. <bio...@gm...>]

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 <bio...@gm... 
> <mailto:bio...@gm...>> 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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