RMSF Plot

YED

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Dec 26, 2023, 2:11:58 PM12/26/23

to carma molecular dynamics

It would be great to have a RMSF plot in this great software.

Nicholas M. Glykos

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Dec 26, 2023, 3:01:58 PM12/26/23

to YED, carma molecular dynamics

> It would be great to have a RMSF plot in this great software.

If you mean to calculate RMSF from average, carma does that since its first
public version. This is mentioned in

https://utopia.duth.gr/glykos/carma.html#section_47

If you do the calculation with grcarma, the RMSFs will also be present in
the 'average' structure, in the B-factor column (last) :

ATOM 1 CA VAL A 1 -9.526 -26.222 -9.308 1.00 1.85
ATOM 2 CA GLU A 2 -9.135 -22.780 -8.161 1.00 1.41
ATOM 3 CA GLU A 3 -11.215 -20.423 -6.553 1.00 1.40
ATOM 4 CA ARG A 4 -10.658 -16.773 -5.845 1.00 1.03
ATOM 5 CA PRO A 5 -13.113 -13.946 -5.599 1.00 1.10
ATOM 6 CA SER A 6 -11.666 -12.284 -8.603 1.00 1.06
............
............

--

Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

YED

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Dec 26, 2023, 4:38:26 PM12/26/23

to carma molecular dynamics

Hi Nicholas,
Thank you for the response. I'm trying to get RMSF using cartesian PCA but it seems to produce an average structure for each cluster. Is there any way to calculate RMSF for the entire trajectory?

26 Aralık 2023 Salı tarihinde saat 23:01:58 UTC+3 itibarıyla Nicholas M. Glykos şunları yazdı:

Nicholas M. Glykos

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Dec 26, 2023, 4:49:05 PM12/26/23

to YED, carma molecular dynamics

> Thank you for the response. I'm trying to get RMSF using cartesian PCA but
> it seems to produce an average structure for each cluster. Is there any way
> to calculate RMSF for the entire trajectory?

Yes, there is. You first do 'fitting' of the whole trajectory to remove
rotations/translations, and then using the fitted trajectory (which is
complete and not clustered), you calculate the average structure which will
give you the RMSFs as a by-product.

This will be much easier to do with grcarma.

YED

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Dec 27, 2023, 3:35:29 AM12/27/23

to carma molecular dynamics

Thank you very much. I used the correct task in grcarma and it worked. I hope you have a great day.

27 Aralık 2023 Çarşamba tarihinde saat 00:49:05 UTC+3 itibarıyla Nicholas M. Glykos şunları yazdı:

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