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#34989 - 05/12/15 03:08 PM How to Highlight B-Values of Side Chains?
rossi Offline
Forum Member

Registered: 03/31/05
Posts: 53
Loc: New York City
Hello:

I am trying to see the effect of side-chain fluctuation on molecular permeation through a transmembrane protein channel.

The idea is create a pdb file with a column of b-values related to the RMSF values of the MD trajectory.

I am using Lennart's script to do this, and everything is working fine.

What I tried was to set the b-values of all heavy atom main-chain atoms to 1.0 with the scalar command. Then, all the B side-chain values were set equal to the calculated RMSF value from the trajectory, using the correct formula relating RMSF fluctuation to b-value.

But, the above method blows up in visualization programs. I think this is probably due to the fact that all main-chain atoms are equal to 1, and the algorithm cannot handle this.

The putty representation takes the values from the b-factor of the CA atom. Theus, one should store ALL fluctuation values on the CA atoms, leaving all other atoms with 0.0, any other value or something like that. Larger RMSF fluctuations from side-chain residues would show up in the representation algorithm based on larger CA values.

I am using CHARMM to compute the RMSF of atoms over the trajectory, and the CHARMM script of Lennart computes the RMSF values ok, but it doesn't seem to be flexible enough to allow for adding the side chain RMSF to the CA RMSF. At least, my brain isn't flexible enough to do this task within the CHARMM scripting language. I have played around with the scalar wmain, wcomp, etc commands. But, wmain, for example, has separate locations for CAs and CBs, but how to add them together?

Can someone please provide me with a way to add the side-chain fluctuations to the CA atom fluctuations?

Thanks so much for your help.

Kind regards,

Angelo

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#34990 - 05/12/15 03:30 PM Re: How to Highlight B-Values of Side Chains? [Re: rossi]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
The rmsf-residue script gets the side chaing average value into the z-coordinete of all side-chain atoms. What you need is a way to get this value into wmain of the CA atoms.
One way to this for each residue is to get rside as in the script, and then:
coor set xdir @rside ydir 0.0 zdir 0.0 sele "residue i" end

finally, after you have done this for all residues:
put the distance of each atom into wmain. since all atoms have the side-chain average rmsf as X and Y=Z=0, this distance is X=sidechain RMSF:

coor dist weig

and get the real x,y,z back from the sca3,4,5 arrays

I have not tried it but it may work.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#34991 - 05/13/15 09:57 AM Re: How to Highlight B-Values of Side Chains? [Re: lennart]
rossi Offline
Forum Member

Registered: 03/31/05
Posts: 53
Loc: New York City
Dear Lennart:

Very nice and very tricky. It worked!!! Hoooray!!

Here is the tail end of the script according to your suggestions:

.
.
.
coor stat sele ires @ires .and. side end
set rside = ?zave
! This command puts side chain rmsf of residue into the x coordinate component
coor set xdir @rside ydir 0.0 zdir 0.0 sele ires @ires end
incr rside by 0.0
trim rside to 12
.
.
.
!Put the X (RMSF values for side chains), Y=Z=0 components into wmain array
coor dist weigh

!compute B-factors from RMSF values
set pi = 3.1415927
calc factor = ( 8.0 * @pi * @pi ) / 3.0
scalar wmain mult @factor

!Recover coordinates for printing
scalar x = sca3
scalar y = sca4
scalar z = sca5
.
.
.
write coor pdb select protein end name cx26_sidechain_rmsf_bfactor.pdb
* coordinates
*
close unit 1


And here are a view of the entries from the resulting PDB file.
ATOM 36 N TRP 3 7.993 -9.797 3.643 1.00 33.30 PROA
ATOM 37 HN TRP 3 7.586 -10.437 4.247 1.00 33.30 PROA
ATOM 38 CA TRP 3 9.374 -10.004 3.332 1.00 33.30 PROA
ATOM 39 HA TRP 3 9.875 -9.087 3.515 1.00 33.30 PROA
ATOM 40 CB TRP 3 9.989 -11.074 4.217 1.00 33.30 PROA
ATOM 41 HB1 TRP 3 9.586 -12.004 3.982 1.00 33.30 PROA
ATOM 42 HB2 TRP 3 11.005 -11.128 4.029 1.00 33.30 PROA
ATOM 43 CG TRP 3 9.839 -10.908 5.660 1.00 33.30 PROA
ATOM 44 CD1 TRP 3 9.358 -11.760 6.475 1.00 33.30 PROA
ATOM 45 HD1 TRP 3 9.029 -12.678 6.184 1.00 33.30 PROA
ATOM 46 NE1 TRP 3 9.355 -11.265 7.707 1.00 33.30 PROA
ATOM 47 HE1 TRP 3 9.064 -11.669 8.450 1.00 33.30 PROA
ATOM 48 CE2 TRP 3 9.852 -10.071 7.707 1.00 33.30 PROA
ATOM 49 CD2 TRP 3 10.173 -9.806 6.440 1.00 33.30 PROA
ATOM 50 CE3 TRP 3 10.706 -8.648 6.149 1.00 33.30 PROA
ATOM 51 HE3 TRP 3 10.972 -8.423 5.198 1.00 33.30 PROA
ATOM 52 CZ3 TRP 3 10.899 -7.755 7.147 1.00 33.30 PROA
ATOM 53 HZ3 TRP 3 11.301 -6.856 6.948 1.00 33.30 PROA
ATOM 54 CZ2 TRP 3 10.045 -9.188 8.694 1.00 33.30 PROA
ATOM 55 HZ2 TRP 3 9.796 -9.384 9.657 1.00 33.30 PROA
ATOM 56 CH2 TRP 3 10.568 -8.022 8.400 1.00 33.30 PROA
ATOM 57 HH2 TRP 3 10.723 -7.326 9.148 1.00 33.30 PROA
ATOM 58 C TRP 3 9.639 -10.336 1.887 1.00 33.30 PROA
ATOM 59 O TRP 3 10.632 -9.940 1.332 1.00 33.30 PROA
ATOM 60 N GLY 4 8.727 -11.036 1.222 1.00 0.00 PROA
ATOM 61 HN GLY 4 7.936 -11.354 1.686 1.00 0.00 PROA
ATOM 62 CA GLY 4 8.813 -11.299 -0.190 1.00 0.00 PROA
ATOM 63 HA1 GLY 4 8.068 -12.012 -0.420 1.00 0.00 PROA
ATOM 64 HA2 GLY 4 9.783 -11.639 -0.425 1.00 0.00 PROA
ATOM 65 C GLY 4 8.550 -10.100 -1.024 1.00 0.00 PROA
ATOM 66 O GLY 4 9.158 -9.904 -2.044 1.00 0.00 PROA
ATOM 67 N THR 5 7.653 -9.226 -0.581 1.00 31.34 PROA
ATOM 68 HN THR 5 7.140 -9.445 0.213 1.00 31.34 PROA
ATOM 69 CA THR 5 7.395 -7.942 -1.197 1.00 31.34 PROA
ATOM 70 HA THR 5 7.241 -8.103 -2.236 1.00 31.34 PROA
ATOM 71 CB THR 5 6.177 -7.257 -0.643 1.00 31.34 PROA
ATOM 72 HB THR 5 6.323 -7.005 0.400 1.00 31.34 PROA
ATOM 73 OG1 THR 5 5.072 -8.098 -0.736 1.00 31.34 PROA
ATOM 74 HG1 THR 5 4.651 -8.032 -0.230 1.00 31.34 PROA
ATOM 75 CG2 THR 5 5.836 -6.017 -1.422 1.00 31.34 PROA
ATOM 76 HG21 THR 5 5.957 -5.733 -1.773 1.00 31.34 PROA
ATOM 77 HG22 THR 5 5.511 -5.818 -1.682 1.00 31.34 PROA
ATOM 78 HG23 THR 5 5.759 -5.544 -1.397 1.00 31.34 PROA
ATOM 79 C THR 5 8.567 -7.013 -1.070 1.00 31.34 PROA
ATOM 80 O THR 5 8.971 -6.378 -2.022 1.00 31.34 PROA

Thanks so much for your help.

Warm regards,

Angelo

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