From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 08 2016 - 21:24:45 CST

Hi,
  Sure, color by "molecule" or else manually choose the colorIDs using
color by "colorID".

Cheers,
  John

On Fri, Dec 09, 2016 at 12:37:12AM +0000, Wong Li Zhe wrote:
> Thank you for the reply, Ashar and John!
>
> Just one quick question, would it be possible to differentiate the
> superimposed structures with colour code? (From the Superpose output)
>
> For instance, structure A in blue and structure B in red?
>
> Best regards,
>
> Li Zhe
>
> ---------------------------------------------------------------------------
>
> From: Ashar Malik <asharjm_at_gmail.com>
> Sent: Wednesday, 7 December, 2016 12:56:55 PM
> To: Wong Li Zhe; vmd-l_at_ks.uiuc.edu; John Stone
> Subject: Re: vmd-l: Superimpose
>
> Sorry accidentally replied to just you instead of the list.
> The thread is intact ...
> Following on your latest set of questions:
>
> That is not the superpose I was talking about.
> Use it from here if you don't want to install :
> [1]http://www.ebi.ac.uk/msd-srv/ssm/
> Hit the launch PDBeFOLD button. On the following page. Select coordinate
> files from the dropdown and upload both pdb files that you want to
> compare.
> In the results summary page - if you click the index you will see a
> rotation matrix like this
>
> -0.421 -0.104 -0.901 X -16.794
>
> 0.199 -0.980 0.021 * Y + 26.754
>
> -0.885 -0.170 0.433 Z 37.528
>
> Remove the 4th column -- and set up a matrix to reflect the values from
> your alignment.
>
> Well, when I input the 2 protein structures with different number of
> residues, PROMALD generated 2 PDB files based on their alignment.
>
> What I have done is that, I then open the 2 PDB files and look for
> matching residues sequence. For instance, residue ILE, ARG, ASN, LEU are
> in position 1000, 1001, 1002, 1003 of protein A and 534, 535, 536, 537
> of protein B.
>
> Since you persist on doing it the hard way :: follow my last email.
> Once you have selected that 1000 should line up with 534 and 1001 with 535
> etc
> start VMD
> load the two structures (first load the structure which has residues
> 1000,1001 etc and then the other)
> since you know the residues across the two structures are identical now
> you can remove the backbone keyword because identical residues mean
> identical number of atoms.
> use the following
> set prot_0 [atomselect 0 "resid 1000 1001 1002 1003 ..."]
> put all your residues numbers in the above selection from 1 of the
> structures
> set prot_1 [atomselect 1 "resid 534 535 536 537 ... "]
> put all your residues numbers in the above selection from the other of
> the 2 structures
> set f [measure fit $prot_0 $prot_1]
> set r [measure rmsd $prot_0 $prot_1]
> puts "RMSD between selections is :::"$r
> The above will return an RMSD value between your selections
> set all_0 [atomselect 0 all]
> $all_0 move $f
> the last two commands will put one structure on top of the other which is
> what you want.
>
>
> Those protein residues sequence that doesn't match, I deleted them based
> on the alignment file generated.
>
> Please don't delete lines/residues from the PDB file. When you will load
> it back into VMD - there will be GAPS and I don't see the point of viewing
> any alignment like that.
> On Wed, Dec 7, 2016 at 5:55 PM, Ashar Malik <[2]asharjm_at_gmail.com> wrote:
>
> Sorry accidentally replied to just you instead of the list.
> The thread is intact ...
> Following on your latest set of questions:
>
> That is not the superpose I was talking about.
> Use it from here if you don't want to install :
> [3]http://www.ebi.ac.uk/msd-srv/ssm/
> Hit the launch PDBeFOLD button. On the following page. Select coordinate
> files from the dropdown and upload both pdb files that you want to
> compare.
> In the results summary page - if you click the index you will see a
> rotation matrix like this
>
> -0.421 -0.104 -0.901 X -16.794
>
> 0.199 -0.980 0.021 * Y + 26.754
>
> -0.885 -0.170 0.433 Z 37.528
>
> Remove the 4th column -- and set up a matrix to reflect the values from
> your alignment.
>
> Well, when I input the 2 protein structures with different number of
> residues, PROMALD generated 2 PDB files based on their alignment.
>
> What I have done is that, I then open the 2 PDB files and look for
> matching residues sequence. For instance, residue ILE, ARG, ASN, LEU
> are in position 1000, 1001, 1002, 1003 of protein A and 534, 535, 536,
> 537 of protein B.
>
> Since you persist on doing it the hard way :: follow my last email.
> Once you have selected that 1000 should line up with 534 and 1001 with
> 535 etc
> start VMD
> load the two structures (first load the structure which has residues
> 1000,1001 etc and then the other)
> since you know the residues across the two structures are identical now
> you can remove the backbone keyword because identical residues mean
> identical number of atoms.
> use the following
> set prot_0 [atomselect 0 "resid 1000 1001 1002 1003 ..."]
> put all your residues numbers in the above selection from 1 of the
> structures
> set prot_1 [atomselect 1 "resid 534 535 536 537 ... "]
> put all your residues numbers in the above selection from the other of
> the 2 structures
> set f [measure fit $prot_0 $prot_1]
> set r [measure rmsd $prot_0 $prot_1]
> puts "RMSD between selections is :::"$r
> The above will return an RMSD value between your selections
> set all_0 [atomselect 0 all]
> $all_0 move $f
> the last two commands will put one structure on top of the other which
> is what you want.
>
>
> Those protein residues sequence that doesn't match, I deleted them
> based on the alignment file generated.
>
> Please don't delete lines/residues from the PDB file. When you will load
> it back into VMD - there will be GAPS and I don't see the point of
> viewing any alignment like that.
>
> ---------------------------------------------------------------------------
>
> From: Ashar Malik <[4]asharjm_at_gmail.com>
> Sent: Wednesday, 7 December, 2016 10:32:14 AM
> To: Wong Li Zhe
> Subject: Re: vmd-l: Superimpose
>
> Hi,
>
> Not sure why but I didn't get any transformation matrix from
> Superpose, hence, I couldn't view it using VMD.
>
> Did you use superpose from the CCP4 suite of programs
> here: [5]http://www.ccp4.ac.uk/html/superpose.html
> Once it is installed properly you type
> superpose protein1.pdb protein2.pdb
> A lot of stuff will flash on the screen. In the stdout you will find a
> few lines like
> Query protein1.pdb
> and Target protein2.pdb
> have been superposed. Superposition matrix (to be applied
> to ref.pdb) is
> Rx Ry Rz T
> 1.000 0.000 -0.000 -0.000
> 0.000 1.000 -0.000 0.000
> -0.000 -0.000 1.000 -0.000
> If you open protein1 and protein2 in VMD and then apply the above
> matrix from superpose onto protein1 it should superimpose the two
> proteins in VMD graphics window for you.
>
> Anyway, I used another server (PROSMALS3D) to run alignment and etc
> as what has been suggested by you.
>
> I don't remember suggesting PROSMAL!!!!
> Did you get an output like in the attached PDF.
>
> Managed to edit the PDB file manually using Excel and removed those
> unwanted residues.
>
> What do you mean removed the unwanted residues? Did you just delete
> the lines? If you were just deleting lines - you could have just
> deleted them in the PDB file (open the PDB file in a text editor -
> like gedit/nano). Which lines are you deleting ? Are you deleting
> those which are not aligning sequentially, because the output that I
> have attached is a sequence output. This server that you are using
> produces a sequence alignment --- even if you do cut down by deleting
> lines/residues - the remaining residues will NOT be equal as they
> STILL have different number of atoms. VMD will not superpose unless
> you have an equal number of atoms. You should refer to my previous
> email and do selections manually on the backbone atoms only. If you
> don't to and want to continue using your method you can delete lines
> but for the structure in VMD you would still have to select backbone
> atoms - so that the two selections are equal. I don't understand why
> you would want to do this. Because the deleted lines means an
> incomplete structure will be aligned - I don't see how that will offer
> any useful information. You could use the transformation matrix from
> aligning the edited structure on the whole. But that would give you
> the same answer which I have already told you ....
> from both structures select equal number of residues and from them
> select backbone atoms only. superimpose them.
>
>
> Prior to superimpose both protein structures on VMD, I tried
> converting from Excel to PDB but somehow it doesn't work with all
> those funny alphabets present in the file.
>
> A couple of things here. 1) A PDB file is a highly formatted file
> which each column assigned to a certain value. see
> here: [6]http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
> Look at the Record : Atom entry. There are more details in that and an
> example read it. 2) How did you convert the excel file to PDB ? PDB is
> just a text file. Did you save it as an excel file and open that excel
> file with a word editor? That would obviously not work because Excel
> has its own format - which is why you may see unfamiliar characters.
>
>
> I wonder do you have any insights on this?
>
> If you want to continue using PROMALS3D - you can get the residues
> that align -- so e.g. if your file tells you that residues
> 1,20,22,34,56 from protein 1 align with 3,21,22,35,57 in protein 2 --
> (notice they are equal in number of residues - both 5 in number) --
> start VMD
> you should load protein1 into VMD
> you should load protein2 into VMD
> set prot_0 [atomselect 0 "resid 1 20 22 34 56 and backbone"]
> set prot_1 [atomselect 1 "resid 3 21 22 35 57 and backbone"]
> set f [measure fit $prot_0 $prot_1]
> set r [measure rmsd $prot_0 $prot_1]
> puts "RMSD between selections is :::"$r
> set all_0 [atomselect 0 all]
> $all_0 move $f
> like i said in my previous email - YOU DO NOT NEED to delete
> lines/edit/use excel/convert or anything of that sort.
> Use promals3d to find which residues you wait to align. once you have
> those - use the code I gave you - change the number of residues to
> match what you get from promals3d. use the code. You will get your
> answer.
>
>
> I have tried online conversion and it doesn't work.
>
> Any thoughts on this?
>
> Thank you in advance.
>
> Best regards,
>
> Li Zhe
>
> --
> Best,
> /A
>
> --
> Best,
> /A
>
> --
> Best,
> /A
>
> References
>
> Visible links
> 1. http://www.ebi.ac.uk/msd-srv/ssm/
> 2. mailto:asharjm_at_gmail.com
> 3. http://www.ebi.ac.uk/msd-srv/ssm/
> 4. mailto:asharjm_at_gmail.com
> 5. http://www.ccp4.ac.uk/html/superpose.html
> 6. http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/