Re-reading what I wrote, here is clarification:
Protein X reads residue indices from pdb, starts at 103, ends at 173,
Your results are for sequence 1-70, You want to see in the structure why in
your results segment 46-53 is unique.
select 46-53 results in no atoms selected, because you are off with the
numbering. Instead you need to calulate 46+103=149 (and perhaps +1, never
sure about that) and 53+103=156 and re-issue the command
select 149-156.
Then you want to know, if the loop in positions 125-132 in the structure,
which you pick by cursor on screen is somehow identified in your
calculation based on the 70aa sequence. Now 125-103=22 (?) and 132-103=129
(?) is needed to convert the screen structure indexing into your tables. Ad
so forth.
Re C
How Rasmo'sl renumber x worked was that if there were gaps in the readed
indices e.g.
ATOM 11 NH2 ARG A 103 -10.684 12.480 58.277 1.00 25.62
RADA N
ATOM 12 N PRO A 108 -14.360 5.552 63.412 1.00 22.41
RADA N
it renumbered all sequentially so the virtual result was something like
ATOM 11 NH2 ARG A 1 -10.684 12.480 58.277 1.00 25.62 RADA
N
ATOM 12 N PRO A 2 -14.360 5.552 63.412 1.00 22.41
RADA N
which of course was a problem, because the you have no clue where you are
(bug in the rasmol sort of)
The desired outcome of renumber 1 (if residue 103 is the first in the
molecule) would be something like
ATOM 11 NH2 ARG A 1 -10.684 12.480 58.277 1.00 25.62 RADA
N
ATOM 12 N PRO A 6 -14.360 5.552 63.412 1.00 22.41
RADA N
103->1
(104)->2
(105)->3
(106)->4
(107)->5
108-> 6
Petr
Dr. Petr Pancoska
Department of Pathology
SUNY Stony Brook, NY 11794
phone: (631)-444-3030
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"Miguel"
<[EMAIL PROTECTED]>
Sent by: To
jmol-users-admin@ jmol-users@lists.sourceforge.net
lists.sourceforge cc
.net
Subject
Re: [Jmol-users] renumbering in
12/21/2004 12:14 Jmol
PM
Please respond to
[EMAIL PROTECTED]
sourceforge.net
Petr wrote:
> Trying "renumber x" in the Rasmol Scripts console results in Script
> command not implemented: renumber.
True, that is not implemented.
A year ago when I was working on the scripting engine I did not understand
how it worked, and noone has asked for it.
> Cannot find any replacement functionality in the docs. This is relatively
> important function for transferring sequence analysis into 3D picture.
Please explain ... I do not understand what you mean.
> PDB files unfortunately sometimes contain numbering that starts not where
> one would like to so it is painful to re-calculate everything to the new
> indexing.
> renumber was an easy remedy for that - any suggestions how to do that?
I now understand that the residue sequence numbers are often not
sequential, and that insertion codes add to the complexity.
I can probably implement 'renumber' ... but the idea of changing the raw
data makes me nervous ... I fear it will have unforseen repercussions.
So first ...
I do not understand what the value of 'renumber' is. It seems to me that
it would break all of the scripts associated with that .pdb file.
Q: What is the benefit of using 'renumber'? What are you trying to
accomplish?
Miguel
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