On 9/02/2011 4:52 PM, bharat gupta wrote:
Tsjerk,
Sorry for asking that .. actually I made a silly mistake while
selecting residues.. After plotting the graphs for common regions I
found that first 100 amino acids shows a lot of fluctuations (compared
to the one without any loop insertion) ..
Tsjerk,
Sorry for asking that .. actually I made a silly mistake while selecting
residues.. After plotting the graphs for common regions I found that first
100 amino acids shows a lot of fluctuations (compared to the one without any
loop insertion) ... Does the insertion caused a great change in t
We can't know that. We don't have your files (and we don't want them).
Check what you did, and what index groups you have. Write out the
structure for the index group and have a look. We're not a substitute
for your brain here... :p
Cheers,
Tsjerk
On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta wr
Thanks for the advice and while creating the index file for first 100 common
residues it found that both structures shows different no.of atoms. .. how
is that possible ??
On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar wrote:
> Hi Bharat,
>
> You can do it with post-processing the data you obt
You calculate rmsf of both proteins separately and then plot them together
and look the region of your interest..
On Wed, Feb 9, 2011 at 10:28, bharat gupta wrote:
> I used the -res option ... and I got the rmsf in terms of residues but
> still the problem is that the two structures contain
Hi Bharat,
You can do it with post-processing the data you obtain from g_rmfs, if
it's okay that the fit uses all residues in either case. Otherwise,
you can make an two index files, including only the residues that are
common to both.
Hope it helps,
Tsjerk
On Wed, Feb 9, 2011 at 5:58 AM, bhara
I used the -res option ... and I got the rmsf in terms of residues but still
the problem is that the two structures contain different amount of residues
due to loop replacement in one structure.. In that case how shall proceed to
check the effect of loop insertion on the overall topology of the pro
try -res option
On Wed, Feb 9, 2011 at 08:51, Justin A. Lemkul wrote:
>
>
> bharat gupta wrote:
>
>> Actually after loop incorporation I want to check which region of the
>> protein shows much deviation , which I think can be done by plotting rmsf
>> values from both proteins.. but the problem h
bharat gupta wrote:
Actually after loop incorporation I want to check which region of the
protein shows much deviation , which I think can be done by plotting
rmsf values from both proteins.. but the problem here is that one
structure which contains loops has more no. of atoms as compared to
Actually after loop incorporation I want to check which region of the
protein shows much deviation , which I think can be done by plotting rmsf
values from both proteins.. but the problem here is that one structure which
contains loops has more no. of atoms as compared to other str. without loop
in
bharat gupta wrote:
Hi,
I want to calculate the RMSF of residues and not of protein ... how can
this be done with g_rmsf..
Also I want to see the rmsf of certain residues .. for which I created
the .ndx file containint those residues only .. and after using g_rmsf
with index file gives th
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