enced this?
best
Kanika
On Wed, Jun 28, 2017 at 6:13 PM, Tsjerk Wassenaar wrote:
> Hi Kanika,
>
> Try
>
> set two_sided_lighting
>
> Cheers,
>
> Tsjerk
>
> On Jun 28, 2017 17:14, "kanika sharma" wrote:
>
>> Dear PyMolers
>>
>&g
you mat try:
>>
>> import center_of_mass
>>
>> com SelectionObjectName, state=1#Create a pseudoatom representing the Object
>> COG and store it as "SelectionObjectName_COM"
>>
>>
>>
>> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma
>
ps://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object
> COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26,
1, myobj and chain A and resi 100 and name NH1+NH2
> ```
>
> and to place a pseudoatom at a specific XYZ coordinate, pass the `pos`
> parameter with a 3-tuple of floats:
>
> ```
> pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
> ```
>
> Hope that helps.
>
> Cheers,
&
Dear PyMol Users,
I asked this question but no body replied so I am trying again.
I am struggling here two things.
1). I want to place a pseudo
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
a
pseudo
atom in the centre of a cavity in t
Dear PyMol Users,
I am struggling here two things.
1). I want to place a pseudoatom in the charge centre of a non aromatic
residue, like arginine.
2). Is it possible to place another pseudoatom in the centre of a cavity in
the protein? I am thinking how can I define the co ordinates of the
positio
residues face to face.
I hope something is possible
--
*Regards,*
*
*
*Kanika Sharma*
Project Assistant
Indian Institute of Technology
SCFBio
Delhi
8010212156
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index.php/Rotkit
>
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>
>
> 2011/10/7 kanika sharma
>
>> Hello everyone,
>> I Have a protein with 2 chains.
>> I h
Hello everyone,
I Have a protein with 2 chains.
I have to rotate the second chain of the protein by 60,120,180,240 degrees
each.
Is there a script in PyMol that can do that?
Best,
Kanika
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can i get to know whether my proteins are in same plane or different plane
in pymol..?
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>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma
> wrote:
> > i have attached a small section of the file after applying the matrix..
> > the spacing between x,y and z axis is abnormal
>
&
i have attached a small section of the file after applying the matrix..
the spacing between x,y and z axis is abnormal
part.pdb
Description: Protein Databank data
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On Mon, Apr 11, 2011 at 12:04 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Kanika,
>
> > I opened a file 1alu in pymol and ran script CenterOfMass.py. When I gave
> > the command com 1alu, state=1, it displays a message
> >
> > AttributeError: 'module' objec
I opened a file 1alu in pymol and ran script CenterOfMass.py. When I gave
the command com 1alu, state=1, it displays a message
AttributeError: 'module' object has no attribute 'get_legal_name'...
Iam unable to figure out why is this so.,
--
After going through the script library and tutorial, I couldn't find
information about calculating the radius of gyration. Is this possible
in pymol? And after this I want to generate a virtual cube around it
of a specific length.
Thanks,
Kanika
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I get the mistake..
Thanks all..
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Should not the positions of ASU's generated by REMARK290 be same as the
symmetry mates generated?
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I used symexp command for 3QK9 using distance of 2.75 to generate
ASU(asymmetric unit). Does symexp generate these symmetry mates from the
remark290 of PDB file? I couldnot find the code for symexp in pymolwiki. Can
anyone help out?
Regards,
Kanika
--
-
I hope this makes my point clear
1BX7...the author determined structure is monomeric..PISA generate dimeric
assembly
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.00 0.00 0.000.0
REMARK
1BX7...the author determined structure is monomeric..PISA generate dimeric
assembly
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.00 0.00 0.000.0
REMARK 350 BIOMT2 1 0.00 1.00
ya,i get it...
Thanks...
On Thu, Mar 3, 2011 at 5:58 PM, Tsjerk Wassenaar wrote:
> Hi Kanika,
>
> > REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
>
> It says 'author determined'. It doesn't say how, though. But look at
> the following:
>
> # Get the molecule
> fetch 1b8e,async=0
>
> # C
protein 1b8e says its a dimer by its pdb file info as:
BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.00 0.00 0.000.0
REMARK 350 BIOMT2 1 0.00 1.00 0.00
the symexp data may not always be consistent with the biomt
transformations..although they turn out to be..
considering the case of 3hh7...the biological unit and asymm unit are
same...to form a dimer of this protein...i cannot find a clue by biomt data
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A,
my protein is 3m2m..iv downloaded the biological assembly 1 for this..
http://www.rcsb.org/pdb/explore/explore.do?structureId=3M2M
to generate dimer for this the BIOMT data is like this from the pdb
filei dont know how will this work if its an identity matrix..
REMARK 350 BIOMOLECULE: 1
REM
tein is not from the PDB, you can still try pisa (
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts
> protein coordinate files uploaded by the users and determines the "stable
> dimer" or else-mer of your protein.
>
> hope these help!
> hongbo
>
>
> O
this is an identity matrix so will not make any change,i thinkbut the
file says so...
can any one help me...!!
Regards,
Kanika
On Mon, Feb 28, 2011 at 1:26 PM, kanika sharma wrote:
> M really sorry for the wrong information guys...script helped a lot..
>
> If my protein is a dime
t; your best in providing correct information and thinking along.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma
> wrote:
> > Iv applied the foll eq:
> >
> > load 1b8e.pdb, A
> > create B,A
> > alter_state 1,B,(x,y,z)=(x,-y
e. For a full biomt record (R
> t), with R being the rotation matrix (first three columns) and t the
> translation vector (last column), you would have to make the equation
> reflect the matrix operation Rp+t.
>
>
> Hope it helps,
>
>
> Tsjerk
>
>
> On Feb 28, 201
Does anyone know how to apply these biometric constraints to generate a
dimer of my molecule
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK
350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.00 0.00 0.000.0
REMARK 350
Hi,
i am working to generate a dimer of my protein..I have made a duplicate of
my proteinCan any one tell me how to rotate my molecule to get maximum
stability..???
Regards..
Kanika
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