Hello --
I am trying to transform an object to align it's major axis with the x-axis
at z = 0 in the camera coordinate space. Sample pdb file (just a simple
scale bar) is attached.
My thought process is as follows:
1. Convert <1, 0, 0> in camera space to model space (vector A)
2. Find vector tha
Thanks to all. It worked for me.
Thanks and Cheers!
On Wed, Jul 2, 2014 at 6:47 PM, Rajintha Bandaranayake
wrote:
> Monica,
>
> Try:
>
> align PDB1//A/80-120+160-220/, PDB2//A/80-120+160-220/
> or if you want to align using the alpha carbons,
> align PDB1//A/80-120+160-220/CA, PDB2//A/80-120+16
Monica,
Try:
align PDB1//A/80-120+160-220/, PDB2//A/80-120+160-220/
or if you want to align using the alpha carbons,
align PDB1//A/80-120+160-220/CA, PDB2//A/80-120+160-220/CA
Cheers,
-Rajintha
On Wed, Jul 2, 2014 at 7:22 AM, Monica Mittal
wrote:
> Dear all
> I need to align lets say resi 80-
Hi Monica,
I haven't tested, but maybe you could try:
align PDB1 and (resi 80-120 or resi 160-220), PDB2 and (resi 80-120 or resi
160-220)
I.e. expanding the selection to both streches. Running sequential
alignments will replace existing ones.
How this may help.
/Andreas
On Jul 2, 2014 1:24 PM,
Dear all
I need to align lets say resi 80-120 and 160-220 from one protein to resi
80-120 and 160-220 in second protein. How can i do this.
I tried following:
align PDB1 and resi 80-120, PDB2 and resi 80-120
this is for one set but how to do for two sets 80-120 as well as 160-220
simultaneously.
Th
Hi Jordan,
Regarding your post script,
> PS. In the newest release of pymol for mac, I have noticed that when I click
> on a letter in the sequence (when the s option is toggled) it selects the
> entire chain rather than the individual amino acid.
Your mouse selecting mode is "chains". Click o
Hi Jordan,
you can first intra_fit the multi-state object and then align its first
state to the input structure.
# this will fit all states to the first state
intra_fit multimodel
# align first state to input structure
align multimodel, input, mobile_state=1
http://pymolwiki.org/index.php/intr
Hi Pymol!
I have a question about movies, but has nothing to do with the movie commands,
so don't worry.
I have 750 states that are dumped directly into pymol where each "move" from
my modeling program, is a new state. I want to compare this to the input
structure which only has one state.
I
Hi Sajeewa,
have you tried one of the alignment commands (align, super, cealign)?
http://pymolwiki.org/index.php/Align
You can't align "files", only "objects". So if your session files
contain only one object each, this is trivial. If they contain multiple
objects which need to be aligned in c
Hello,
I have three intramolecular tunnels in three pymol session (.pse) files.
Two .pse files are corresponding to the same snapshot in molecular
dynamics. The third .pse file is
for a different snapshot. I want to merge these .pse files using commands
like
load first.pse
load second.pse,partial
Hi Abhi,
On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma
wrote:
> I want to align different models of a multimodel pdb file.
>
> How can I do that without extracting models as identical pdb.
>
> cheers,
> Abhi
Try the intra_fit command.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Rese
I want to align different models of a multimodel pdb file.
How can I do that without extracting models as identical pdb.
cheers,
Abhi
I have a pdb and xplor file which contain two units of the same
protein/inhibitor complex. What I am trying to do is align the two
proteins to each other so I can compare the subunits. I can accomplish
this by reading in the pdb file twice and aligning the b unit from the
second pdb file to the
I recently tried aligning a movie object of a morph
(with 32 states) to a single pdb and it seemed to work
although I dont know what state of the movie it
aligned to. I was wondering if you can specify which
state you want to align to and what was aligned by
default.
Thanks
Jason Lamoureux
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