Re: [PyMOL] Problem using pymol

[Spencer Bliven]

> Please let me know how can I renumber protein chains to avoid overlap and
> give it a uniqu chain id.
>

You can manually modify chain IDs with the alter
 command. For instance, to rename
chain A to X:

alter chain A, chain = "X"

To automatically select unique chain IDs, you can install the flatten_obj
 script.


> How can I change .pse file to .pdb file?
>

Use the 'Save molecule' option in the file menu, or the save
 command.

-Spencer
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[PyMOL] Problem with pymol

[soumi]

Respected Sir,

   Can I build a model using missing residues through Pymol ? If it 
is,Please 

tell me the way.



With Regards,

SoumiDas--
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[PyMOL] (no subject)

[Dan Lin]

Dear all:

It appears that pymol only interpolates motions that include rotations by
moving the object along an arc. I would like to make a movie that does not
do this, but rather, moves the object along a straight line while rotating
the object. Unfortunately, I'm absolutely at a loss about how I could do
this. Would anybody have any suggestions about where to look for this
information?

Thanks,
Dan
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Re: [PyMOL] how to close displaying a molecule

[Tsjerk Wassenaar]

Hi Smith,

You can delete the object:

delete B

Cheers,

Tsjerk

On Fri, Dec 11, 2015 at 8:19 AM, Smith Liu  wrote:

> Dear All,
>
> Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb
> and have only A.pdb displayed?
>
> Smith
>
>
>
>
>
>
> --
>
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] how to close displaying a molecule

[Albert]

just click the b.pdb on the Pymol object manager bar to undisplay it.

That's the basic of basic usage of Pymol. Wouldn't it be nice if you 
spend a few minutes to go through Pymol manual?




On 12/11/2015 08:19 AM, Smith Liu wrote:

Dear All,

Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close 
B.pdb and have only A.pdb displayed?


Smith



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[PyMOL] how to close displaying a molecule

[Smith Liu]

Dear All,


Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb and 
have only A.pdb displayed?


Smith

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[PyMOL] Fw: on load new B-factors

[Smith Liu]

in addition, now it occurs "[Errno 2] No such file or directory: 
'newBfactors.txt', although I have specified the directory of  
'newBfactors.txt'. It seems this error message has no relation with which 
directory I put 'newBfactors.txt'.


Any advice?


Smith







 Forwarding messages 
From: "Smith Liu" 
Date: 2015-12-10 22:27:03
To: "pymol-users@lists.sourceforge.net" 
Subject: [PyMOL] on load new B-factors

Dear All,


When I use "loadBfacts mol, [startaa, [source, [visual Y/N]]]", I meet the 
following error message,


"File "Some_directory\parse.py", line 250, in parse
self.result=app(layer.kw[0],layer.args,layer.kw_args)
File "loadBfacts.py",line 16, in loadBfacts
obj=cmd.get_object_list(mol)[0]
TypeError: ‘NoneType' object is unsubscriptable"


Will you please tell me how to clear this error?


In addition, for the newBfactors.txt, each line was for one residue rather than 
for the one atom, right?  If my PDB starting at resi 100 ending at resi 400, 
the newBfactors.txt should start at resi 1 and end at resi 400 in order to have 
pymol color the whole molecule correctly based on new B-factors, am I right or 
not?


Smith








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[PyMOL] on load new B-factors

[Smith Liu]

Dear All,


When I use "loadBfacts mol, [startaa, [source, [visual Y/N]]]", I meet the 
following error message,


"File "Some_directory\parse.py", line 250, in parse
self.result=app(layer.kw[0],layer.args,layer.kw_args)
File "loadBfacts.py",line 16, in loadBfacts
obj=cmd.get_object_list(mol)[0]
TypeError: ‘NoneType' object is unsubscriptable"


Will you please tell me how to clear this error?


In addition, for the newBfactors.txt, each line was for one residue rather than 
for the one atom, right?  If my PDB starting at resi 100 ending at resi 400, 
the newBfactors.txt should start at resi 1 and end at resi 400 in order to have 
pymol color the whole molecule correctly based on new B-factors, am I right or 
not?


Smith



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