[PyMOL] help

[Clarisa Alvarez]

Hello everyone:
I need help because I have a pdb of a monomer but I know that it is a dimer
by crystallographic symmetry,  how can I make a new molecule of it? because
I could make it by generate/symmetry mate...but I could not save it...any
help will be great!
Thanks in advance!
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Re: [PyMOL] Atoms appears on cartoon at high resolution

[Thomas Holder]

Hi Lucile,

Thanks for the pse (off-list). Please hide the "nonbonded" representation:

PyMOL> hide nonbonded

Nonbonded rep is shown by default. In ray tracing, those are rendered as 
cylinders, with a radius that depends on the zoom level, that's why you may not 
see them when zooming in.

Cheers,
  Thomas

On 07 Oct 2015, at 09:48, Thomas Holder  wrote:

> Hi Lucile,
> 
> This picture looks unusual, can you give some details on how you created it? 
> E.g. is this a full-atom protein structure, or a CA-only or pseudo-atom 
> coarse grain model? Did you modify any settings?
> 
> The spheres look like "nb_spheres" representation, so maybe you simply need 
> to hide them:
> 
> PyMOL> hide nb_spheres
> 
> Cheers,
>  Thomas
> 
> On 06 Oct 2015, at 04:00, Lucile Fischer  wrote:
> 
>> Hello, 
>> thanks for providing such an useful list.
>> My question is : can we avoid the appearance of "blobs" at atom locations 
>> when ray tracing at high resolution an helix cartoon? (see attached picture)
>> thanks in advance
>> Lucile
>> 
>> 
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] help

[Osvaldo Martin]

Hi Clarisa,

If I understand correctly you generate the dimer, but you are not able to
save it. Wich error did you get? Did you select all the object when saving
the file?

By the way, may be you will find this wiki page
 useful.

Cheers,
Osvaldo.

On Wed, Oct 7, 2015 at 5:00 PM, Clarisa Alvarez 
wrote:

Hello everyone:
> I need help because I have a pdb of a monomer but I know that it is a
> dimer by crystallographic symmetry,  how can I make a new molecule of it?
> because I could make it by generate/symmetry mate...but I could not save
> it...any help will be great!
> Thanks in advance!
>
>
> --
>
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Re: [PyMOL] help

[Roger Rowlett]

Clarisa,

Depending on what you want to do with the file, you may not need to save 
a new PDB at all.


You could for example,

 * Issue the command symexp ,,(all),4.0 to generate nearby
   symmetry mates, then remove the objects you don't need to form the
   proper dimer. ( is your PDB file object)
 * The select File...Save Molecule and select all the objects to save
   using shift-clicks. (but this may be unnecessary--see below)

When you do this both chains will have the same chain identifers (e.g. 
chain A) This could be clumsy later if you are doing further 
manipulations of the structure and you save the molecule as a single PDB 
with two identical chain identifiers. In this case, every selection you 
made would be a double selection (one in both chains.) You can change 
the chain identifier for the symmetry chain easily enough in a text 
editor, I suppose, but this is an extra step.


Alternatively, if you simply want to work with your new dimer structure 
in Pymol, there is no need to alter the chain numbers after doing the 
proper symmetry expansion. Rather, you can select individual items in 
one chain or the other by selecting the original or symmetry object. 
This might be useful, for example, if you want to highlight one active 
site and its interaction with the neighboring chain. I usually assign 
object names to the two monomers as "achain" and "bchain" to make 
manipulation of the structure easier. So, for example,


 * "Select asite, resi 42+44+98 and achain" might select active site
   residues from the original chain
 * "Select otherres, resi 33 and bchain" might select interactigin
   residues form your symmetry expanded chain.
 * No need to save the molecule as a separate PDB. Just save the
   session file.

Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu


On 10/7/2015 11:00 AM, Clarisa Alvarez wrote:

Hello everyone:
I need help because I have a pdb of a monomer but I know that it is a 
dimer by crystallographic symmetry,  how can I make a new molecule of 
it? because I could make it by generate/symmetry mate...but I could 
not save it...any help will be great!

Thanks in advance!


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[PyMOL] how to setup environment for APBS?

[Albert]

Hello:

I noticed that each time when I try to use APBS plugin, pymol always ask 
to specify the location of:

apbs
psize.py
pdb2pqr.py

I am just wondering can we somehow write the location of those program 
into .pymolrc file so that each time Pymol APBS plugin can find it 
automatically?

thanks a lot

Albert

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Re: [PyMOL] APBS problem

[Andreas Forster]

Hi Albert,

I apologize that I take your email for a grumpy old man's rant, but I feel
this mailing list is getting washed out with poorly formulated questions.

What happened to specifying what OS you use, what version of PyMOL, what
version of the apbs plugin.  Also, to give answers, it would help to know
what settings you chose for the calculation of the electrostatic
potential.  There's a bunch of buttons to click.  Which ones did you
choose?  What step have you already taken to overcome the problem?

Basically, I'm asking new users to spend a leisurely coffee break reading
http://www.catb.org/~esr/faqs/smart-questions.html and then ask better
question.

The answer to your problem:  /tmp/1-PE0.dx needs to be generated.  That's
all I can infer from the information you gave.

All best.


Andreas


On Thu, Oct 8, 2015 at 4:30 PM, Albert  wrote:

> Hello:
>
> I am trying to calculate the protein surface electstatic properities by
> APBS plugin in pymol. But it always failed with messages:
>
> Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?
>
> Does anybody has any idea how to solve this problem?
>
> thx a lot
>
>
>
>
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[PyMOL] APBS problem

[Albert]

Hello:

I am trying to calculate the protein surface electstatic properities by 
APBS plugin in pymol. But it always failed with messages:

Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?

Does anybody has any idea how to solve this problem?

thx a lot



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Re: [PyMOL] APBS problem

[Albert]

thanks a lot for reply.

Problem solved after I specify the maloc library path explicitly in my 
tcsh environment.


setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib



On 10/08/2015 05:02 PM, Andreas Forster wrote:

Hi Albert,

I apologize that I take your email for a grumpy old man's rant, but I 
feel this mailing list is getting washed out with poorly formulated 
questions.


What happened to specifying what OS you use, what version of PyMOL, 
what version of the apbs plugin.  Also, to give answers, it would help 
to know what settings you chose for the calculation of the 
electrostatic potential.  There's a bunch of buttons to click.  Which 
ones did you choose?  What step have you already taken to overcome the 
problem?


Basically, I'm asking new users to spend a leisurely coffee break 
reading http://www.catb.org/~esr/faqs/smart-questions.html 
 and then ask 
better question.


The answer to your problem: /tmp/1-PE0.dx needs to be generated.  
That's all I can infer from the information you gave.


All best.


Andreas


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Re: [PyMOL] how to setup environment for APBS?

[Osvaldo Martin]

Hi Albert,

As far as I know you can set the environmental variables APBS_BINARY_DIR,
APBS_PSIZE_DIR and  APBS_PDB2PQR_DIR or just set the values for this
variable inside the plugin.

Anyone knows any other method?

Cheers,
Osvaldo


On Thu, Oct 8, 2015 at 4:54 PM, Albert  wrote:

> Hello:
>
> I noticed that each time when I try to use APBS plugin, pymol always ask
> to specify the location of:
>
> apbs
> psize.py
> pdb2pqr.py
>
> I am just wondering can we somehow write the location of those program
> into .pymolrc file so that each time Pymol APBS plugin can find it
> automatically?
>
> thanks a lot
>
> Albert
>
>
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