Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

[Matic Kisovec]

Hello Brenton,

I used the pdd2pqr provided by Ubuntu repositories (version 1.8) and installed 
it directly(with Synaptic) from there.
The path on my Xubuntu system is: /usr/share/pdb2pqr/pdb2pqr.py

I also tried setting something up on Windows but gave up eventually.

Good luck and all the best,
Matic


On 14. 04. 2015 08:39, Brenton Horne wrote:

Hi,

pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
1.8 versions; in a previous question I was advised to use the 1.8
version) and consequently APBS tools doesn't work. I have tried turning
the pdb2pqr.py.in into pdb2pqr.py by removing the "in" extension, but
the APBS failed to set up the grid after I did this. Is there any way
around this?

Thanks for your time,
Brenton

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Re: [PyMOL] APBS plugin not working on both Ubuntu & Windows 7

[David Hall]

There is an "INSTALL" file that provides instructions. The first step,
calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in

If you want to manually do it, it just changes the first line in the file
to point to your python installation. But, since there's a whole bunch of
other things ./configure appears to do, I suggest following the steps in
the INSTALL file.

-David


On Tue, Apr 14, 2015 at 2:39 AM, Brenton Horne 
wrote:

> Hi,
>
> pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
> 1.8 versions; in a previous question I was advised to use the 1.8
> version) and consequently APBS tools doesn't work. I have tried turning
> the pdb2pqr.py.in into pdb2pqr.py by removing the "in" extension, but
> the APBS failed to set up the grid after I did this. Is there any way
> around this?
>
> Thanks for your time,
> Brenton
>
>
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
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Re: [PyMOL] Cartoon putty in pymol

[Osvaldo Martin]

Hi, Wenfu

The putty representation uses the values on the b-factor column of the pdf
file and your file has the same value for each atom (0.0), hence the error.
If you want to have residues with different width you need different
b-factor values for different residues. If, on the other hand you are OK
with all residues having the same width, just do

set cartoon_putty_transform, 2

Cheers,
Osvaldo.



On Mon, Apr 13, 2015 at 10:34 AM,  wrote:

>  Hi pymol users,
>
>  I have a pdb file, which is from the result of a molecular dynamics
> simulation. I want to present the structure with cartoon putty in pymol.
> But I can only make it cartoon putty in Macpymol 0.99 version. When I use
> pymol1.7 or 1.3 version, the error is like this: Extrude-Warning: invalid
> putty settings (division by zero)
> I attach part of the pdb file and hope to get your suggestions.
>
>  Thanks,
> Wenfu
>
> =
>
> Please note that this e-mail and any files transmitted from
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[PyMOL] pymol crash when ray

[maw1]

Hi pymol users,

I am just using pymol to open one super big molecular model (20 megadaltons). 
My pymol1.7 is on linux system and the computer has 32 CPU with 62GB memory 
storage.
When I try to use command ray to make a high quality image, the pymol crash 
with error message like this: Pymol ran out of memory storage and you need to 
decease the quality of the image.

I have tried to set the hash_max 10, 30 or 60 and it won’t work. Also I use 
protein backbone to present the whole structure.
I will appreciate any suggestions.

Thanks,
Wenfu

=

 Please note that this e-mail and any files transmitted from
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 and protected from disclosure under applicable law. If the reader of
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 you are hereby notified that any reading, dissemination, distribution,
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 is strictly prohibited.  If you have received this communication in
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 and deleting this message, any attachments, and all copies and backups
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Re: [PyMOL] pymol crash when ray

[Osvaldo Martin]

Hi Wenfu,

Did you get the same error if you do the raytraicing from a script?

Probably you could try with this
 approximation to render
your molecule.

Cheers,
Osvaldo.

On Tue, Apr 14, 2015 at 5:12 PM,  wrote:

 Hi pymol users,
>
>  I am just using pymol to open one super big molecular model (20
> megadaltons). My pymol1.7 is on linux system and the computer has 32 CPU
> with 62GB memory storage.
> When I try to use command ray to make a high quality image, the pymol
> crash with error message like this: Pymol ran out of memory storage and you
> need to decease the quality of the image.
>
>  I have tried to set the hash_max 10, 30 or 60 and it won’t work. Also I
> use protein backbone to present the whole structure.
> I will appreciate any suggestions.
>
>  Thanks,
> Wenfu
>
>
>
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
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> exercises
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​
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Re: [PyMOL] pymol crash when ray

[H. Adam Steinberg]

one more thing…

Delete all objects that you are not using for this particular rendering (save 
it as a separate file). I have found this speeds up rendering times.


> On Apr 14, 2015, at 7:49 PM, H. Adam Steinberg  
> wrote:
> 
> For an instantaneous rendering of any PyMOL scene that won't crash your 
> machine use the DRAW command instead of the RAY command. You will loose 
> features like shadows and depth cue.
> 
> When I have to render huge PyMOL scenes like you describe below, I create 
> them in a way that I can RAY them in sections (for example, ray the back 
> section, then the front) and then reassemble those sections in Photoshop.
> 
> You can also change how PyMOL uses memory from the Settings menu. Choose 
> Settings/Rendering/Memory and then choose use most, but I seem to remember 
> there is some limitation that actually makes PyMOL render without crashing 
> when you choose use less.
> 
>> On Apr 14, 2015, at 3:12 PM, m...@mskcc.org  wrote:
>> 
>> Hi pymol users,
>> 
>> I am just using pymol to open one super big molecular model (20 
>> megadaltons). My pymol1.7 is on linux system and the computer has 32 CPU 
>> with 62GB memory storage.
>> When I try to use command ray to make a high quality image, the pymol crash 
>> with error message like this: Pymol ran out of memory storage and you need 
>> to decease the quality of the image. 
>> 
>> I have tried to set the hash_max 10, 30 or 60 and it won’t work. Also I use 
>> protein backbone to present the whole structure.
>> I will appreciate any suggestions.
>> 
>> Thanks,
>> Wenfu
>> 
>> --
>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>> Develop your own process in accordance with the BPMN 2 standard
>> Learn Process modeling best practices with Bonita BPM through live exercises
>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- 
>>  event?utm_
>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net 
>> )
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users 
>> 
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 
>> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] Protein classification

[Abdul Ajees]

Dear all,
I have a set of 200 methyltransferase protein structures. For protein - ligand 
interactions study, I would like to classify the proteins in to different 
groups. I have tried to classify the proteins based on sequence but it is not 
satisfactory in view point of structures. Based on the previous suggestions I 
have used the DALI server results like Z-score, RMS deviation for grouping.  I 
am ended up 35-40 groups for 200 structures. However, The results are not still 
not convincing enough. 
I have also tried, Pymol - superimpose and Chimera - structure based sequence 
alignment, but both the program are crashing for 200 structures.  
I will be thankful to you, if you suggest any alternative idea or online tools.
Thank you in advance.
With regardsAbdul Ajees--
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