Re: [PyMOL] show the long helix filament

2016-01-13 Thread Lukáš Pravda 
Hi Yeping,

 

What is the PDB id you are working with? Perhaps you have to download the 
biological assembly rather than asymmetric unit. I’d suggest you to go to the 
PDBe entry (pdbe.org/PDBID) and from the quick links select download ‘Assembly 
composition XML’. Take a look which assembly id has ‘preferred’ attribute se to 
‘True’ and download corresponding assembly. 

 

Hope it helps

 

Lukas Pravda

Central European Institute of Technology (CEITEC)

 

From: sunyeping [mailto:sunyep...@aliyun.com] 
Sent: Wednesday, January 13, 2016 9:31 AM
To: pymol-users 
Subject: [PyMOL] show the long helix filament

 

 

Dear all,

 

I am studying a published protein molecule which was claimed to be helical 
symmetric. The pdb file contain 3 copies of this molecule arranged in 
head-to-tail patern. The author claims that this interation is repeated in a 
directional manner along the P31 screw axis. Does anyone know how to show the 
whole long helix filament rather that just three protomer of this molecule? Can 
pymol do this?

 

Best regards.

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

 

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Re: [PyMOL] show the long helix filament

2016-01-13 Thread Spencer Bliven 
For such cases I generate the symmetry partners using either the symexp
 command or the supercell
 script. Both scripts result in
lots of extra objects, which you then have to winnow down to a single
helix. Supercell can be nice since you can specify how man unit cells to
generate along a particular axis and it draws the unit cells.

-Spencer

On Wed, Jan 13, 2016 at 10:35 AM, Lukáš Pravda  wrote:

> Hi Yeping,
>
>
>
> What is the PDB id you are working with? Perhaps you have to download the
> biological assembly rather than asymmetric unit. I’d suggest you to go to
> the PDBe entry (pdbe.org/PDBID) and from the quick links select download
> ‘Assembly composition XML’. Take a look which assembly id has ‘preferred’
> attribute se to ‘True’ and download corresponding assembly.
>
>
>
> Hope it helps
>
>
>
> Lukas Pravda
>
> Central European Institute of Technology (CEITEC)
>
>
>
> *From:* sunyeping [mailto:sunyep...@aliyun.com]
> *Sent:* Wednesday, January 13, 2016 9:31 AM
> *To:* pymol-users 
> *Subject:* [PyMOL] show the long helix filament
>
>
>
>
>
> Dear all,
>
>
>
> I am studying a published protein molecule which was claimed to be helical
> symmetric. The pdb file contain 3 copies of this molecule arranged in
> head-to-tail patern. The author claims that this interation
> is repeated in a directional manner along the P31 screw axis. Does anyone
> know how to show the whole long helix filament rather that just three
> protomer of this molecule? Can pymol do this?
>
>
>
> Best regards.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
>
>
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>
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Re: [PyMOL] PyMOL + APBS plugin

2016-01-13 Thread Thomas Holder 
Hi Matic,

1. If you have conflicting (non-unique) file names, you have two options:
  a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
  b) Set the "auto_rename_duplicate_objects" setting

2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days 
ago. If you don't want to recompile, you can also install the updated plugin 
manually from here: http://pymolwiki.org/index.php/Apbsplugin

3. Use the "matrix_copy" command to transfer the transformation matrix from the 
molecular object to the map object after alignment (matrix_copy foo_1, 
foo_1_map)

Hope that helps.

Cheers,
  Thomas 

On 13 Jan 2016, at 13:19, Matic Kisovec  wrote:

> Dear all,
> 
> I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I 
> use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 
> 1.8.0.0.
> 
>   • First I tried to perform a couple of APBS calculations through the 
> APBS plugin window and all went great. Then I did a batch pdb2pqr 
> transformation on my local machine and then a batch apbs calculation also on 
> my local machine. Both directly in terminal (no connection with Pymol). I 
> more or less followed these instructions: http://jamiebaxter.com/blog/?p=890 
> . After the calculations I ended up with all the standard files (.in, .pqr 
> and .dx). The issue was that I was not able to load them in Pymol. After 
> loading .pqr and .dx the tab 'Visualization' in APBS plugin windows kept 
> saying to load a molecule and a map. And after clicking the button 'Update' 
> nothing happened. There was no error reported. First I thought there has to 
> be something wrong with the manual procedure of generating .pqr and .dx 
> files. More or less by accident I figured out the problem is in the names of 
> files. I generated them to be identical and the only difference was the 
> extension (for example foo_1.pqr and foo_1.dx). If I changed one of the names 
> (I just tried .dx for now) and added or deleted a single character everything 
> went smoothly once loaded in Pymol. Is this a problem/bug only in my case 
> since the APBS plugin also creates temporary files with identical names?
>   • Another possible bug is present in the 'Visualization' tab of APBS 
> plugin. If one uses the button 'Update' in the 'Maps and Molecules' field 
> (the one marked in orange in this image: 
> https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses 
> the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and 
> 'Molecular Surface'. They keep on moving downwards until you loose the from 
> the screen (see the image in the previous link to see this). 'Field lines' 
> fields keep appearing after each click on the 'Update' button. Of course one 
> can restrain from using the mentioned 'Update' button since it seems to me 
> that it is not really necessary at all. But still it is a strange behaviour.
>   • This is just a question not an issue really. Is there an easy way to 
> visualise multiple aligned proteins with their electrostatic surfaces 
> simultaneously? I tried 'set grid_mode' and it works but not if I do an 
> alignment after loading the pqr structure and the APBS map. I suppose I 
> could/should align them before doing the calculations but since I didn't it 
> would be great if it is possible to do this during visualization.
> Hopefully somebody can look into this or at least find this through googling 
> and in this way save a couple of minutes or hours.
> All the best,
> Matic Kisovec

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] PyMOL + APBS plugin

2016-01-13 Thread Matic Kisovec 
Dear Thomas,

thank you for these short and perfect answers.

  1.  All fine now.
  2.  Updated the plugin and the GUI bug is gone. One more thing though. 
Whenever I click the button to either set temporary file locations or to set 
program locations in APBS GUI window I immediately get a Segmentation fault 
error (/usr/local/bin/pymol: line 3:  9250 Segmentation fault  (core 
dumped)).
  3.  Also works great.

Thank you again for your quick reply! Your help is invaluable to me (and 
probably to many other users of Pymol).
Keep up the good work!

Kind regards,
Matic


On 13. 01. 2016 20:01, Thomas Holder wrote:

Hi Matic,

1. If you have conflicting (non-unique) file names, you have two options:
  a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
  b) Set the "auto_rename_duplicate_objects" setting

2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days 
ago. If you don't want to recompile, you can also install the updated plugin 
manually from here: http://pymolwiki.org/index.php/Apbsplugin

3. Use the "matrix_copy" command to transfer the transformation matrix from the 
molecular object to the map object after alignment (matrix_copy foo_1, 
foo_1_map)

Hope that helps.

Cheers,
  Thomas

On 13 Jan 2016, at 13:19, Matic Kisovec 
 wrote:



Dear all,

I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I 
use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0.

• First I tried to perform a couple of APBS calculations through the 
APBS plugin window and all went great. Then I did a batch pdb2pqr 
transformation on my local machine and then a batch apbs calculation also on my 
local machine. Both directly in terminal (no connection with Pymol). I more or 
less followed these instructions: http://jamiebaxter.com/blog/?p=890 . After 
the calculations I ended up with all the standard files (.in, .pqr and .dx). 
The issue was that I was not able to load them in Pymol. After loading .pqr and 
.dx the tab 'Visualization' in APBS plugin windows kept saying to load a 
molecule and a map. And after clicking the button 'Update' nothing happened. 
There was no error reported. First I thought there has to be something wrong 
with the manual procedure of generating .pqr and .dx files. More or less by 
accident I figured out the problem is in the names of files. I generated them 
to be iden
tical and the only difference was the extension (for example foo_1.pqr and 
foo_1.dx). If I changed one of the names (I just tried .dx for now) and added 
or deleted a single character everything went smoothly once loaded in Pymol. Is 
this a problem/bug only in my case since the APBS plugin also creates temporary 
files with identical names?
• Another possible bug is present in the 'Visualization' tab of APBS 
plugin. If one uses the button 'Update' in the 'Maps and Molecules' field (the 
one marked in orange in this image: 
https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses 
the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and 
'Molecular Surface'. They keep on moving downwards until you loose the from the 
screen (see the image in the previous link to see this). 'Field lines' fields 
keep appearing after each click on the 'Update' button. Of course one can 
restrain from using the mentioned 'Update' button since it seems to me that it 
is not really necessary at all. But still it is a strange behaviour.
• This is just a question not an issue really. Is there an easy way to 
visualise multiple aligned proteins with their electrostatic surfaces 
simultaneously? I tried 'set grid_mode' and it works but not if I do an 
alignment after loading the pqr structure and the APBS map. I suppose I 
could/should align them before doing the calculations but since I didn't it 
would be great if it is possible to do this during visualization.
Hopefully somebody can look into this or at least find this through googling 
and in this way save a couple of minutes or hours.
All the best,
Matic Kisovec





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[PyMOL] Issue visualizing Delphi electrostatic potential map

2016-01-13 Thread Gmail 
I am having trouble visualizing Delphi generated maps in pymol. I've followed a 
number of tutorials online but they are all quite outdated so that may be a 
factor. I'm using the newest version of Delphi (v6.2) and PyMol v1.7. I am able 
to generate the electrostatic potential map in Delphi, however, after renaming 
it to a .phi file and loading it into a PyMol session with the PDB structure 
used to generate it, the view moves to a location very far away from my 
structure, so the electrostatic potential cannot be projected onto the 
protein's surface. There is no error reported in the output. Does anyone know 
how I can fix this?

Thanks,

TS
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