[PyMOL] Query about inserting ligand at preferred base pairs of DNA

[Sneha Kandapal]

Hello Team,

I need help in inserting ligand to base pair in DNA. I have a drug molecule and 
want to insert in between the base pairs I am interested in ( it is 12-mer 
dsDNA). I tried to follow the tutorials but cannot find something where I can 
insert ligand into the custom DNA sequence I have generated.

I will appreciate if you can please help me or guide me where I can study and 
understand how to do it.

Thank you,
Sneha
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Re: [PyMOL] query

[Thomas Holder]

Hi Ankita,

set depth_cue, 0

http://pymolwiki.org/index.php/Depth_cue

Cheers,
  Thomas

On 27 Apr 2016, at 11:06, H. Adam Steinberg  wrote:

> Scrolling the mouse will not move the molecule, it will reduce the fog that 
> pymol puts in the image, making it less gray.
> 
> Sent from my iPhone
> 
> On Apr 27, 2016, at 6:45 AM, ankita mehta  wrote:
> 
>> No, I can not do this becos i have to show the complex that is protein in a 
>> fix orientation.
>> Suggest some alternative..
>> Thanks!
>> 
>> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:
>> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and 
>> down! 
>> Usually (if you have not changed any settings), SCROLLING UP should solve 
>> your problem.
>> 
>> Cheers.
>> 
>> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta  wrote:
>> Hii,
>> I want to save the image in pymol
>> I am using white background but it gives me dull colouring of the protein 
>> which is at the background than the protein part at foreground.
>> I want a unified sceme for all protein .
>> pls suggest.
>> thanks!

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] query

[H. Adam Steinberg]

Scrolling the mouse will not move the molecule, it will reduce the fog that 
pymol puts in the image, making it less gray.

Sent from my iPhone

> On Apr 27, 2016, at 6:45 AM, ankita mehta  wrote:
> 
> No, I can not do this becos i have to show the complex that is protein in a 
> fix orientation.
> Suggest some alternative..
> Thanks!
> 
>> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:
>> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and 
>> down! 
>> Usually (if you have not changed any settings), SCROLLING UP should solve 
>> your problem.
>> 
>> Cheers.
>> 
>>> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta  
>>> wrote:
>>> Hii,
>>> I want to save the image in pymol
>>> I am using white background but it gives me dull colouring of the protein 
>>> which is at the background than the protein part at foreground.
>>> I want a unified sceme for all protein .
>>> pls suggest.
>>> thanks!
>>> 
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> 
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Re: [PyMOL] query

[ankita mehta]

No, I can not do this becos i have to show the complex that is protein in a
fix orientation.
Suggest some alternative..
Thanks!

On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:

> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
> down!
> Usually (if you have not changed any settings), SCROLLING UP should solve
> your problem.
>
> Cheers.
>
> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta 
> wrote:
>
>> Hii,
>> I want to save the image in pymol
>> I am using white background but it gives me dull colouring of the protein
>> which is at the background than the protein part at foreground.
>> I want a unified sceme for all protein .
>> pls suggest.
>> thanks!
>>
>>
>> --
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>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
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Re: [PyMOL] query

[Dheeraj Prakaash]

Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
down!
Usually (if you have not changed any settings), SCROLLING UP should solve
your problem.

Cheers.

On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta 
wrote:

> Hii,
> I want to save the image in pymol
> I am using white background but it gives me dull colouring of the protein
> which is at the background than the protein part at foreground.
> I want a unified sceme for all protein .
> pls suggest.
> thanks!
>
>
> --
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> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
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>
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[PyMOL] query

[ankita mehta]

Hii,
I want to save the image in pymol
I am using white background but it gives me dull colouring of the protein
which is at the background than the protein part at foreground.
I want a unified sceme for all protein .
pls suggest.
thanks!
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[PyMOL] Query of running script of Contact Map Visualizer Plugin

[Suhaila Haji Mohd Hussin]

Hello I know the plugin mentioned above (in the Subject) will work if I go to 
Plugin  Manage Plugins  Install  contact_map_visualizer I get that. But 
nothing happens if I run the plugin if I go to File  Run  
contact_map_visualizer.py I do this because I need it for my project, 
preferably running the script via this method. Can anyone please tell me why it 
is not working on the second method? I know it's a plugin and it's just a 
python script anyway, no? Regards,Suhaila--
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[PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin

[Suhaila Haji Mohd Hussin]

Hello especially for those who are experienced using Contact Map Visualizer 
Plugin. About generating a contact map, after typing the following command as 
shown:
 
g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm

It gives us a list of group selection to analyze such as below: Select group 
for analysis
 Group 0 ( System) has  2616 elements
 Group 1 (Protein) has  2470 elements
 Group 2 (  Protein-H) has  2470 elements
 Group 3 (C-alpha) has   314 elements
 Group 4 (   Backbone) has   934 elements
 Group 5 (  MainChain) has  1246 elements
 Group 6 (   MainChain+Cb) has  1540 elements
 Group 7 (MainChain+H) has  1246 elements
 Group 8 (  SideChain) has  1224 elements
 Group 9 (SideChain-H) has  1224 elements
 Group10 (Prot-Masses) has  2470 elements
 Group11 (non-Protein) has   146 elements
 Group12 (Ion) has 2 elements
 Group13 ( CL) has 2 elements
 Group14 (  Water) has   144 elements
 Group15 (SOL) has   144 elements
 Group16 (  non-Water) has  2472 elements
 Group17 ( Water_and_ions) has   146 elements My question is that is it 
possible to modify that group selection? I want to add in group analysis on 
alpha helix  beta sheet.For example Group 18 (Alpha helix) has 999 elements. 
If it is possible? How  where can I do that?  Hope you reply a.s.a.p
 
Many thanks,
Suhaila

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Re: [PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin

[Tsjerk Wassenaar]

Hi Suheila,

The CMV requires the contact map and the structure to match. So to get
what you want, it's easiest to load the structure in pymol, and save
only the part you want to analyze:

save helix.pdb, ss h
save sheet.pdb, ss s

Then you can run g_mdmat on each of those, and load the result back in pymol.

Hope it helps,

Tsjerk

On Mon, Mar 19, 2012 at 6:20 PM, Suhaila Haji Mohd Hussin
bell_beaut...@hotmail.com wrote:
 Hello especially for those who are experienced using Contact Map Visualizer
 Plugin. About generating a contact map, after typing the following command
 as shown:

 g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm

 It gives us a list of group selection to analyze such as below:

 Select group for analysis
 Group 0 ( System) has 2616 elements
 Group 1 ( Protein) has 2470 elements
 Group 2 ( Protein-H) has 2470 elements
 Group 3 ( C-alpha) has 314 elements
 Group 4 ( Backbone) has 934 elements
 Group 5 ( MainChain) has 1246 elements
 Group 6 ( MainChain+Cb) has 1540 elements
 Group 7 ( MainChain+H) has 1246 elements
 Group 8 ( SideChain) has 1224 elements
 Group 9 ( SideChain-H) has 1224 elements
 Group 10 ( Prot-Masses) has 2470 elements
 Group 11 ( non-Protein) has 146 elements
 Group 12 ( Ion) has 2 elements
 Group 13 ( CL) has 2 elements
 Group 14 ( Water) has 144 elements
 Group 15 ( SOL) has 144 elements
 Group 16 ( non-Water) has 2472 elements
 Group 17 ( Water_and_ions) has 146 elements

 My question is that is it possible to modify that group selection? I want to
 add in group analysis on alpha helix  beta sheet.
 For example Group 18 (Alpha helix) has 999 elements.

 If it is possible? How  where can I do that?

 Hope you reply a.s.a.p

 Many thanks,
 Suhaila

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Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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Re: [PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin

[Suhaila Haji Mohd Hussin]

 OK. I can see a  bit clearer now :) Yet which leads me to another question. 
About the group selection analysis below: Select group for analysis
Group 0 ( System) has 2616 elements
Group 1 ( Protein) has 2470 elements
Group 2 ( Protein-H) has 2470 elements
Group 3 ( C-alpha) has 314 elements
Group 4 ( Backbone) has 934 elements
Group 5 ( MainChain) has 1246 elementsGroup 6 ( MainChain+Cb) has 1540 
elementsGroup 7 ( MainChain+H) has 1246 elements
Group 8 ( SideChain) has 1224 elements
Group 9 ( SideChain-H) has 1224 elements
Group 10 ( Prot-Masses) has 2470 elements
Group 11 ( non-Protein) has 146 elements
Group 12 ( Ion) has 2 elements
Group 13 ( CL) has 2 elements
Group 14 ( Water) has 144 elements
Group 15 ( SOL) has 144 elements
Group 16 ( non-Water) has 2472 elements
Group 17 ( Water_and_ions) has 146 elements What are those really? I don't have 
biology background really. All I know is that Protein (Secondary structure) has 
one or more chains and in it hasamino acids. And the protein consists of alpha 
helix and beta sheets. Basically my project is to plot contact map on the 
selected chain ( consisting alpha helix  beta sheets) of a protein.I'm just a 
bit confused what are those groups for? I mean I don't really need those. I 
just need to plot on a chain. Many thanks,Suhaila Date: Mon, 19 Mar 2012 
19:37:12 +0100
 Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map 
 Visualizer Plugin
 From: tsje...@gmail.com
 To: bell_beaut...@hotmail.com
 CC: pymol-users@lists.sourceforge.net
 
 Hi Suheila,
 
 The CMV requires the contact map and the structure to match. So to get
 what you want, it's easiest to load the structure in pymol, and save
 only the part you want to analyze:
 
 save helix.pdb, ss h
 save sheet.pdb, ss s
 
 Then you can run g_mdmat on each of those, and load the result back in pymol.
 
 Hope it helps,
 
 Tsjerk
 
 On Mon, Mar 19, 2012 at 6:20 PM, Suhaila Haji Mohd Hussin
 bell_beaut...@hotmail.com wrote:
  Hello especially for those who are experienced using Contact Map Visualizer
  Plugin. About generating a contact map, after typing the following command
  as shown:
 
  g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
 
  It gives us a list of group selection to analyze such as below:
 
  Select group for analysis
  Group 0 ( System) has 2616 elements
  Group 1 ( Protein) has 2470 elements
  Group 2 ( Protein-H) has 2470 elements
  Group 3 ( C-alpha) has 314 elements
  Group 4 ( Backbone) has 934 elements
  Group 5 ( MainChain) has 1246 elements
  Group 6 ( MainChain+Cb) has 1540 elements
  Group 7 ( MainChain+H) has 1246 elements
  Group 8 ( SideChain) has 1224 elements
  Group 9 ( SideChain-H) has 1224 elements
  Group 10 ( Prot-Masses) has 2470 elements
  Group 11 ( non-Protein) has 146 elements
  Group 12 ( Ion) has 2 elements
  Group 13 ( CL) has 2 elements
  Group 14 ( Water) has 144 elements
  Group 15 ( SOL) has 144 elements
  Group 16 ( non-Water) has 2472 elements
  Group 17 ( Water_and_ions) has 146 elements
 
  My question is that is it possible to modify that group selection? I want to
  add in group analysis on alpha helix  beta sheet.
  For example Group 18 (Alpha helix) has 999 elements.
 
  If it is possible? How  where can I do that?
 
  Hope you reply a.s.a.p
 
  Many thanks,
  Suhaila
 
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 -- 
 Tsjerk A. Wassenaar, Ph.D.
 
 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands
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Re: [PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin

[Suhaila Haji Mohd Hussin]

I see!
Many thanks 
Tsjerk! XD

 Date: Mon, 19 Mar 2012 20:59:08 +0100
 Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map 
 Visualizer Plugin
 From: tsje...@gmail.com
 To: bell_beaut...@hotmail.com
 
 Hi Suheila,
 
 These groups are for selecting specific subgroups of a protein or of
 the solvent. But they don't seem to be important for what you want to
 do. Just choose 'protein'.
 
 Cheers,
 
 Tsjerk
 
 On Mon, Mar 19, 2012 at 7:58 PM, Suhaila Haji Mohd Hussin
 bell_beaut...@hotmail.com wrote:
 
   OK. I can see a  bit clearer now :)
 
  Yet which leads me to another question. About the group selection analysis
  below:
 
 
  Select group for analysis
  Group 0 ( System) has 2616 elements
  Group 1 ( Protein) has 2470 elements
  Group 2 ( Protein-H) has 2470 elements
  Group 3 ( C-alpha) has 314 elements
  Group 4 ( Backbone) has 934 elements
  Group 5 ( MainChain) has 1246 elements
  Group 6 ( MainChain+Cb) has 1540 elements
  Group 7 ( MainChain+H) has 1246 elements
  Group 8 ( SideChain) has 1224 elements
  Group 9 ( SideChain-H) has 1224 elements
  Group 10 ( Prot-Masses) has 2470 elements
  Group 11 ( non-Protein) has 146 elements
  Group 12 ( Ion) has 2 elements
  Group 13 ( CL) has 2 elements
  Group 14 ( Water) has 144 elements
  Group 15 ( SOL) has 144 elements
  Group 16 ( non-Water) has 2472 elements
  Group 17 ( Water_and_ions) has 146 elements
 
  What are those really? I don't have biology background really. All I know is
  that Protein (Secondary structure) has one or more chains and in it has
  amino acids. And the protein consists of alpha helix and beta sheets.
  Basically my project is to plot contact map on the selected chain (
  consisting alpha helix  beta sheets) of a protein.
  I'm just a bit confused what are those groups for? I mean I don't really
  need those. I just need to plot on a chain.
 
  Many thanks,
  Suhaila
  Date: Mon, 19 Mar 2012 19:37:12 +0100
  Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map
  Visualizer Plugin
  From: tsje...@gmail.com
  To: bell_beaut...@hotmail.com
  CC: pymol-users@lists.sourceforge.net
 
 
  Hi Suheila,
 
  The CMV requires the contact map and the structure to match. So to get
  what you want, it's easiest to load the structure in pymol, and save
  only the part you want to analyze:
 
  save helix.pdb, ss h
  save sheet.pdb, ss s
 
  Then you can run g_mdmat on each of those, and load the result back in
  pymol.
 
  Hope it helps,
 
  Tsjerk
 
  On Mon, Mar 19, 2012 at 6:20 PM, Suhaila Haji Mohd Hussin
  bell_beaut...@hotmail.com wrote:
   Hello especially for those who are experienced using Contact Map
   Visualizer
   Plugin. About generating a contact map, after typing the following
   command
   as shown:
  
   g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
  
   It gives us a list of group selection to analyze such as below:
  
   Select group for analysis
   Group 0 ( System) has 2616 elements
   Group 1 ( Protein) has 2470 elements
   Group 2 ( Protein-H) has 2470 elements
   Group 3 ( C-alpha) has 314 elements
   Group 4 ( Backbone) has 934 elements
   Group 5 ( MainChain) has 1246 elements
   Group 6 ( MainChain+Cb) has 1540 elements
   Group 7 ( MainChain+H) has 1246 elements
   Group 8 ( SideChain) has 1224 elements
   Group 9 ( SideChain-H) has 1224 elements
   Group 10 ( Prot-Masses) has 2470 elements
   Group 11 ( non-Protein) has 146 elements
   Group 12 ( Ion) has 2 elements
   Group 13 ( CL) has 2 elements
   Group 14 ( Water) has 144 elements
   Group 15 ( SOL) has 144 elements
   Group 16 ( non-Water) has 2472 elements
   Group 17 ( Water_and_ions) has 146 elements
  
   My question is that is it possible to modify that group selection? I
   want to
   add in group analysis on alpha helix  beta sheet.
   For example Group 18 (Alpha helix) has 999 elements.
  
   If it is possible? How  where can I do that?
  
   Hope you reply a.s.a.p
  
   Many thanks,
   Suhaila
  
  
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  --
  Tsjerk A. Wassenaar, Ph.D.
 
  post-doctoral researcher
  Molecular Dynamics Group
  * Groningen Institute for Biomolecular Research and Biotechnology
  * Zernike Institute for Advanced Materials
  University of Groningen
  The Netherlands
 
 
 
 -- 
 Tsjerk A. Wassenaar, Ph.D.
 
 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands

[PyMOL] Query on Contact Map Visualizer

[Suhaila Haji Mohd Hussin]

Hello guys,

Regarding the subject mentioned above, I'm wondering if PDB file has more than 
one chain, will the generation of contact map using g_mdmat from Gromacs
still produce a map of all chains?

Don't I have a choice to choose one chain?

Refer the subject above for more details:
http://www.pymolwiki.org/index.php/Contact_map_visualizer

Cheers,
Suhaila.
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Re: [PyMOL] Query on Contact Map Visualizer

[Tsjerk Wassenaar]

Hi Suhaila,

From what I understand from the wiki, you have to have a match between
the PDB and the contact map. If your contact map was made on a
structure with multiple chains, all chains will be in there. If you
want to select a single chain, you have to extract that chain from
thhe PDB file, then run g_mdmat, and then load the PDB file and the
map into Pymol.

Hope it helps,

Tsjerk

On Mon, Mar 12, 2012 at 1:43 PM, Suhaila Haji Mohd Hussin
bell_beaut...@hotmail.com wrote:
 Hello guys,

 Regarding the subject mentioned above, I'm wondering if PDB file has more
 than one chain, will the generation of contact map using g_mdmat from
 Gromacs
 still produce a map of all chains?

 Don't I have a choice to choose one chain?

 Refer the subject above for more details:
 http://www.pymolwiki.org/index.php/Contact_map_visualizer

 Cheers,
 Suhaila.

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Re: [PyMOL] query

[Vitali Stanevich]

here it is:
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts

vitali

On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-scie...@yahoo.co.in 
rjayashree13-scie...@yahoo.co.in wrote:

 Thank you. It works, but it does not bring out the type of interaction
 responsible for interface contact-hydrogen bonding or electrostatic
 interaction etc.
  I am using another tool called PSAP for analyzing inter-molecular
 interactions (iris.physics.iisc.ernet.in/psap)
 It gives me the residues involved in hydrogen bonding, now using Pymol I
 can label these residues, but is there any way to depict these hydrogen
 bonds also and the distances?

 Dr. Jayashree Ramana

  http://www.juit.ac.in/bio/jsr.php

   --
 *From:* Vitali Stanevich stanev...@wisc.edu
 *To:* rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in

 *Cc:* pymol-users@lists.sourceforge.net 
 pymol-users@lists.sourceforge.net
 *Sent:* Sunday, 20 November 2011 1:57 PM
 *Subject:* Re: [PyMOL] query

 check this out:
 http://www.pymolwiki.org/index.php/InterfaceResidues

 if you want faster and easier, but less reliable (in my opinion) way, you
 can analyze your .pdb with PISA:
 http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

 vitali

 On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in 
 rjayashree13-scie...@yahoo.co.in wrote:

 I have a PDB file for a dimeric protein. Is it possible to depict the
 intersubunit contacts for any PDB file? Is Pymol alone sufficient for this
 purpose or will it only help visualization?
 Could you also tell me which commands in Pymol can I use for this purpose?
 I have tried a lot but could not get an answer to this. I will be very
 thankful for the favour.

 Dr. Jayashree Ramana

  http://www.juit.ac.in/bio/jsr.php


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Re: [PyMOL] query

[Vitali Stanevich]

check this out:
http://www.pymolwiki.org/index.php/InterfaceResidues

if you want faster and easier, but less reliable (in my opinion) way, you
can analyze your .pdb with PISA:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

vitali

On Sun, Nov 20, 2011 at 1:51 AM, rjayashree13-scie...@yahoo.co.in 
rjayashree13-scie...@yahoo.co.in wrote:

 I have a PDB file for a dimeric protein. Is it possible to depict the
 intersubunit contacts for any PDB file? Is Pymol alone sufficient for this
 purpose or will it only help visualization?
 Could you also tell me which commands in Pymol can I use for this purpose?
 I have tried a lot but could not get an answer to this. I will be very
 thankful for the favour.

 Dr. Jayashree Ramana

 http://www.juit.ac.in/bio/jsr.php


 --
 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
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[PyMOL] query

[kumud agarwal]

hi
I built a peptide using pymol. When I labelled the residues they are numbered 
fron 2 and not from 1 i.e. the first residues in my peptide is ALA and when I 
labelled this residue it is labelled as ALA-2 and not ALA-1. 

I want to ask why it is not labelled starting from 1 instead of 2?
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Re: [PyMOL] query

[Jason Vertrees]

Hi Kumud,

I don't know,. Maybe because Warren wanted to label the end cap as residue
number 1. Anyone else know?

Regardless if you want to renumber your sequence, just type the following
or download the zero_residues script from the PyMOLWiki (
http://www.pymolwiki.org/index.php/Zero_residues):

# adjust all residue identifiers by subtracting 'N'
# from their index. Replace 'N' with whatever
# you want

alter mySeq, resi=str(int(resi)-N)

# update the sequence display

sort

Cheers,

-- Jason

On Sat, Nov 19, 2011 at 10:19 AM, kumud agarwal meet_ku...@yahoo.co.inwrote:

 hi
 I built a peptide using pymol. When I labelled the residues they are
 numbered fron 2 and not from 1 i.e. the first residues in my peptide is ALA
 and when I labelled this residue it is labelled as ALA-2 and not ALA-1.

 I want to ask why it is not labelled starting from 1 instead of 2?


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 All the data continuously generated in your IT infrastructure
 contains a definitive record of customers, application performance,
 security threats, fraudulent activity, and more. Splunk takes this
 data and makes sense of it. IT sense. And common sense.
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[PyMOL] query about secondary structure alteration

[sangeeta kundu]

Dear Sir,

  * I want too assign the secondary structure of my protein according
to DSSP classification,  I used the following commands*
*  alter A/22:28/,  ss='S'*
   * or*
 *alter A/45:50?, ss= 'H' *
  *and so on  followed by *
 *  rebuild*
*   cartoon automatic*
*   show cartoon*
*   But the problem is that the structure  remains the same, without
any alteration.*
*   I tried the same commands in case of other proteins, where it
works, but it failed in case of my protein. The protein is a globular
one  with  70  rsidues, having a crystal structure.  It has a single
chain only, so I used alter /22:28/, ss= 'S' , I am interested to know
what type of  classification does Pymol follow for secondary structure
classification ,  and  where the problem lies so that I can not alter my
structure. Thanks in advance.*
**
**
*regards*
*SANGEETA *

Re: [PyMOL] Pymol Query

[Marc Saric]

 I have recently downloaded Pymol and can't get the protein structure 
 to display on the main screen, files are being uploaded and are 
 visible in the side bar and if I try to randomly alter colours on the
 protein parts of it appear though I can't be sure of what I am
 looking at as the program hasn't diplayed it. Is this a program fault
 or a simple menu preference?

Hi Vicki,

it would help if you would let us know some more details:

What type of hardware do you use (graphics-card, CPU)?
Which operation system do you use?
Which version of Pymol do you use?
What files did you want to display (non-standard PDB-files sometimes
produce errors or are displayed invisible)?
Are there any error messages in the console-window upon loading?

Pymol normaly loads and displays PDB-files with a standard-layout and
centers them on the screen (unlike some other/older programs like O,
where it is considered a feature NOT to center the display (i.e. you see
nothing after loading)).

-- 
Bye,

Marc Saric

[PyMOL] Pymol Query

[vfs3]

Query

I have recently downloaded Pymol and can't get the protein structure to display
on the main screen, files are being uploaded and are visible in the side bar
and if I try to randomly alter colours on the protein parts of it appear though
I can't be sure of what I am looking at as the program hasn't diplayed it. Is
this a program fault or a simple menu preference?

Vicki Symigton



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Re: [PyMOL] Query variable value

[Sebastien Moretti]

PyExperts:

When inside PyMOL, how do I find out the value of a variable without 
using 'set'?


For example, I can type:
 set specular, 1
and then I know, specular = 1.

But how do I find out specular's (or ANY variable's) value without 
changing it?


Thanks,

Olivier


Hello Olivier,
For PyMOL variables, defined with
set variable_name,variable_value
, you can get it with
get variable_name


For other variables (Python variables), defined like it:
variable_name=variable_value
you can get it with
print variable_name
or use it simply with
variable_name


I hope this will help you.

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13402 Marseille cedex

Re: [PyMOL] Query variable value

[Ezequiel H Panepucci]

Olivier,

But how do I find out specular's (or ANY variable's) value without 
changing it?


I wrote a little extension called 'grepset' that does what you want and it 
is great for finding out about other settings.


It is available at the pymol wiki site:

http://www.pymolwiki.org/index.php/Grepset

Cheers,
Zac

[PyMOL] Query variable value

[Olivier Julien]

PyExperts:

When inside PyMOL, how do I find out the value of a variable without 
using 'set'?


For example, I can type:
 set specular, 1
and then I know, specular = 1.

But how do I find out specular's (or ANY variable's) value without 
changing it?


Thanks,

Olivier

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Dr Brian D. Sykes Lab
Department of Biochemistry
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Edmonton (AB) Canada T6G 2H7
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Email: ojul...@ualberta.ca
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