[PyMOL] foggy state just for one of the molecules

[Oganesyan, Vaheh]

Hello PyMOLers,

Happy New Year!

Is there a way to show one of the molecules on image in a foggy state 
irrespective of depth-cue? I want to make an illustration showing how one 
molecule blocks another for interaction with ligand/receptor.

Thanks in advance.

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01D80228.40A93CD0]
R | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
vaheh.oganes...@astrazeneca.com

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Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is discontinued)

[Oganesyan, Vaheh]

Hi Thomas,

Can you also mention appropriate graphics cards that pair well with the Volfoni 
hardware?

Thank you.

From: Thomas Holder 
Sent: Tuesday, July 7, 2020 10:03 AM
To: David Krause 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Which 3D setup for a new installation? (Since 3D Vision is 
discontinued)

Hi David,

I won't be able to really give a future proof recommendation, but at least I 
can say that we have emitters and glasses from Volfoni which work so far as a 
suitable replacement for Nvidia's 3D vision.

emitter: Volfoni ActivHub RF one (VPES-07000)
glasses: Volfoni EDGE RF 3D (VPEG-03210)

A new technology that we at Schrödinger are pretty excited about is the Looking 
Glass display. We think this has much more potential than VR to be a useful 
tool for drug discovery and research.
https://lookingglassfactory.com/schrodinger

Cheers,
Thomas


> On Jul 2, 2020, at 3:48 PM, David Krause 
> mailto:kra...@biochem2.uni-frankfurt.de>> 
> wrote:
>
> Dear List,
>
>
> one of our research groups needs a new 3D PyMol setup.
> Looking through the wiki 
> (https://pymolwiki.org/index.php/Stereo_3D_Display_Options)
>  the most prominent way to do 3D seemed through Nvidia's 3D Vision,
> but since 3D Vision is discontinued, i struggle a bit to find a good and 
> future proof 3D solution.
>
> Can you recommend a 3D Setup?
> Should we go VR?
>
> We're planning to use the Commercial PyMol version, not the open source one.
>
>
> --
> Mit freundlichen Grüßen / With kind regards
>
> David Krause
> IT
> Institute of Biochemistry II
>
> Gustav Embden-Zentrum der Biochemie
> Goethe University Frankfurt - Medical Faculty
>
> University Hospital - Building 75
> Theodor-Stern-Kai 7
> 60590 Frankfurt am Main
> Germany
>
> +49 (0)69 6301 84971 (Phone)
> +49 (0)69 6301 84975 (Fax)
> kra...@biochem2.uni-frankfurt.de
>
>
>
> ___
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] renumber

[Oganesyan, Vaheh]

Thank you Jared.

From: Jared Sampson 
Sent: Monday, June 15, 2020 4:47 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh -

I wasn't saying it can't be done, just that pdbset is my preferred way to 
handle renumbering when going in the insertion code --> integer direction.

Within PyMOL, here is one way (you'll have to repeat for each chain you wish to 
renumber):

```
# see: 
https://pymolwiki.org/index.php/Pymol.stored<https://pymolwiki.org/index.php/Pymol.stored>
from pymol import stored

# store the current residue numbers in a list
stored.oldresi = []
iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi)

# make a list of the new residue numbers
stored.newresi = list(range(1, len(stored.oldresi)+1))

# zip them together into a lookup dict
stored.hash = dict(zip(stored.oldresi, stored.newresi))

# change the residue numbers for each atom in your chain
alter polymer.protein and chain L, resi=stored.hash[resi]
```

Hope that helps.

Cheers,
Jared



From: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Reply: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Date: June 15, 2020 at 3:57:24 PM
To: Jared Sampson 
<mailto:jared.samp...@columbia.edu>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> 
<mailto:pymol-users@lists.sourceforge.net>
Subject:  RE: [PyMOL] renumber


Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
mailto:jared.samp...@columbia.edu>>
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber<http://www.ccp4.ac.uk/html/pdbset.html#renumber>

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared


From: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Reply: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
<mailto:blaine-moo...@ouhsc.edu>, Jarrett Johnson 
<mailto:jarrett.john...@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> 
<mailto:pymol-users@lists.sourceforge.net>
Subject:  Re: [PyMOL] renumber



Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber=DwMGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOc

Re: [PyMOL] renumber

[Oganesyan, Vaheh]

Jared,

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

Thanks.

From: Jared Sampson 
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hi Vaheh -

Try `pdbset` from the CCP4 suite.

http://www.ccp4.ac.uk/html/pdbset.html#renumber<http://www.ccp4.ac.uk/html/pdbset.html#renumber>

```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```

Hope that helps.

Cheers,
Jared


From: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Reply: Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) 
<mailto:blaine-moo...@ouhsc.edu>, Jarrett Johnson 
<mailto:jarrett.john...@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> 
<mailto:pymol-users@lists.sourceforge.net>
Subject:  Re: [PyMOL] renumber


Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>; 
Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber=DwMGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI=<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber=DwMGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI=>>
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py=DwQGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw=<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py=DwQGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw=>>

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com%3cmailto:vaheh.oganes...@astrazeneca.com>>>
 wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

Re: [PyMOL] renumber

[Oganesyan, Vaheh]

Blain,

The command will not change the numbering of amino acids starting from #1. But 
if you got missing ones, like in my case, it will. Except for those having also 
letter in the number field. I mean the numbering used for CDRs of antibodies, 
not alternatives. Hence, my question, is there a command that will ignore the 
letters in the number field and renumber the amino acids in the order they 
appear in the file.

Thank you.

From: Mooers, Blaine H.M. (HSC) 
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh ; Jarrett Johnson 

Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber

Hi Vaheh,

alter vh, resi=str(int(resi)+0)

will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419


From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [EXTERNAL] Re: [PyMOL] renumber

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn't because there are residue numbers with 
letters. Is there a command that will either remove the letters or won't pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page 
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber=DwMGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI=<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber=DwMGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI=>>
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run 
renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py=DwQGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw=<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py=DwQGaQ=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw=>>

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com%3cmailto:vaheh.oganes...@astrazeneca.com>>>
 wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn't 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Re: [PyMOL] renumber

[Oganesyan, Vaheh]

Thank you Jarrett,

Then the command

alter vh, resi=str(int(resi)+0)

should work, right? But it doesn’t because there are residue numbers with 
letters. Is there a command that will either remove the letters or won’t pay 
attention to them and renumber sequentially.

Regards,


From: Jarrett Johnson 
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber

Hello,

The command shown on this page  
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber>
 is not one that comes with PyMOL by default. Try downloading the script and 
importing it via the `run` command in the PyMOL command-line:

run renumber.py

and then you should be able to use the command as shown on the Wiki page.

Hope that helps,
Jarrett J.

On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh 
mailto:vaheh.oganes...@astrazeneca.com>> wrote:

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn’t 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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--

Jarrett Johnson | Senior Developer
[Schrodinger Logo]<https://www.schrodinger.com/>

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[PyMOL] renumber

[Oganesyan, Vaheh]

Hello PyMOLers,

Wiki uses renumber command to alter residue numbers, but PyMOL doesn't 
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?


Regards,

Vaheh

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Re: [PyMOL] feature request

[Oganesyan, Vaheh]

Thomas and Jared,
I’m not sure what will be the best solution, but as a start, color of the 
object name may stay white if more than one color is used. Because you both 
found this as an interesting idea allows me to ask similar question now 
regarding labels. What if we can get label_color match the residue color. I 
vaguely remember something like this discussed x number of years ago, but do 
not remember why not. Could label become property of the object and not just a 
property of a session?

Thank you.


From: Jared Sampson 
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh ; Thomas Holder 

Cc: pymol-users 
Subject: Re: [PyMOL] feature request

Hi Thomas and Vaheh -

This is indeed an interesting idea.  I was thinking about this in terms of 
implementation, and what the edge cases might be.  I wonder what would be the 
mechanism for assigning the color if the object is not just a single color.  
Would it be the color that is the dominant color of the object over all 
(visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object 
name according to the colors in the spectrum (like the "spectrum" and "rainbow" 
menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different 
representations—would there be a hierarchy in terms of choosing , e.g. surface 
> cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` 
setting to turn the menu object name coloring on/off.  (Perhaps different modes 
could correspond to different ways of choosing the displayed color.)  It might 
also be useful to include object-level (or named-selection-level) settings to 
override the global setting and specify the color or spectrum directly, e.g.:

set internal_gui_name_color, red, obj1
set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might 
work!

Cheers,
Jared


On October 1, 2019 at 5:13:07 AM, Thomas Holder 
(thomas.hol...@schrodinger.com<mailto:thomas.hol...@schrodinger.com>) wrote:
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a 
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do 
you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh 
> mailto:vaheh.oganes...@astrazeneca.com>> 
> wrote:
>
> Thomas and other PyMOL developers,
>
> It looks as if we color the object name similar to the object color it will 
> be easier to distinguish which structure am I manipulating now. While models 
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>
> Thank you.
> Regards,
>
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> 
> AstraZeneca
> R | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046
> vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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[PyMOL] feature request

[Oganesyan, Vaheh]

Thomas and other PyMOL developers,

It looks as if we color the object name similar to the object color it will be 
easier to distinguish which structure am I manipulating now. While models can 
be colored, the names of the models can't.
Anybody else think it might be helpful?

Thank you.
Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046 
vaheh.oganes...@astrazeneca.com



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[PyMOL] label color

[Oganesyan, Vaheh]

Hello PyMOLers,

In version 2.2.3 under Win upon ray-tracing label color changes. Is there a way 
to prevent that from happening?

Thank you.

Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046
vaheh.oganes...@astrazeneca.com

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[PyMOL] aberrant behavior of mouse clicks in PyMOL

[Oganesyan, Vaheh]

Hi All,


I’m experiencing very annoying behavior of mouse clicks when there are more 
than one molecule in ASU. Upon opening the window cartoon mode is showing. If I 
click on the part of first listed molecule then all look good. However, if I 
click on the part of the second molecule then another residue gets picked up 
from the first one. Now, if I do “show as cartoon” while it is already showing 
cartoon, then the behavior goes back to normal.
Question: Do I have computer hardware issue, (personal hardware issue ), or 
this is a bug?
Thank you.

Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046
vaheh.oganes...@astrazeneca.com



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[PyMOL] PyMOL 2.0.4 mouse middle button

[Oganesyan, Vaheh]

Dear all,

In recent past in PyMOL one could move the center of the screen using mouse 
middle button (clock-hold-move). Now middle button invokes zooming. Would 
anyone know how the center can be moved now?

Thank you.


Regards,

Vaheh Oganesyan, PhD
www.medimmune.com




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Re: [PyMOL] tube width

[Oganesyan, Vaheh]

Found it: set cartoon_tube_radius, number

Regards,

Vaheh Oganesyan
www.medimmune.com

From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, August 22, 2017 11:52 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] tube width

Hello PyMOLers,

When presenting in cartoon tube mode how one can change the tube width?


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

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[PyMOL] tube width

[Oganesyan, Vaheh]

Hello PyMOLers,

When presenting in cartoon tube mode how one can change the tube width?


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

To the extent this electronic communication or any of its attachments contain 
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[PyMOL] smooth-ribbon

[Oganesyan, Vaheh]

Hey PyMOLers,

Would you know how to show smooth ribbon?
I can use cartoon_oval_length command to get almost what I want, however only 
for helices. Thanks in advance.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


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Re: [PyMOL] smooth-ribbon

[Oganesyan, Vaheh]

Found:

hide everything
show cartoon
cartoon tube
set cartoon_tube_radius, (number)


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


-Original Message-
From: Oganesyan, Vaheh
Sent: Monday, November 23, 2015 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: smooth-ribbon

Hey PyMOLers,

Would you know how to show smooth ribbon?
I can use cartoon_oval_length command to get almost what I want, however only 
for helices. Thanks in advance.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com


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information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
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have received this electronic communication in error, please reply to the 
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[PyMOL] coloring based on alignment

[Oganesyan, Vaheh]

Colleagues,

Was wondering if there is a functionality built  in PyMOL for coloring of the 
molecule based on sequence identity/similarity? This topic was discussed 
briefly in 2007 and the answer was from Robert Campbell suggesting using his 
scripts. Seems to be a good tool to have for anyone.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com



To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
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Re: [PyMOL] measuring wizard

[Oganesyan, Vaheh]

Thank you reply, Thomas.

Invoking

alter all, ID = index

didn't help.

Regards,

Vaheh Oganesyan
www.medimmune.com


-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Friday, October 02, 2015 4:05 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] measuring wizard

Hi Vaheh,

What PyMOL version do you use? Version 1.4 to 1.6 couldn't handle duplicated 
IDs with dynamic_measures=1. So either set dynamic_measures to 0, or assign 
unique IDs with:

alter all, ID = index

Cheers,
  Thomas

On 02 Oct 2015, at 14:58, Oganesyan, Vaheh <oganesy...@medimmune.com> wrote:

> Hi PyMOL users,
>
> In measuring wizard I'm consistently facing an annoying property that allows 
> me to measure only one distance between object1 and symmetry mate invoked 
> through symexp command. Whenever I click another atom on symmetry mate a 
> completely different atom from object1 is being chosen. Is it a bug in 
> program or am I doing something wrong?
>
>
> Regards,
>
> Vaheh Oganesyan
> MedImmune, ADPE
> www.medimmune.com

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
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have received this electronic communication in error, please reply to the 
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[PyMOL] measuring wizard

[Oganesyan, Vaheh]

Hi PyMOL users,

In measuring wizard I'm consistently facing an annoying property that allows me 
to measure only one distance between object1 and symmetry mate invoked through 
symexp command. Whenever I click another atom on symmetry mate a completely 
different atom from object1 is being chosen. Is it a bug in program or am I 
doing something wrong?


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
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Re: [PyMOL] measuring wizard

[Oganesyan, Vaheh]

Thank you. Will upgrade.

Regards,

Vaheh Oganesyan
www.medimmune.com


-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
Sent: Friday, October 02, 2015 4:34 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] measuring wizard

Hi Vaheh,

I checked the release notes, there was actually a picking bug related to 
measurement labels, this was fixed in 1.7.6.2. As an immediate workaround, hide 
all labels before creating the next measurement.

Cheers,
  Thomas

On 02 Oct 2015, at 16:15, Oganesyan, Vaheh <oganesy...@medimmune.com> wrote:

> Thank you reply, Thomas.
>
> Invoking
>
> alter all, ID = index
>
> didn't help.
>
> Regards,
>
> Vaheh Oganesyan
> www.medimmune.com
>
>
> -Original Message-
> From: Thomas Holder [mailto:thomas.hol...@schrodinger.com]
> Sent: Friday, October 02, 2015 4:05 PM
> To: Oganesyan, Vaheh
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] measuring wizard
>
> Hi Vaheh,
>
> What PyMOL version do you use? Version 1.4 to 1.6 couldn't handle duplicated 
> IDs with dynamic_measures=1. So either set dynamic_measures to 0, or assign 
> unique IDs with:
>
> alter all, ID = index
>
> Cheers,
>  Thomas
>
> On 02 Oct 2015, at 14:58, Oganesyan, Vaheh <oganesy...@medimmune.com> wrote:
>
>> Hi PyMOL users,
>>
>> In measuring wizard I'm consistently facing an annoying property that allows 
>> me to measure only one distance between object1 and symmetry mate invoked 
>> through symexp command. Whenever I click another atom on symmetry mate a 
>> completely different atom from object1 is being chosen. Is it a bug in 
>> program or am I doing something wrong?
>>
>>
>> Regards,
>>
>> Vaheh Oganesyan
>> MedImmune, ADPE
>> www.medimmune.com

--
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PyMOL Principal Developer
Schrödinger, Inc.

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[PyMOL] transparent figure

[Oganesyan, Vaheh]

Hello PyMOLers,

I’m wondering if the figure can have transparent background?


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

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[PyMOL] white background

[Oganesyan, Vaheh]

Dear PyMOL developers,

The latest incentive version of PyMOL 1.7.6.0 fails to show residue numbering 
in the sequence in the upper part of the screen when the background has been 
chosen to be white (i.e., it does not change the color of the font) . Also, 
unlike previous versions, after choosing Display/Sequence the sequence will 
appear only after clicking inside the viewer window. I don’t think either of 
the mentioned are special features. Can it be fixed, please?

Thank you.
Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
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Re: [PyMOL] selecting all instead of just one aa

[Oganesyan, Vaheh]

Thanks, really easy, feel very special. By not choosing MouseSelection 
ModeChains how else one gets into that mode? Just curious.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pitt.edu]
Sent: Thursday, September 25, 2014 2:19 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selecting all instead of just one aa

Hi,
Go to the Mouse Menu  Selection Mode  Residues

Matt Baumgartner
On 09/25/2014 01:48 PM, Oganesyan, Vaheh wrote:
All,

During my PyMOL session I've accidentally entered into a mode when by 
clicking one amino acid whole chain becomes selected. How can I turn it off? It 
is a quite elaborate scene to start it over. Thank you for help.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
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Re: [PyMOL] selecting all instead of just one aa

[Oganesyan, Vaheh]

I see. Great help, Thank you.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pitt.edu]
Sent: Thursday, September 25, 2014 3:01 PM
To: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selecting all instead of just one aa

In the bottom right it says 'Selecting Residues'. If you click on that it will 
cycle through the other selection levels.
Matt

On 09/25/2014 02:25 PM, Oganesyan, Vaheh wrote:
Thanks, really easy, feel very special. By not choosing MouseSelection 
ModeChains how else one gets into that mode? Just curious.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pitt.edu]
Sent: Thursday, September 25, 2014 2:19 PM
To: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] selecting all instead of just one aa

Hi,
Go to the Mouse Menu  Selection Mode  Residues

Matt Baumgartner
On 09/25/2014 01:48 PM, Oganesyan, Vaheh wrote:
All,

During my PyMOL session I've accidentally entered into a mode when by 
clicking one amino acid whole chain becomes selected. How can I turn it off? It 
is a quite elaborate scene to start it over. Thank you for help.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com
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and any

[PyMOL] migration from monitor to wall mounted screen and projector

[Oganesyan, Vaheh]

Hi all,

I'm planning migration from CRT monitor to wall mounted screen with projector 
that will support stereo. Mid-range emitter like AE125 for small office (4m by 
4m) like mine is sufficient. I'm looking for advise on projector and screen. It 
looks like ViewSonic PJD7820HD ($699) with native (at least 1280 x 1024 at 120 
Hz) support should work.
Have any of you tried this? What are other options for projector and are there 
preferences for wall mount screens?

Thank you.

Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

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Re: [PyMOL] regarding APBS tools in PyMOL

[Oganesyan, Vaheh]

Thank you, Carsten,

I’ll give it a try. Do you think it may be related to memory allocation since 
it does run on smaller objects?
I’ve found that upon starting APBS in PyMOL the apbs.exe file in the Program 
locations window is in quotes. Removing those makes it run but still on small 
objects.


Regards,

Vaheh
8-5851

From: Schubert, Carsten [JRDUS] [mailto:cschu...@its.jnj.com]
Sent: Tuesday, April 22, 2014 5:59 PM
To: Oganesyan, Vaheh; pymol-users
Subject: RE: regarding APBS tools in PyMOL

Hi Vaheh,

my recollection is a bit hazy, but I remember having some issues with the 
distributed APBS version earlier this year. Try downloading the latest APBS and 
run the plug-in generated input file using the latest version from the 
commandline. If that works you may have to swap the APBs binary or adjust the 
path to APBS accordingly.

HTH

Carsten

From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, April 22, 2014 9:45 AM
To: pymol-users
Subject: [PyMOL] regarding APBS tools in PyMOL

Colleagues,

The latest PyMOL version 1.7.0.3 looks like having issues with molecule size 
when APBS is being used. I’m loading whole molecule consisting of ~500 aa and 
APBS plugin after setting up the grid and after starting APBS run few seconds 
later opens a window with message: APBS stopped working. Close Program. If I 
load a portion of the molecule (and it doesn’t matter which, but should be less 
than 200 aa) then it works fine.
It is being run on Intel Core i7, 64-bit with 8 GB RAM.
Did anyone see such behavior?

Regards,

Vaheh
8-5851

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[PyMOL] regarding APBS tools in PyMOL

[Oganesyan, Vaheh]

Colleagues,

The latest PyMOL version 1.7.0.3 looks like having issues with molecule size 
when APBS is being used. I’m loading whole molecule consisting of ~500 aa and 
APBS plugin after setting up the grid and after starting APBS run few seconds 
later opens a window with message: APBS stopped working. Close Program. If I 
load a portion of the molecule (and it doesn’t matter which, but should be less 
than 200 aa) then it works fine.
It is being run on Intel Core i7, 64-bit with 8 GB RAM.
Did anyone see such behavior?

Regards,

Vaheh
8-5851

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[PyMOL] labels in version 1.7.0.1

[Oganesyan, Vaheh]

PyMOLers,

I've installed PyMOL version 1.7.0.1 on my new laptop running Win 7, 64-bit. 
Number of issues:

1. Side-by-side stereo shows only one side in cross- or wall-eye mode and both 
when ray-traced;
2. Labels can be generated, but I can move in editing mode only the label that 
was generated last.

I'm assuming this has something to do with my setup. If someone has seen these 
and found solution, please share.

Regards,

Vaheh
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Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white

[Oganesyan, Vaheh]

Engin,

If you go to Edit_all and change the seq_view_label_color to grey the numbers 
will become visible with white bkgr.

 Vaheh




-Original Message-
From: Engin Özkan [mailto:eoz...@stanford.edu]
Sent: Wednesday, September 04, 2013 4:40 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set 
to white

I forgot to explicitly say, this is only for the Sequence View panel, which has 
a black background regardless of the background parameter. And it applies to 
both sequence numbers and chain labels. Sequences themselves are displayed 
correctly.

Engin

On 9/4/13 12:59 PM, Engin Özkan wrote:
 Hi everybody,

 Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue
 numbers in the sequence if the background is set to white. I have been
 playing with all the seq_view_* settings (thanks for documenting them
 clearly within the Edit All Settings window!), especially
 seq_view_label_color, and this setting works if the background is not
 set to white. If the background is white (regardless of opaque
 background or not), many colors I tried display no font (or likely
 black font), *but* some colors do, and some colors display incorrect colors.

 RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and
 white for sequence numbers do not show. Grey, purple and brown look
 fine, but pink is a dimmed light blue, orange is green, and aquamarine
 is brown. After having too much fun with these colors, I thought I
 report this.

 Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version
 catches an error as it is starting, which may be related:
 libpng warning: iCCP: known incorrect sRGB profile

 Working on a Mac 10.6.8.

 Best,
 Engin

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[PyMOL] sequence file extraction

[Oganesyan, Vaheh]

I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to 
extract the sequence info.
I'm typing save objectname.fasta in old version and get the fasta file. In 
1.4.1 it complains
=
Traceback (most recent call last):
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py, line 254, in 
parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py, line 535, in 
save
st = _self.get_fastastr(selection)
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py, line 178, in 
get_fastastr
if seq.has_key(obj):
AttributeError: 'str' object has no attribute 'has_key'
=

Is there now a different way of extracting sequence info in PyMOL?

Thank you.

 Vaheh
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Re: [PyMOL] sequence file extraction

[Oganesyan, Vaheh]

Never mind. After restarting the computer fasta file is being written.

 Vaheh




-Original Message-
From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com]
Sent: Tuesday, December 27, 2011 11:16 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] sequence file extraction

I'm using ver. 1.4.1 and it looks like PyMOL recently lost the ability to 
extract the sequence info.
I'm typing save objectname.fasta in old version and get the fasta file. In 
1.4.1 it complains
=
Traceback (most recent call last):
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py, line 254, in 
parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py, line 535, in 
save
st = _self.get_fastastr(selection)
  File C:\Program Files\PyMOL\PyMOL/modules\pymol\exporting.py, line 178, in 
get_fastastr
if seq.has_key(obj):
AttributeError: 'str' object has no attribute 'has_key'
=

Is there now a different way of extracting sequence info in PyMOL?

Thank you.

 Vaheh
To the extent this electronic communication or any of its attachments contain 
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Re: [PyMOL] Ca trace

[Oganesyan, Vaheh]

Thank you Warren,

 

That exactly is what I wanted.

 

___ 
Vaheh 



From: Warren DeLano [mailto:war...@delsci.com] 
Sent: Wednesday, March 04, 2009 8:45 PM
To: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Ca trace

 

Vaheh,

 

PyMOL cannot draw a decent cartoon from CA-coordinates only.

 

set cartoon_trace_atoms

 

cartoon tube

 

show cartoon, name ca

 

Is about the best it can do.

 

Cheers,

Warren

 

 

 



From: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com] 
Sent: Wednesday, March 04, 2009 2:46 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Ca trace

 

Colleagues,

 

If the PDB file contains only Ca atoms and PyMOL shows them as
non-bonded atoms what one should do to display them as a ribbon? The
1rh2 entry is one of them.

 

Thank you.

 

___ 
Vaheh 




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electronic communication in error, please reply to the sender advising
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cooperation.




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information that is not in the public domain, such information is considered by 
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[PyMOL] Ca trace

[Oganesyan, Vaheh]

Colleagues,

 

If the PDB file contains only Ca atoms and PyMOL shows them as
non-bonded atoms what one should do to display them as a ribbon? The
1rh2 entry is one of them.

 

Thank you.

 

___ 
Vaheh 




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[PyMOL] two objects with synchronous rotation about their axes

[Oganesyan, Vaheh]

Is there a way in pymol to create such two objects that will rotate with
mouse each around its own axis?
I hope I'm clear.

Oganesyan Vaheh
Antibody Discovery
MedImmune, Inc.
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Re: [PyMOL] APBS

[Oganesyan, Vaheh]

Dear Robert,

Thank you for your note. You were right. I downloaded i386 for my Linux
computer and it runs. The funny part is that my computer has 64 bit
Xeon processor.
Go figure ...

Vaheh Oganesyan

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Robert
Campbell
Sent: Wednesday, May 30, 2007 11:06 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS

Hi Vaheh,

* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
 I did not get much luck with those recommendations either. I was doing
exactly the same. Something is phishy with my pymol and/or APBS
installation. I did check for different pdb files, so it is not pdb
related. The roor message is below:


==
 Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs',
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
 OSError Exception in Tk callback
   Function: function lambda at 0xf608448c (type: type
'function')
   Args: ()
 Traceback (innermost last):
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.
py, line 1747, in __call__
 return apply(self.func, args)
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py, line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py, line 132, in _doCommand
 return command(name)
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line
1101, in execute
 (retval,progout) =
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),
))
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line
317, in run
 retcode =
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOU
T)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in
call
 return Popen(*args, **kwargs).wait()
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in
__init__
 errread, errwrite)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in
_execute_child
 raise child_exception
 OSError: [Errno 8] Exec format error

 ^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca
http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] APBS

[Oganesyan, Vaheh]

I did not get much luck with those recommendations either. I was doing exactly 
the same. Something is phishy with my pymol and/or APBS installation. I did 
check for different pdb files, so it is not pdb related. The roor message is 
below:
==
Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', 
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
OSError Exception in Tk callback
  Function: function lambda at 0xf608448c (type: type 'function')
  Args: ()
Traceback (innermost last):
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, 
line 1747, in __call__
return apply(self.func, args)
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 132, in _doCommand
return command(name)
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 1101, in 
execute
(retval,progout) = 
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 317, in run
retcode = 
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in call
return Popen(*args, **kwargs).wait()
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in __init__
errread, errwrite)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in 
_execute_child
raise child_exception
OSError: [Errno 8] Exec format error
==
Comments and solutions are appreciated.

VO

-Original Message-
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
 
I also continually had this problem unless I got pqr coordinates  
(with hydrogens)

below is the instructions I wrote for myself and group so that I  
would be able to do it again next time (getting old and the memory  
isn't what it used to be)

pqr corrdinates - Can do it on the web at

http://pdb2pqr.sourceforge.net/

http://agave.wustl.edu/pdb2pqr/server.html

I just used the defaults


Under plugins go to APBS tools

Choose use another PQR.  (maybe if you select Use PDB2PQR it might do  
this automatically without first going on line to do it?)


default configuration



Each time I've always had to set the APBS binary location.  The other  
sections leave blank



default Temporary File Locations



To start APBS 1st select Set Grid, then do Run APBS - I don't know  
why the buttons are placed in that order.  Also, it seems you must  
click on Run APBS twice before it launches.  Run Top in unix window  
to make sure it runs

For Hfq, ~400 residues, APBS took about a minute.

Go to Visualization and click on Update



For most reasonable looking Molecular Surfaces I turn off Solvent  
Accessible Surface and turn on Color by potential on sol. acc. surf.   
Select Show.  If you change the range you must also click on Update


When I tried to do this with another loaded structure, it actually  
looked like it mapped the first EPS onto the surface of the second  
structure.


Make sure to remove waters (and probably everyother non-protein  
residue).  EP on the left was done with waters in structure.  Notice  
red surface where ever water molecules appeare


non-linear Bolzman

Linear Bolzman

On May 24, 2007, at 1:16 PM, Michael Lerner wrote:

 Hi,

 Can you try installing the most recent version of my plugin from
 http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
 the normal Install Plugin menu option .. there's no need to do things
 by hand anymore)?  It fixes some problems and gives better error
 messages on others.

 Thanks,

 -Michael

 -- 
 Biophysics Graduate Student
 Carlson Lab, University of Michigan
 http://www.umich.edu/~mlerner


 On 5/24/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote:




 I'll appreciate some help with APBS plugin.



 In both Win or Lin the same error appears:



 ObjectMapLoadDXFile-Error: Unable to open file!



 After googling with this error message I've checked all of the
 possibilities:

 Map file is loaded OK, folders with apbs.exe and psize.py files do  
 not
 contain blanks,

 the *.pqr file is created using pdb2pqr server with and without chain
 identifier.



 At this point I do not know what else to try. Before (about 1 year  
 ago) I've
 used it with no problems.

 Could someone point me to the problem?

 Windows version is 0_99rc6 installed using binaries.

 Thanks in advance.



 Vaheh Oganesyan


 - 
 
 This SF.net

[PyMOL] APBS

[Oganesyan, Vaheh]

I'll appreciate some help with APBS plugin.
 
In both Win or Lin the same error appears:
 
ObjectMapLoadDXFile-Error: Unable to open file!
 
After googling with this error message I've checked all of the
possibilities:
Map file is loaded OK, folders with apbs.exe and psize.py files do not
contain blanks, 
the *.pqr file is created using pdb2pqr server with and without chain
identifier.
 
At this point I do not know what else to try. Before (about 1 year ago)
I've used it with no problems.
Could someone point me to the problem?
Windows version is 0_99rc6 installed using binaries.
Thanks in advance.
 
Vaheh Oganesyan