pymol-users Mailing List for PyMOL Molecular Graphics System

I'm also unable to checkout from that url from two separate networks
and machines.

Error message:
    svn: E210002: Unable to connect to a repository at URL
'svn://svn.code.sf.net/p/pymol/code/trunk/pymol'
    svn: E210002: Network connection closed unexpectedly

~Paul

--
Paul Rigor
http://www.ics.uci.edu/~prigor
"What we observe is not nature itself, but nature exposed to our
method of questioning" ~ Werner Karl Heisenberg



On Wed, Apr 30, 2014 at 10:46 AM, Nat Echols <nat...@gm...> wrote:
> I'm getting the same error for a completely unrelated SourceForge repository
> (but strangely, another works fine).  I suspect they're having server
> problems - it wouldn't be the first time.
>
> -Nat
>
>
> On Wed, Apr 30, 2014 at 1:39 PM, Andreas Förster <doc...@gm...>
> wrote:
>>
>> Dear all,
>>
>> trying to update PyMOL with the usual
>>
>> svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>>
>> I get an "svn: Network connection closed unexpectedly" error.
>>
>> This is on two different computers/OSs.  Has anything changed?
>>
>> Thanks.
>>
>>
>> Andreas
>>
>>
>> --
>>                    Andreas Förster
>>       Crystallization and X-ray Facility Manager
>>             Centre for Structural Biology
>>                Imperial College London
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform
>> available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

I'm getting the same error for a completely unrelated SourceForge
repository (but strangely, another works fine).  I suspect they're having
server problems - it wouldn't be the first time.

-Nat


On Wed, Apr 30, 2014 at 1:39 PM, Andreas Förster <doc...@gm...>wrote:

> Dear all,
>
> trying to update PyMOL with the usual
>
> svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>
> I get an "svn: Network connection closed unexpectedly" error.
>
> This is on two different computers/OSs.  Has anything changed?
>
> Thanks.
>
>
> Andreas
>
>
> --
>                    Andreas Förster
>       Crystallization and X-ray Facility Manager
>             Centre for Structural Biology
>                Imperial College London
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Dear all,

trying to update PyMOL with the usual

svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol

I get an "svn: Network connection closed unexpectedly" error.

This is on two different computers/OSs.  Has anything changed?

Thanks.


Andreas


-- 
                   Andreas Förster
      Crystallization and X-ray Facility Manager
            Centre for Structural Biology
               Imperial College London

Hi PyMol community,

Is there such thing as a site comparing hardware performance for PyMol? What would be the ideal system/OS to run PyMol?

Best regards to all,
Marcelo

Wishing you all the best Jason, it has been fantastic to be involved with this bb with you as the key guy. Always there to answer the questions

From: Jason Vertrees [mailto:jas...@gm...]
Sent: Thursday, 24 April 2014 9:00 p.m.
To: pymol-users; cc...@ji...
Subject: [PyMOL] Farewell

Greetings PyMOLers and CCP4ers worldwide,

It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse<—to" rel="nofollow">http://www.linkedin.com/in/jasonvertrees/>—to follow one of my dreams—helping lead technology and science at a new startup<http://www.realmassive.com>. March 30th marked my last day at Schrödinger and supporting PyMOL.

Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it.

Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed.

It's been great fun. I wish you all the best.

Cheers,

-- Jason

--
Jason Vertrees, PhD
(e) Jas...@gm...<mailto:Jas...@gm...>
(o) +1 (603) 374-7120

Hi Yeping -

It doesn’t look like Spectrumbar supports additional labeling, but you could add labels at each end by using pseudoatoms at the positions where you want the labels to appear (see the second example at http://pymolwiki.org/index.php/Pseudoatom).

For the 2D gradient box, you can create whatever intermediate labels you like, just keep the same scale.  For example, if your bar covers data values from -0.3 to +2.3 and you make it 260 pixels wide, then each 10px accounts for 0.1 unit.  So “0.0” will be 30px from the left side, “+0.5” will be at 80px, and so forth.  After you create it at that scale, you can resize it as you wish and the relative positions will remain the same.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Apr 28, 2014, at 10:20 PM, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:

Dear Jared,

Thank you for the reply. But I still have a couple of questions:

     As for the spectrumbar<" rel="nofollow">http://pymolwiki.org/index.php/Spectrumbar> script, how could I assign a particular data value to a particular color?  By using the command:

spectrumbar blue, white, red

I can get a spectrumbar. If the range of my data is -0.3~2.3, maybe I can label two end of the bar with -0.3 and 2.3 manually, respectively. But if I want to label more data to the bar? How shold I do?

      As you suggest, I can simplely get a 2D box with a linear gradient fill. But the question is the same with above: how could I correctly label the bar according my data set?

Best regards,


Yeping

------------------------------------------------------------------
发件人：Sampson, Jared <Jar...@ny...<mailto:Jar...@ny...>>
发送时间：2014年4月29日(星期二) 04:36
收件人：孙业平 <sun...@al...<mailto:sun...@al...>>
抄　送：pymol-users <pym...@li...<mailto:pym...@li...>>
主　题：Re: [PyMOL] gradually changed colors with b-factor colum

Hi Yeping -

I was about to suggest Sean Law’s new spectrumbar<" rel="nofollow">http://pymolwiki.org/index.php/Spectrumbar> script, but I see he beat me to it.  You’ll have to adjust the positioning of the bar with some trial and error.  Also, in case you get a “NameError: global name 're' is not defined” error, simply change the 4th line from:

    from re import *

to

    import re

I’ve just submitted a pull request<" rel="nofollow">https://github.com/Pymol-Scripts/Pymol-script-repo/pull/55> with this fix, but if you download the script before it’s accepted, you'll have to make the change yourself.

Alternatively, you could fairly easily create a simple 2D box with a gradient fill in e.g. Inkscape or Illustrator with the appropriate colors and add the labels manually.  So long as you specify a linear gradient, it should be fairly consistent with the PyMOL values.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 27, 2014, at 8:50 AM, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:

Dear proessor Holder and pymol users,

I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:

spectrum b, blue_white_red, byres=1

But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps:

  1.  Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.
  2.  Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much.




Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------
发件人：Thomas Holder <sp...@us...<mailto:sp...@us...>>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sun...@al...<mailto:sun...@al...>>
抄　送：pymol-users <pym...@li...<mailto:pym...@li...>>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms:

PyMOL>run path/to/spectrumany.py
PyMOL>spectrumany b, white blue, name CA

If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script:
http://pymolwiki.org/index.php/AlphaToAll

Hope that helps.

Cheers,
Thomas

On 10 Dec 2013, at 01:04, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:

> Hi, professor Holder,
>
> Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> 发件人：Thomas Holder <sp...@us...<mailto:sp...@us...>>
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 <sun...@al...<mailto:sun...@al...>>
> 抄　送：pymol-users <pym...@li...<mailto:pym...@li...>>
> 主　题：Re: [PyMOL] gradually changed colors with flexibility
>
> Hi Yeping,
>
> use the spectrum command:
>
> PyMOL> spectrum b, blue_white_red
>
> http://pymolwiki.org/index.php/Spectrum
>
> Cheers,
> Thomas
>
> On 09 Dec 2013, at 11:30, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:
>
> > Dear all,
> >
> > I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------------------
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=================================

Hi,

What is the command to set bond angles ??

Regards
--------------
BHARAT

Dear Jared,Thank you for the reply. But I still have a couple of questions:
     As for the spectrumbar script, how could I assign a particular data value to a particular color?  By using the command:spectrumbar blue, white, redI can get a spectrumbar. If the range of my data is -0.3~2.3, maybe I can label two end of the bar with -0.3 and 2.3 manually, respectively. But if I want to label more data to the bar? How shold I do?
      As you suggest, I can simplely get a 2D box with a linear gradient fill. But the question is the same with above: how could I correctly label the bar according my data set?Best regards,
Yeping------------------------------------------------------------------
发件人：Sampson, Jared <Jar...@ny...>
发送时间：2014年4月29日(星期二) 04:36
收件人：孙业平 <sun...@al...>
抄　送：pymol-users <pym...@li...>
主　题：Re: [PyMOL] gradually changed colors with b-factor colum






Hi Yeping - 



I was about to suggest Sean Law’s new spectrumbar script, but I see he beat me to it.  You’ll have to adjust the positioning of the bar with some trial and error.  Also, in case you get a “NameError:
 global name 're' is not defined” error, simply change the 4th line from:



    from re import *



to 



    import re



I’ve just submitted a pull request with this fix, but if you download the script before it’s accepted, you'll have to make the change yourself.



Alternatively, you could fairly easily create a simple 2D box with a gradient fill in e.g. Inkscape or Illustrator with the appropriate colors and add the labels manually.  So long as you specify a linear gradient, it should be fairly consistent with the
 PyMOL values.



Hope that helps. 



Cheers,
Jared


--

Jared Sampson

Xiangpeng Kong Lab

NYU Langone Medical Center

http://kong.med.nyu.edu/







On Apr 27, 2014, at 8:50 AM, sunyeping <sun...@al...> wrote:




Dear proessor Holder and pymol users,





I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:





spectrum b, blue_white_red, byres=1 







But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar),
 this can be done with the following steps:


Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically
 created colors made by b-factor script) and show the b-factor bar as lines (or sticks).



Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much.   











Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences




------------------------------------------------------------------

发件人：Thomas Holder <sp...@us...>

发送时间：2013年12月11日(星期三) 12:49

收件人：孙业平 <sun...@al...>

抄　送：pymol-users <pym...@li...>

主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility




Hi Yeping,



the spectrum command has a "byres" argument to operate on the residue level:



PyMOL>spectrum b, blue_white_red, byres=1



There is no white_blue color ramp, but there is a script which provides this:

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

It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms:



PyMOL>run path/to/spectrumany.py

PyMOL>spectrumany b, white blue, name CA



If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script:

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



Hope that helps.



Cheers,

Thomas



On 10 Dec 2013, at 01:04, sunyeping <sun...@al...> wrote:



> Hi, professor Holder,

> 

> Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual
 atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks.


> 

> Yeping Sun

> 

> Institute of Microbiology, Chinese Academy of Sciences

> 

> 

> ------------------------------------------------------------------

> 发件人：Thomas Holder <sp...@us...>

> 发送时间：2013年12月10日(星期二) 04:50

> 收件人：孙业平 <sun...@al...>

> 抄　送：pymol-users <pym...@li...>

> 主　题：Re: [PyMOL] gradually changed colors with flexibility

> 

> Hi Yeping,

> 

> use the spectrum command:

> 

> PyMOL> spectrum b, blue_white_red

> 

> http://pymolwiki.org/index.php/Spectrum

> 

> Cheers,

> Thomas

> 

> On 09 Dec 2013, at 11:30, sunyeping <sun...@al...> wrote:

> 

> > Dear all,

> > 

> > I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.

> > 

> > Yeping Sun

> > 

> > Institute of Microbiology, Chinese Academy of Sciences



------------------------------------------------------------------------------

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This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.

=================================

Hi Yeping -

I was about to suggest Sean Law’s new spectrumbar<" rel="nofollow">http://pymolwiki.org/index.php/Spectrumbar> script, but I see he beat me to it.  You’ll have to adjust the positioning of the bar with some trial and error.  Also, in case you get a “NameError: global name 're' is not defined” error, simply change the 4th line from:

    from re import *

to

    import re

I’ve just submitted a pull request<" rel="nofollow">https://github.com/Pymol-Scripts/Pymol-script-repo/pull/55> with this fix, but if you download the script before it’s accepted, you'll have to make the change yourself.

Alternatively, you could fairly easily create a simple 2D box with a gradient fill in e.g. Inkscape or Illustrator with the appropriate colors and add the labels manually.  So long as you specify a linear gradient, it should be fairly consistent with the PyMOL values.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 27, 2014, at 8:50 AM, sunyeping <sun...@al...<mailto:sun...@al...>> wrote:

Dear proessor Holder and pymol users,

I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:

spectrum b, blue_white_red, byres=1

But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps:

  1.  Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.
  2.  Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much.




Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------
发件人：Thomas Holder <sp...@us...<mailto:sp...@us...>>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sun...@al...<mailto:sun...@al...>>
抄　送：pymol-users <pym...@li...<mailto:pym...@li...>>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms:

PyMOL>run path/to/spectrumany.py
PyMOL>spectrumany b, white blue, name CA

If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script:
http://pymolwiki.org/index.php/AlphaToAll

Hope that helps.

Cheers,
Thomas

On 10 Dec 2013, at 01:04, sunyeping <sun...@al...> wrote:

> Hi, professor Holder,
>
> Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> 发件人：Thomas Holder <sp...@us...>
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 <sun...@al...>
> 抄　送：pymol-users <pym...@li...>
> 主　题：Re: [PyMOL] gradually changed colors with flexibility
>
> Hi Yeping,
>
> use the spectrum command:
>
> PyMOL> spectrum b, blue_white_red
>
> http://pymolwiki.org/index.php/Spectrum
>
> Cheers,
> Thomas
>
> On 09 Dec 2013, at 11:30, sunyeping <sun...@al...> wrote:
>
> > Dear all,
> >
> > I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.
> >
> > Yeping Sun
> >
> > Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
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=================================

You can try the spectrumbar script:
http://www.pymolwiki.org/index.php/Spectrumbar
Best,
Sean 		 	   		  

Jason -

I’d also like to express my appreciation for all you’ve done to benefit the PyMOL community.  You have, time and again, proven yourself to be an extremely responsive and helpful leader both in developing the software and in enabling others to learn to use it.  Like many on these lists, I’m sure, after hearing of Warren’s untimely passing 5 years ago, I was saddened of course, but also concerned about what would happen to PyMOL without him.  Fortunately, it couldn’t have landed in better hands.  I wish you all the best in your new endeavor.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On Apr 24, 2014, at 9:29 AM, Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:

Dear Jason,

thank you so much for you deep commitment and your invaluable contributions to PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed to give it a new home at Schrödinger. We are sorry to see you leave and will truly miss you here.

To me personally, you have been a great mentor and guide and I can hardly enumerate what I learned from you. I owe you deep gratitude.

It is my honour to now take the lead on PyMOL and serve the community and our sponsors as best as I can. The PyMOL team at Schrödinger is strongly dedicated to continuously improve PyMOL and keep the PyMOL spirit alive.

Cheers,
 Thomas

On 24 Apr 2014, at 05:00, Jason Vertrees <jas...@gm...<mailto:jas...@gm...>> wrote:

Greetings PyMOLers and CCP4ers worldwide,

It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse—to follow one of my dreams—helping lead technology and science at a new startup. March 30th marked my last day at Schrödinger and supporting PyMOL.

Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it.

Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed.

It's been great fun. I wish you all the best.

Cheers,

-- Jason

--
Jason Vertrees, PhD
(e) Jas...@gm...<mailto:Jas...@gm...>
(o) +1 (603) 374-7120

--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

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This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

Dear proessor Holder and pymol users,I previously tried to color a protein structure accord to a set of customer data. I replaced the b factor of individual Ca atoms and colored the structure with the command:spectrum b, blue_white_red, byres=1 But I think I need a color scale bar to show the range of the data set. According to PymolWiki (http://www.pymolwiki.org/index.php/Advanced_Coloring#Creating_a_Color_bar), this can be done with the following steps:Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Make CA's to be separated by 5 Angstroem.Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).Could you tell me how to assign blue_white_red color for these increment? And if the range of my data set is -0.8 to 2.3, how to make the color gradient reflect this range? Thank you very much.   
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
------------------------------------------------------------------
发件人：Thomas Holder <sp...@us...>
发送时间：2013年12月11日(星期三) 12:49
收件人：孙业平 <sun...@al...>
抄　送：pymol-users <pym...@li...>
主　题：Re: [PyMOL] 答复： gradually changed colors with flexibility

Hi Yeping,

the spectrum command has a "byres" argument to operate on the residue level:

PyMOL>spectrum b, blue_white_red, byres=1

There is no white_blue color ramp, but there is a script which provides this:
http://pymolwiki.org/index.php/Spectrumany
It doesn't have the byres argument. If you only show cartoon, just limit the selection to CA atoms:

PyMOL>run path/to/spectrumany.py
PyMOL>spectrumany b, white blue, name CA

If you want to show all atoms, you can map the CA atom b-factor to all residue atoms with this script:
http://pymolwiki.org/index.php/AlphaToAll

Hope that helps.

Cheers,
  Thomas

On 10 Dec 2013, at 01:04, sunyeping <sun...@al...> wrote:

> Hi, professor Holder,
> 
> Thank you for the reply, but how can I do this on the level of individual amino acids in stead of atom? I have two homolog stuctures and I want to map the difference between the b factors of the corresonding residues of these two stuctures rather than individual atoms. And I want to use gradually deepened color from white to blue. Could you explain more in detail? Thanks.  
> 
> Yeping Sun
> 
> Institute of Microbiology, Chinese Academy of Sciences
> 
> 
> ------------------------------------------------------------------
> 发件人：Thomas Holder <sp...@us...>
> 发送时间：2013年12月10日(星期二) 04:50
> 收件人：孙业平 <sun...@al...>
> 抄　送：pymol-users <pym...@li...>
> 主　题：Re: [PyMOL] gradually changed colors with flexibility
> 
> Hi Yeping,
> 
> use the spectrum command:
> 
> PyMOL> spectrum b, blue_white_red
> 
> http://pymolwiki.org/index.php/Spectrum
> 
> Cheers,
> Thomas
> 
> On 09 Dec 2013, at 11:30, sunyeping <sun...@al...> wrote:
> 
> > Dear all,
> > 
> > I want to show amino acids in a structure according to their flexibility (B factor) by gradually changed colors. Can pymol do this? Thanks.
> > 
> > Yeping Sun
> > 
> > Institute of Microbiology, Chinese Academy of Sciences

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Dear all,
I am trying to map b factor onto a structure by gradually changing color. I use the following command: 
pymol>spectrum b, blue_white_red, byres=1It seems to work. But I don't know how to make pymol show a color bar presenting the range of b factor. Could you help me? Thanks.Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

I have been able to use this script successfully in the past but now for some reason I cannot. I load my structure and in the command line type
run show_bumps.py
show_bumps (selection of what I want to show bumps for), showbumps

and while I get a vanderwaal strain printed out on the command line, I do not get any  disks to show up to illustrate the bad/good contacts (like i do with the mutagenesis wizard).  Maybe I am typing my selection in wrong? So for example, if I want to see any steric clashes residue 6 has with surrounding residues in my structure, I would type in
show_bumps resi 6, showbumps

Thanks in advance.

Dear Jason,

thank you so much for you deep commitment and your invaluable contributions to PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed to give it a new home at Schrödinger. We are sorry to see you leave and will truly miss you here.

To me personally, you have been a great mentor and guide and I can hardly enumerate what I learned from you. I owe you deep gratitude.

It is my honour to now take the lead on PyMOL and serve the community and our sponsors as best as I can. The PyMOL team at Schrödinger is strongly dedicated to continuously improve PyMOL and keep the PyMOL spirit alive.

Cheers,
  Thomas

On 24 Apr 2014, at 05:00, Jason Vertrees <jas...@gm...> wrote:

> Greetings PyMOLers and CCP4ers worldwide,
> 
> It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse—to follow one of my dreams—helping lead technology and science at a new startup. March 30th marked my last day at Schrödinger and supporting PyMOL.
> 
> Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it.
> 
> Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed.
> 
> It's been great fun. I wish you all the best.
> 
> Cheers,
> 
> -- Jason
> 
> --
> Jason Vertrees, PhD
> (e) Jas...@gm...
> (o) +1 (603) 374-7120

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Spencer,

yes it's a private variable and as such was never supposed to serve as
X11 (or Tkinter) availability check... but: I would (and did) also use
it, since it's the best option to check this right now.

Cheers,
  Thomas

Spencer Bliven wrote, On 04/22/14 10:46:
> I just found the pymol._ext_gui property, which seems to be None if X11
> is off and a positive number if X11 is present. Seeing as it's a private
> variable, is it ok to use this to check for X11 presence?
> 
> -Spencer
> 
> 
> On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven <sb...@uc...
> <mailto:sb...@uc...>> wrote:
> 
>     Here's what I'm currently using. It seems to work so far. Looking
>     through the PyMol binary I see about 50 possible names though, so it
>     would be nice if there were a built-in way to detect X11.
> 
>     def hasTk():
>         """ Make an educated guess as to whether Tk is installed,
>         hopefully without triggering any installation on Macs
>         """
>         hasTk = True
>         if sys.platform=="darwin": #Mac
>             # Hack: check the path for entries containing 'X11'
>             hasTk = any([ "X11" in p.upper() for p in sys.path])
>        
>         if hasTk:
>             try:
>                 import Tkinter
>             except ImportError:
>                 hasTk = False
> 
>         return hasTk
> 
> 
>     On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven <sb...@uc...
>     <mailto:sb...@uc...>> wrote:
> 
>         I'm working on a plugin with a command line interface and a
>         light-weight tk interface through the plugins menu. This works
>         fine on Linux, Windows, and open-source Mac builds, but not on
>         MacPyMol.app. Importing Tkinter causes PyMol to quit with a
>         prompt to install X11 (but not an ImportError, as far as I can
>         tell). If X11 is installed there are no errors, but there is not
>         a plugins menu, so I'd rather not bother loading and
>         initializing the Tk interface to the plugin.
> 
>         How can I detect whether Tk is available?
> 
>         I can think of two approaches, but haven't figured out the
>         correct commands for either. (1) Check the name that pymol was
>         started with. "MacPyMol.app" does not have Tk, while
>         "PyMOLX11Hybrid.app" does.  I'm not sure how to get the name
>         (maybe could be guessed from sys.path?), and I know there are a
>         lot more variants than those two available. (2) Check for the
>         existence of the plugins menu. But this would have to be done
>         without importing Tk and triggering the X11 check.
> 
>         Is there a simple way to do this I'm overlooking?
> 
>         Thanks,
>         -Spencer

-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

Hi DJ,

with little scripting experience, this might be challanging. However,
it's possible of course. The PSICO module has a "map_new_apbs" and a
"apbs_surface" function.

psico.electrostatics.apbs_surface
psico.electrostatics.map_new_apbs

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

Hope that helps as a starting point.

Cheers,
  Thomas

Dhananjay wrote, On 04/23/14 04:02:
> Dear all,
> 
> Is there any way to use apbs through pml script.
> I have 40-50 pqr files and I wish to see them all in surface
> representation.
> However, default surface is not enough for me.
> Therefore, wish to run apbs.
> I want to make automated script to get apbs calculated surface
> representation.
> 
> Could any one suggest me how I can start.
> 
> I have little experience in writing .pml scripts.
> 
> Thank you in advance.
> 
> -- DJ

-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

Hi Meginir,

there are several "center of mass" scripts on the PyMOLWiki. If you have
PSICO installed, try this:

python
sele = 'yourobject'
cmd.alter(sele, 'q=1') # SDF files load with q=0
for i in range(1, cmd.count_states() + 1):
  cmd.alter_state(i, sele, '(x,y,z)=(x-%f,y-%f,z-%f)' %
tuple(psico.querying.centerofmass(sele, i)))
python end

Cheers,
  Thomas

meginir urestal wrote, On 04/23/14 05:15:
> Hi,
> 
> I have an sdf file with several ligands. The problem I am facing is that
> each of the ligands is in a different patch of space. Does anyone know
> of a way to center all the ligands around the same point for easy viewing?
> 
> Thanks,

-- 
Thomas Holder
PyMOL
Schrödinger, Inc.

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:CSC...@it...]
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:Oga...@Me...]
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

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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. 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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. 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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Hi,

I have an sdf file with several ligands. The problem I am facing is that
each of the ligands is in a different patch of space. Does anyone know of a
way to center all the ligands around the same point for easy viewing?

Thanks,

Dear all,

Is there any way to use apbs through pml script.
I have 40-50 pqr files and I wish to see them all in surface
representation.
However, default surface is not enough for me.
Therefore, wish to run apbs.
I want to make automated script to get apbs calculated surface
representation.

Could any one suggest me how I can start.

I have little experience in writing .pml scripts.

Thank you in advance.

-- DJ

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:Oga...@Me...]
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

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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. 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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Hi,

After installing Dynoplot I was able to start it via the plugins menu
(which works fine), but when I try starting it via the command line it
throws an error (please see the log file).

Eventually I'd like to use Dynoplot in combination with "Monitor file
continuously" one to visualize the output from the structure
calculation on the fly.

Thank you,
Vitaly

I just found the pymol._ext_gui property, which seems to be None if X11 is
off and a positive number if X11 is present. Seeing as it's a private
variable, is it ok to use this to check for X11 presence?

-Spencer


On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven <sb...@uc...> wrote:

> Here's what I'm currently using. It seems to work so far. Looking through
> the PyMol binary I see about 50 possible names though, so it would be nice
> if there were a built-in way to detect X11.
>
> def hasTk():
>     """ Make an educated guess as to whether Tk is installed,
>     hopefully without triggering any installation on Macs
>     """
>     hasTk = True
>     if sys.platform=="darwin": #Mac
>         # Hack: check the path for entries containing 'X11'
>         hasTk = any([ "X11" in p.upper() for p in sys.path])
>
>     if hasTk:
>         try:
>             import Tkinter
>         except ImportError:
>             hasTk = False
>
>     return hasTk
>
>
> On Mon, Apr 14, 2014 at 10:46 AM, Spencer Bliven <sb...@uc...> wrote:
>
>> I'm working on a plugin with a command line interface and a light-weight
>> tk interface through the plugins menu. This works fine on Linux, Windows,
>> and open-source Mac builds, but not on MacPyMol.app. Importing Tkinter
>> causes PyMol to quit with a prompt to install X11 (but not an ImportError,
>> as far as I can tell). If X11 is installed there are no errors, but there
>> is not a plugins menu, so I'd rather not bother loading and initializing
>> the Tk interface to the plugin.
>>
>> How can I detect whether Tk is available?
>>
>> I can think of two approaches, but haven't figured out the correct
>> commands for either. (1) Check the name that pymol was started with.
>> "MacPyMol.app" does not have Tk, while "PyMOLX11Hybrid.app" does.  I'm not
>> sure how to get the name (maybe could be guessed from sys.path?), and I
>> know there are a lot more variants than those two available. (2) Check for
>> the existence of the plugins menu. But this would have to be done without
>> importing Tk and triggering the X11 check.
>>
>> Is there a simple way to do this I'm overlooking?
>>
>> Thanks,
>> -Spencer
>>
>
>

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

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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. 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 and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.