pymol-users Mailing List for PyMOL Molecular Graphics System

Hi

 Thank you Seth and Adam for vouching for the missing residue option.
Thank you Thomas for considering the request for implememntation.

Best Regards
Priyan

On Mon, Sep 29, 2014 at 7:04 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Seth and Adam,
>
> thanks a lot for the feature request and for explaining why this is
> useful. The sequence viewer part should not be too difficult, actually. Of
> course I remember the "cartoon dash" request, Seth. Working on PyMOL's
> cartoon code is not the easiest task (for historical reasons) but we are
> working on getting improvements like this in.
>
> Cheers,
>   Thomas
>
> On 27 Sep 2014, at 10:22, H. Adam Steinberg <h.a...@gm...>
> wrote:
>
> > Phenomenal idea! I fully agee! :)
> >
> > On Sep 27, 2014, at 2:22 AM, Seth Harris <se...@gm...> wrote:
> >
> >> Hi Thomas et al,
> >>
> >> There was a recent question on the board about missing residues and the
> possibility of reading SEQRES headers and PyMOL being able to show the
> missing bits in the sequence view, perhaps with the amino acid letters
> grayed out to distinguish the gap. I know the reply was "PyMOL doesn't
> currently" do this, but it seemed to then end "full stop" rather than,
> "...but it's a fantastic idea". I'd like to second the idea as a great
> addition! When building structures or viewing and hitting gaps one always
> has to shuffle off to find the sequence or jump back to see how big the gap
> is and what type of residues are supposed to be in there. This would put it
> right there integrated at one's fingertips.
> >>
> >> This also reminds me of something I suggested to you, Thomas, that
> might fit in here of having a "cartoon dash" rendering (at least for loops
> if not helices and strands?) such that one could borrow a loop from a
> homologue or build in a placeholder to provide visual continuity in a model
> while still clearly indicating the disordered regions, but now in a 3D
> ray-traced dashed line that follows the cartoon trajectory rather than the
> usual penciled in job.
> >>
> >> I know in building a new structure I don't often have any SEQRES header
> in place, but if it offered advantages like this it would be easy enough to
> install such.
> >>
> >> Thanks,
> >> Seth
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
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Hi Seth and Adam,

thanks a lot for the feature request and for explaining why this is useful. The sequence viewer part should not be too difficult, actually. Of course I remember the "cartoon dash" request, Seth. Working on PyMOL's cartoon code is not the easiest task (for historical reasons) but we are working on getting improvements like this in.

Cheers,
  Thomas

On 27 Sep 2014, at 10:22, H. Adam Steinberg <h.a...@gm...> wrote:

> Phenomenal idea! I fully agee! :)
> 
> On Sep 27, 2014, at 2:22 AM, Seth Harris <se...@gm...> wrote:
> 
>> Hi Thomas et al,
>> 
>> There was a recent question on the board about missing residues and the possibility of reading SEQRES headers and PyMOL being able to show the missing bits in the sequence view, perhaps with the amino acid letters grayed out to distinguish the gap. I know the reply was "PyMOL doesn't currently" do this, but it seemed to then end "full stop" rather than, "...but it's a fantastic idea". I'd like to second the idea as a great addition! When building structures or viewing and hitting gaps one always has to shuffle off to find the sequence or jump back to see how big the gap is and what type of residues are supposed to be in there. This would put it right there integrated at one's fingertips.
>> 
>> This also reminds me of something I suggested to you, Thomas, that might fit in here of having a "cartoon dash" rendering (at least for loops if not helices and strands?) such that one could borrow a loop from a homologue or build in a placeholder to provide visual continuity in a model while still clearly indicating the disordered regions, but now in a 3D ray-traced dashed line that follows the cartoon trajectory rather than the usual penciled in job.
>> 
>> I know in building a new structure I don't often have any SEQRES header in place, but if it offered advantages like this it would be easy enough to install such.
>> 
>> Thanks,
>> Seth

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Phenomenal idea! I fully agee! :)

On Sep 27, 2014, at 2:22 AM, Seth Harris <se...@gm...> wrote:

> Hi Thomas et al,
> 
> There was a recent question on the board about missing residues and the possibility of reading SEQRES headers and PyMOL being able to show the missing bits in the sequence view, perhaps with the amino acid letters grayed out to distinguish the gap. I know the reply was "PyMOL doesn't currently" do this, but it seemed to then end "full stop" rather than, "...but it's a fantastic idea". I'd like to second the idea as a great addition! When building structures or viewing and hitting gaps one always has to shuffle off to find the sequence or jump back to see how big the gap is and what type of residues are supposed to be in there. This would put it right there integrated at one's fingertips.
> 
> This also reminds me of something I suggested to you, Thomas, that might fit in here of having a "cartoon dash" rendering (at least for loops if not helices and strands?) such that one could borrow a loop from a homologue or build in a placeholder to provide visual continuity in a model while still clearly indicating the disordered regions, but now in a 3D ray-traced dashed line that follows the cartoon trajectory rather than the usual penciled in job.
> 
> I know in building a new structure I don't often have any SEQRES header in place, but if it offered advantages like this it would be easy enough to install such.
> 
> Thanks,
> Seth
> 
>  
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi Thomas et al,

There was a recent question on the board about missing residues and the
possibility of reading SEQRES headers and PyMOL being able to show the
missing bits in the sequence view, perhaps with the amino acid letters
grayed out to distinguish the gap. I know the reply was "PyMOL doesn't
currently" do this, but it seemed to then end "full stop" rather than,
"...but it's a fantastic idea". I'd like to second the idea as a great
addition! When building structures or viewing and hitting gaps one always
has to shuffle off to find the sequence or jump back to see how big the gap
is and what type of residues are supposed to be in there. This would put it
right there integrated at one's fingertips.

This also reminds me of something I suggested to you, Thomas, that might
fit in here of having a "cartoon dash" rendering (at least for loops if not
helices and strands?) such that one could borrow a loop from a homologue or
build in a placeholder to provide visual continuity in a model while still
clearly indicating the disordered regions, but now in a 3D ray-traced
dashed line that follows the cartoon trajectory rather than the usual
penciled in job.

I know in building a new structure I don't often have any SEQRES header in
place, but if it offered advantages like this it would be easy enough to
install such.

Thanks,
Seth

Goetz,

Thanks your site really helped!  I also figured out that when I installed
in windows it did not have the correct permissions so I had to run it as an
administrator to get the plugin to load properly.

Thanks for all your help.

-Joe

On Fri, Sep 26, 2014 at 4:42 AM, Goetz Parsiegla <
Goe...@un...> wrote:

>  Hello Joseph,
>
> I modified the plugin from Daniel Seeliger to adapt it for the use of
> PyMol under windows. Have a look at the tutorial to install the plugin on
> our web page : http://eipl.cnrs-mrs.fr/bioinformatic.php.
>
> I hope it helps ...
>
> Best regards
> Goetz
>
> Le 25/09/2014 18:49, Joseph Brown a écrit :
>
> Matt thanks for the response.  I did try both of those things you
> suggested.  I am using a windows based system, but it is in the directory.
> I even tried uninstalling it and then re-installing to see if that would
> fix it.  I have also rebooted the computer.  I was hoping it was something
> simple that I was just missing due to a lack of experience.
>
>
> On Thu, Sep 25, 2014 at 12:04 PM, Matthew Baumgartner <mp...@pi...>
> wrote:
>
>>  Hi,
>> Did you try restarting pymol?
>>
>> Also, check your startup directory to see if it was moved there. On unix,
>> it's ~/.pymol/startup/ you should see the autodock.py script there.
>>
>> HTH,
>> Matt
>>
>> On 09/25/2014 11:56 AM, Joseph Brown wrote:
>>
>> I am trying to install the autodock vina plugin for PyMOL.   I go to the
>> plugin tab, manage plugins, install and get a message that it installed but
>> it does not appear under the Plugin tab.  If I go to remove it is showing
>> up as being installed.  Any suggestions would be helpful.
>>
>>  -Joe
>>
>>
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> -------------------------------------------------------------------
> Goetz Parsiegla, PhD, Maître de Conférences Aix-Marseille Université (AMU)
>
> Research :
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> UMR 7282 CNRS et Aix-Marseille Université - Director : Frédéric Carrière
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>
> Teaching :
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>
> Email: Goe...@im...
> -------------------------------------------------------------------
>
>

Dear Steinberg

Thank you very much for the idea

Best Regards
Priyan

On Thu, Sep 25, 2014 at 7:33 PM, H. Adam Steinberg <
h.a...@gm...> wrote:

> This is not as simple as you would like but PyMOL does have the ability to
> manually build in missing atoms. And this feature allows you to manually
> fill in missing sequences. I have used it many times to make a specific
> point, noting that the missing AAs were manually added to the figure.
>
> On Sep 25, 2014, at 8:38 AM, ccp4 pymol <ccp...@gm...> wrote:
>
> Thank you Thomas.
>
> Best Regards
> Priyan
>
> On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder <
> tho...@sc...> wrote:
>
>> Hi Priyan,
>>
>> unfortunately PyMOL doesn't have such functionality to include missing
>> atoms in the sequence viewer, neither does it read SEQRES records.
>>
>> Cheers,
>>   Thomas
>>
>> On 21 Sep 2014, at 23:28, Priyadarshan <ccp...@gm...> wrote:
>> > Hello everyone
>> >
>> >  Many a times we have structures solved with residues missing as no
>> electron density was seen. The complete sequence information is given in
>> the SEQRES section of PDB. Is there a way in which we can identify the
>> missing residues readily when we turn on the sequence feature by may be
>> putting it in small letters or italicized etc. This would be like asking
>> pymol to read sequence from SEQRES section and compare it to sequence from
>> the section where coordinates are.
>> >
>> > I am sorry if such a post/request has already been made but I could not
>> find it. Please suggest/direct.
>> >
>> > Thank you.
>>
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger, Inc.
>>
>>
>
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>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
>

I see. Great help, Thank you.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pi...]
Sent: Thursday, September 25, 2014 3:01 PM
To: Oganesyan, Vaheh; pym...@li...
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 Mouse>Selection Mode>Chains how else one gets into that mode? Just curious.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pi...]
Sent: Thursday, September 25, 2014 2:19 PM
To: pym...@li...<mailto:pym...@li...>
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 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.




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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.

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 
> Mouse>Selection Mode>Chains how else one gets into that mode? Just 
> curious.
>
> /Regards,/
>
> //
>
> /Vaheh/
>
> /8-5851/
>
> *From:*Matthew Baumgartner [mailto:mp...@pi...]
> *Sent:* Thursday, September 25, 2014 2:19 PM
> *To:* pym...@li...
> *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 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.
>
>
>     ------------------------------------------------------------------------------
>
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> To the extent this electronic communication or any of its attachments 
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> is considered by MedImmune to be confidential and proprietary. This 
> communication is expected to be read and/or used only by the 
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> information is considered by MedImmune to be confidential and 
> proprietary. This communication is expected to be read and/or used 
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> Thank you for your cooperation. 

Thanks, really easy, feel very special. By not choosing Mouse>Selection Mode>Chains how else one gets into that mode? Just curious.



Regards,

Vaheh
8-5851

From: Matthew Baumgartner [mailto:mp...@pi...]
Sent: Thursday, September 25, 2014 2:19 PM
To: pym...@li...
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 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.



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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,
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 
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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 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.

Matt thanks for the response.  I did try both of those things you
suggested.  I am using a windows based system, but it is in the directory.
I even tried uninstalling it and then re-installing to see if that would
fix it.  I have also rebooted the computer.  I was hoping it was something
simple that I was just missing due to a lack of experience.


On Thu, Sep 25, 2014 at 12:04 PM, Matthew Baumgartner <mp...@pi...>
wrote:

>  Hi,
> Did you try restarting pymol?
>
> Also, check your startup directory to see if it was moved there. On unix,
> it's ~/.pymol/startup/ you should see the autodock.py script there.
>
> HTH,
> Matt
>
> On 09/25/2014 11:56 AM, Joseph Brown wrote:
>
> I am trying to install the autodock vina plugin for PyMOL.   I go to the
> plugin tab, manage plugins, install and get a message that it installed but
> it does not appear under the Plugin tab.  If I go to remove it is showing
> up as being installed.  Any suggestions would be helpful.
>
>  -Joe
>
>
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>
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Hi,
Did you try restarting pymol?

Also, check your startup directory to see if it was moved there. On 
unix, it's ~/.pymol/startup/ you should see the autodock.py script there.

HTH,
Matt

On 09/25/2014 11:56 AM, Joseph Brown wrote:
> I am trying to install the autodock vina plugin for PyMOL.   I go to 
> the plugin tab, manage plugins, install and get a message that it 
> installed but it does not appear under the Plugin tab.  If I go to 
> remove it is showing up as being installed.  Any suggestions would be 
> helpful.
>
> -Joe
>
>
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>
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I am trying to install the autodock vina plugin for PyMOL.   I go to the
plugin tab, manage plugins, install and get a message that it installed but
it does not appear under the Plugin tab.  If I go to remove it is showing
up as being installed.  Any suggestions would be helpful.

-Joe

This is not as simple as you would like but PyMOL does have the ability to manually build in missing atoms. And this feature allows you to manually fill in missing sequences. I have used it many times to make a specific point, noting that the missing AAs were manually added to the figure.

On Sep 25, 2014, at 8:38 AM, ccp4 pymol <ccp...@gm...> wrote:

> Thank you Thomas.
> 
> Best Regards
> Priyan
> 
> On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder <tho...@sc...> wrote:
> Hi Priyan,
> 
> unfortunately PyMOL doesn't have such functionality to include missing atoms in the sequence viewer, neither does it read SEQRES records.
> 
> Cheers,
>   Thomas
> 
> On 21 Sep 2014, at 23:28, Priyadarshan <ccp...@gm...> wrote:
> > Hello everyone
> >
> >  Many a times we have structures solved with residues missing as no electron density was seen. The complete sequence information is given in the SEQRES section of PDB. Is there a way in which we can identify the missing residues readily when we turn on the sequence feature by may be putting it in small letters or italicized etc. This would be like asking pymol to read sequence from SEQRES section and compare it to sequence from the section where coordinates are.
> >
> > I am sorry if such a post/request has already been made but I could not find it. Please suggest/direct.
> >
> > Thank you.
> 
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
> 
> 
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Thank you Thomas.

Best Regards
Priyan

On Thu, Sep 25, 2014 at 5:23 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Priyan,
>
> unfortunately PyMOL doesn't have such functionality to include missing
> atoms in the sequence viewer, neither does it read SEQRES records.
>
> Cheers,
>   Thomas
>
> On 21 Sep 2014, at 23:28, Priyadarshan <ccp...@gm...> wrote:
> > Hello everyone
> >
> >  Many a times we have structures solved with residues missing as no
> electron density was seen. The complete sequence information is given in
> the SEQRES section of PDB. Is there a way in which we can identify the
> missing residues readily when we turn on the sequence feature by may be
> putting it in small letters or italicized etc. This would be like asking
> pymol to read sequence from SEQRES section and compare it to sequence from
> the section where coordinates are.
> >
> > I am sorry if such a post/request has already been made but I could not
> find it. Please suggest/direct.
> >
> > Thank you.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>

Dear all,

We released Incentive PyMOL 1.7.2.2 which fixes the mouse wheel issue on Windows and broken putty cartoon representation. Installers can be downloaded from http://pymol.org/download as usual. Open-Source PyMOL was not affected by those issues.

Cheers,
 The PyMOL Team at Schrödinger

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Gian,

thank you very much! The idea to associate side chain dynamics with the its
B-factor is very attractive for me! However I'm  not sure how to make
ensemble-like view of the side chains in accordance to its B-factors - in
fact as the end of the day (night?!) I'd like to obtain representation of
the conformational distribution of the selected side-chain based on
simulation data  projected on the receptors cartoon diagram - it should
looks like the alignment of the whole ensemble (in transparency view) onto
the averaged (solid-view) structure) not just a colour specter. If you know
how to do it in PyMol based on one pdb please let me know.

James

2014-09-22 10:16 GMT+02:00 Gianluca Santoni <gia...@ib...>:

> I did something similar once.
> For mainchains, you can at first calculate B-factors (similar as in
> crystallography) from md simulation, that would be added to your starting
> (or final, i don't remember) structure.
> then use the cartoon-putty representation to visualize your structure.
>
> You could try using something similar, like for exemple a color spectrum
> of b-factors,for the sidechains.
> In this case don't forget to exclude the N-ter and C-ter from your
> calculations, or they will completly flatten your spectrum.
>
> Cheers,
> Gian
>
>
>
>
> On 9/21/14 9:19 AM, James Starlight wrote:
>
>> Dear Pymol users!
>>
>>
>> In this topic I've decide to put all questions regarding visualisation.
>>
>> This time I'm very intresting whether it possible to add some effect of
>> the  "flexebility" or "ensemble-like dynamics" on the selected elements
>> (e.g selected side-chains to convey a sense of its flexibility like in
>> the molecular dynamics simulation) by introdycing of some filter on this
>> part like some kind of bluring). Of cource I can do it by taking several
>> aligned snapshots from MD and load it in the Pymol but here I wounder if
>> its also possible do from one pdb structure.
>>
>> Thanks for help,
>>
>> James
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Slashdot TV.  Video for Nerds.  Stuff that Matters.
>> http://pubads.g.doubleclick.net/gampad/clk?id=160591471&
>> iu=/4140/ostg.clktrk
>>
>>
>>
>> _______________________________________________
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>
> --
> Gianluca Santoni,
> Dynamop Group
> Institut de Biologie Structurale
> 6 rue Jules Horowitz
> 38027 Grenoble Cedex 1
> France
> _________________________________________________________
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>

Hi Priyan,

unfortunately PyMOL doesn't have such functionality to include missing atoms in the sequence viewer, neither does it read SEQRES records.

Cheers,
  Thomas

On 21 Sep 2014, at 23:28, Priyadarshan <ccp...@gm...> wrote:
> Hello everyone
> 
>  Many a times we have structures solved with residues missing as no electron density was seen. The complete sequence information is given in the SEQRES section of PDB. Is there a way in which we can identify the missing residues readily when we turn on the sequence feature by may be putting it in small letters or italicized etc. This would be like asking pymol to read sequence from SEQRES section and compare it to sequence from the section where coordinates are.
> 
> I am sorry if such a post/request has already been made but I could not find it. Please suggest/direct.
> 
> Thank you.

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

Hi Lei,

those tunnel atoms all have the same name, thus the selection is not unique (not a *single* atom but multiple). For a script like that, it's best to select by atom index.

cmd.iterate("tunnel", 'stored.centers.append("(%s`%d)" % (model, index))')

Cheers,
  Thomas

On 24 Sep 2014, at 23:27, Lei Chen <rai...@gm...> wrote:

> Hi,
> I still have trouble. I am not sure if it is because the tunnel pdb is
> not standard. (it's an output file from another software called
> CAVER.)
> My tunnel pdb looks like:
> ATOM      1  H   FIL T 537     -44.636 -88.973  27.394        5.02
> ATOM      2  H   FIL T 537     -44.620 -88.474  27.363        4.90
> CONECT    1    2
> ATOM      3  H   FIL T 537     -44.574 -87.982  27.350        4.82
> CONECT    2    3
> ATOM      4  H   FIL T 537     -44.568 -87.484  27.315        4.78
> CONECT    3    4
> ATOM      5  H   FIL T 537     -44.561 -86.985  27.279        4.78
> CONECT    4    5
> ATOM      6  H   FIL T 537     -44.554 -86.486  27.243        4.82
> CONECT    5    6
> My codes：
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> stored.centers = []
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
> (model, segi, chain, resn, resi, name))')
> for s in stored.centers:
> print s
> angle = cmd.get_angle(start_point, end_point, s)
> print "%s: %3.2f" % (s, angle)
> cmd.extend( "vertical_distance", vertical_distance );
> 
> output:
> /tunnel//T/FIL`537/H
> GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
> 
> If I use cmd.angle, I get:
> cmd-Error: The 'pk3' selection is undefined.
> 
> 
> On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
>> Hi Lei -
>> 
>> The `get_angle` command needs an atom selection for your “tunnel" atoms,
>> which, like the B-factor as Matt mentioned, you can also get using
>> `iterate`:
>> 
>> ###
>> 
>> # create a list
>> stored.centers = []
>> 
>> # get the macro selection string for each atom in tunnel
>> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
>> segi, chain, resn, resi, name))')
>> 
>> # loop through the list of centers and print each angle
>> for s in stored.centers:
>>    angle = cmd.get_angle('start_point', 'end_point', s)
>>    print "%s: %3.2f" % (s, angle)
>> 
>> ###
>> 
>> Hope that helps.
>> 
>> Cheers,
>> Jared
>> 
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>> 
>> 
>> 
>> 
>> 
>> 
>> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>> 
>> Hi,
>> you can just use the 'angle' command.
>> 
>> cmd.angle('angle1', 'start_point', 'end_point', a)
>> 
>> To print the b-factor you can use the iterate command
>> (http://www.pymolwiki.org/index.php/Iterate)
>> cmd.iterate('(a)', 'print b')
>> 
>> HTH,
>> Matt Baumgartner
>> 
>> 
>> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>> 
>> Hi all,
>> I generate two pseudoatoms "start_point" and "end_point" by
>> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
>> in one chain.
>> I want to measure the angle from each atoms in "tunnel" to "end_point"
>> to "start_point". at the same time, I want to print the B-factor of
>> atoms in "tunnel".
>> To measure the angle, I programmed like this，but it doesn't work.
>> I guess it's because get_angle function needs some particular variable
>> format.
>> By the way, how can I print the b factor of atom?
>> Thanks,
>> Lei
>> 
>> from pymol import cmd, stored
>> def vertical_distance( start_point, end_point, tunnel ):
>> centers = cmd.get_model(tunnel,1)
>> for a in centers.atom:
>> angle= cmd.get_angle(start_point, end_point,a)
>> print angle
>> return (start_point, end_point, tunnel)
>> cmd.extend( "vertical_distance", vertical_distance );

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.

>From the previous task it's OK now

small question about pymol :)

how to prevent removing TER record after editing of the structure using
pymol

e.g I used the following command to load protein-ligand complex (where
there is TER between protein and ligand) and remove hydrogens and than save
back it to new pdb where there were no more TER records

pymol $pdb -c -q -d "remove hydrogens; save
${temp}/${filenamenoextention}_noH.pdb, ${filenamenoextention}" >
${temp}/xz.log

and smth about shell informatics:

how to scan specified string in pdb corresponded to the last line of the
ligand (which is the RES in pdb) and add after this line TER record. E.g
the basic idea:

grep -v "ATOM.*\(RES\|MOL\)" $pdb | # smth with sed  > pdb_with_TER.pdb

now I only would like to know proper reg expression in my case for GREP and
command for SED

James

2014-09-24 11:06 GMT+02:00 James Starlight <jms...@gm...>:

> some additional question about shell scripting (copied from the amber
> forum because I'd like to find as more sollutions of this problem as
> possible):
>
>
> I wounder about possibilities to define disulphide bond between any pairs
> of SG atoms of CYX residues using amber's tleap scripts in some automatic
> fashion.
>
> In my case I use tleap as part of some big script to process many
> models.pdb for further md simulation. Each of the model consist of pair of
> CYX residues (assigned by pdb2pqr) in different positions of its sequence.
> So in script I need firstly to know the number of position for each of CYX
> residues of each model and than to fill this numbers to the tleap input
> files for each model
>
> in bash for one model it will be look like:
>
> #some command to scan the sequence of model.pdb and define pair of its CYX
> residues within it as the k ans i variables
>   printf "source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
> protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
> protein protein.parm7 protein.inpcrd\nquit" > ./tleap.in
>
>
> so my task is only to find some command which will scan model and find
> positions of the CYX within its sequence which could be put to the tleap as
> two digits. It will be better to find those 2 digits using pdb as an input
> and some unix command like sed or grep to find positions
>
> I will be very thankful for any suggestions!
>
> James
>
>
>
> 2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar <ts...@gm...>:
>
>>
>> csplit -b "%03d.pdb" test.pdbqt /^MODEL/ {0} > somelog.log
>>>
>>
>> man csplit:
>>
>> csplit -f blabla -b "%03d.pdb" test.pdbqt /^MODEL/ {1}
>>
>> But you want only the first frame anyway, so no real use for csplit...
>>
>> sed /^ENDMDL/q my_docking.pdb | grep -v "^ROOT\|^ENDROOT\|^TORSDOF
>>> 0\|^MODEL\|^REMARK" |  sed -e 's/^ENDMDL/TER/g' > firstmodel.pdb
>>>
>>
>> sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
>> 0\|MODEL\|REMARK\)/d' my_docking.pdb > firstmodel.pdb
>>
>> ... shorter and one process running in stead of 3.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>

It seems due to the fact that youre selection s is not a valid selection.
Try to simplify it by simply giving
(model, chain, resi, name)
It should be enough to define a single atom, as required by get_angle



On 9/25/14 5:27 AM, Lei Chen wrote:
> Hi,
> I still have trouble. I am not sure if it is because the tunnel pdb is
> not standard. (it's an output file from another software called
> CAVER.)
> My tunnel pdb looks like:
> ATOM      1  H   FIL T 537     -44.636 -88.973  27.394        5.02
> ATOM      2  H   FIL T 537     -44.620 -88.474  27.363        4.90
> CONECT    1    2
> ATOM      3  H   FIL T 537     -44.574 -87.982  27.350        4.82
> CONECT    2    3
> ATOM      4  H   FIL T 537     -44.568 -87.484  27.315        4.78
> CONECT    3    4
> ATOM      5  H   FIL T 537     -44.561 -86.985  27.279        4.78
> CONECT    4    5
> ATOM      6  H   FIL T 537     -44.554 -86.486  27.243        4.82
> CONECT    5    6
> My codes：
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> stored.centers = []
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
> (model, segi, chain, resn, resi, name))')
> for s in stored.centers:
> print s
> angle = cmd.get_angle(start_point, end_point, s)
> print "%s: %3.2f" % (s, angle)
> cmd.extend( "vertical_distance", vertical_distance );
>
> output:
> /tunnel//T/FIL`537/H
> GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
>
> If I use cmd.angle, I get:
> cmd-Error: The 'pk3' selection is undefined.
>
>
> On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
>> Hi Lei -
>>
>> The `get_angle` command needs an atom selection for your “tunnel" atoms,
>> which, like the B-factor as Matt mentioned, you can also get using
>> `iterate`:
>>
>> ###
>>
>> # create a list
>> stored.centers = []
>>
>> # get the macro selection string for each atom in tunnel
>> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
>> segi, chain, resn, resi, name))')
>>
>> # loop through the list of centers and print each angle
>> for s in stored.centers:
>>      angle = cmd.get_angle('start_point', 'end_point', s)
>>      print "%s: %3.2f" % (s, angle)
>>
>> ###
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>>
>>
>>
>> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>>
>> Hi,
>> you can just use the 'angle' command.
>>
>> cmd.angle('angle1', 'start_point', 'end_point', a)
>>
>> To print the b-factor you can use the iterate command
>> (http://www.pymolwiki.org/index.php/Iterate)
>> cmd.iterate('(a)', 'print b')
>>
>> HTH,
>> Matt Baumgartner
>>
>>
>> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>>
>> Hi all,
>> I generate two pseudoatoms "start_point" and "end_point" by
>> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
>> in one chain.
>> I want to measure the angle from each atoms in "tunnel" to "end_point"
>> to "start_point". at the same time, I want to print the B-factor of
>> atoms in "tunnel".
>> To measure the angle, I programmed like this，but it doesn't work.
>> I guess it's because get_angle function needs some particular variable
>> format.
>> By the way, how can I print the b factor of atom?
>> Thanks,
>> Lei
>>
>> from pymol import cmd, stored
>> def vertical_distance( start_point, end_point, tunnel ):
>> centers = cmd.get_model(tunnel,1)
>> for a in centers.atom:
>> angle= cmd.get_angle(start_point, end_point,a)
>> print angle
>> return (start_point, end_point, tunnel)
>> cmd.extend( "vertical_distance", vertical_distance );
>>
>>
>>
>>
>>
>>
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-- 
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz							
38027 Grenoble Cedex 1						
France	
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

Hi,
I still have trouble. I am not sure if it is because the tunnel pdb is
not standard. (it's an output file from another software called
CAVER.)
My tunnel pdb looks like:
ATOM      1  H   FIL T 537     -44.636 -88.973  27.394        5.02
ATOM      2  H   FIL T 537     -44.620 -88.474  27.363        4.90
CONECT    1    2
ATOM      3  H   FIL T 537     -44.574 -87.982  27.350        4.82
CONECT    2    3
ATOM      4  H   FIL T 537     -44.568 -87.484  27.315        4.78
CONECT    3    4
ATOM      5  H   FIL T 537     -44.561 -86.985  27.279        4.78
CONECT    4    5
ATOM      6  H   FIL T 537     -44.554 -86.486  27.243        4.82
CONECT    5    6
My codes：
from pymol import cmd, stored
def vertical_distance( start_point, end_point, tunnel ):
stored.centers = []
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
(model, segi, chain, resn, resi, name))')
for s in stored.centers:
print s
angle = cmd.get_angle(start_point, end_point, s)
print "%s: %3.2f" % (s, angle)
cmd.extend( "vertical_distance", vertical_distance );

output:
/tunnel//T/FIL`537/H
GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.

If I use cmd.angle, I get:
cmd-Error: The 'pk3' selection is undefined.


On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
> Hi Lei -
>
> The `get_angle` command needs an atom selection for your “tunnel" atoms,
> which, like the B-factor as Matt mentioned, you can also get using
> `iterate`:
>
> ###
>
> # create a list
> stored.centers = []
>
> # get the macro selection string for each atom in tunnel
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
> segi, chain, resn, resi, name))')
>
> # loop through the list of centers and print each angle
> for s in stored.centers:
>     angle = cmd.get_angle('start_point', 'end_point', s)
>     print "%s: %3.2f" % (s, angle)
>
> ###
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>
> Hi,
> you can just use the 'angle' command.
>
> cmd.angle('angle1', 'start_point', 'end_point', a)
>
> To print the b-factor you can use the iterate command
> (http://www.pymolwiki.org/index.php/Iterate)
> cmd.iterate('(a)', 'print b')
>
> HTH,
> Matt Baumgartner
>
>
> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>
> Hi all,
> I generate two pseudoatoms "start_point" and "end_point" by
> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
> in one chain.
> I want to measure the angle from each atoms in "tunnel" to "end_point"
> to "start_point". at the same time, I want to print the B-factor of
> atoms in "tunnel".
> To measure the angle, I programmed like this，but it doesn't work.
> I guess it's because get_angle function needs some particular variable
> format.
> By the way, how can I print the b factor of atom?
> Thanks,
> Lei
>
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> centers = cmd.get_model(tunnel,1)
> for a in centers.atom:
> angle= cmd.get_angle(start_point, end_point,a)
> print angle
> return (start_point, end_point, tunnel)
> cmd.extend( "vertical_distance", vertical_distance );
>
>
>
>
>
>
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>
>

Hi Lei -

The `get_angle` command needs an atom selection for your “tunnel" atoms, which, like the B-factor as Matt mentioned, you can also get using `iterate`:

###

# create a list
stored.centers = []

# get the macro selection string for each atom in tunnel
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model, segi, chain, resn, resi, name))')

# loop through the list of centers and print each angle
for s in stored.centers:
    angle = cmd.get_angle('start_point', 'end_point', s)
    print "%s: %3.2f" % (s, angle)

###

Hope that helps.

Cheers,
Jared

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






On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...<mailto:mp...@pi...>> wrote:

Hi,
you can just use the 'angle' command.

cmd.angle('angle1', 'start_point', 'end_point', a)

To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')

HTH,
Matt Baumgartner

On 09/24/2014 06:35 PM, rainfieldcn wrote:
Hi all,
I generate two pseudoatoms "start_point" and "end_point" by
center_of_mass.py. I load an object "tunnel" which has a sets of atoms
in one chain.
I want to measure the angle from each atoms in "tunnel" to "end_point"
to "start_point". at the same time, I want to print the B-factor of
atoms in "tunnel".
To measure the angle, I programmed like this，but it doesn't work.
I guess it's because get_angle function needs some particular variable
format.
By the way, how can I print the b factor of atom?
Thanks,
Lei

from pymol import cmd, stored
def vertical_distance( start_point, end_point, tunnel ):
centers = cmd.get_model(tunnel,1)
for a in centers.atom:
angle= cmd.get_angle(start_point, end_point,a)
print angle
return (start_point, end_point, tunnel)
cmd.extend( "vertical_distance", vertical_distance );






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Hi,
you can just use the 'angle' command.

cmd.angle('angle1', 'start_point', 'end_point', a)

To print the b-factor you can use the iterate command 
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')

HTH,
Matt Baumgartner

On 09/24/2014 06:35 PM, rainfieldcn wrote:
> Hi all,
> I generate two pseudoatoms "start_point" and "end_point" by
> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
> in one chain.
> I want to measure the angle from each atoms in "tunnel" to "end_point"
> to "start_point". at the same time, I want to print the B-factor of
> atoms in "tunnel".
> To measure the angle, I programmed like this，but it doesn't work.
> I guess it's because get_angle function needs some particular variable
> format.
> By the way, how can I print the b factor of atom?
> Thanks,
> Lei
>
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> centers = cmd.get_model(tunnel,1)
> for a in centers.atom:
> angle= cmd.get_angle(start_point, end_point,a)
> print angle
> return (start_point, end_point, tunnel)
> cmd.extend( "vertical_distance", vertical_distance );
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
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