pymol-users Mailing List for PyMOL Molecular Graphics System

Not sure who on the forum would know the answer to this question but I am sure someone will. I used many of the python scripts in pymol for my MS thesis, including the get_distance script that I also made  modifications to. I mentioned all these scritps in my thesis and of course cited the PyMol papers and sourceforge. One of my committee members wants me to have an appendix in my thesis of the get_distance script I modified. My question is, are there any copyright issues with this? Should I just  cite PyMol again and in the appendix on the modified script make sure to note what modifications I did versus what was there originally?  Thanks.

Hi CY and Jared,

Jared, CY is actually right that MacPyMOL won't run if you're not logged in to the Mac desktop. I assume in your test, you were logged in on the imac (WindowServer running for your user).

For this use case, we now provide the "Mac alternative X11-only build" (current: "pymol-v1.7.6.1-Darwin-x86_64.tar.gz") which is built like on a unix system, linked to X11 graphics (requires XQuartz) instead of OSX Cocoa. This version works without a WindowsServer in command line "-c -q" mode. CY, please give that version a try.

Cheers,
  Thomas

On 29 May 2015, at 12:35, Sampson, Jared <Jar...@ny...> wrote:

> Hi CY - 
> 
> If you're using the -c flag, you shouldn't need a windowing system at all.  The following works for me between a MacBook Air and an iMac, both running 10.9.5, with MacPyMOL 1.7.6.0 installed on the iMac.
> 
> ### begin shell ###
> (macbook-air)~ › ssh jared@imac
> Password:
> Last login: Fri May 29 10:37:12 2015 from macbook-air
> (imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd "fetch 3opl, async=0; save tmp.png"
> PyMOL>fetch 3opl, async=0; save tmp.png
> HEADER    HYDROLASE                               01-SEP-10   3OPL
> TITLE     ESBL R164H MUTANT SHV-1 BETA-LACTAMASE
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: BETA-LACTAMASE SHV-1;
> COMPND   3 CHAIN: A;
> COMPND   4 SYNONYM: PIT-2;
> COMPND   5 EC: 3.5.2.6;
> COMPND   6 ENGINEERED: YES;
> COMPND   7 MUTATION: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  Symmetry: Found 4 symmetry operators.
>  CmdLoad: "./3opl.pdb" loaded as "3opl".
>  Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.).
>  ScenePNG: wrote 640x480 pixel image to file "tmp.png".
> (imac)~ › exit
> logout
> Connection to imac closed.
> (macbook-air)~ › 
> ### end shell ###
> 
> The file ~/tmp.png is created on the iMac.  I also used -k to prevent PyMOL from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands.  If you're running a .pml script, you don't need to include -d, just the path to the script (which must be on the remote machine).  As you noted, when it runs I see the MacPyMOL application icon pop into the Dock on the iMac and then disappear as soon as the script finishes.
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
> 
> 
> On May 28, 2015, at 11:28 AM, Yu Chen <ch...@um...> wrote:
> 
>> Hello, 
>> 
>> I am trying to run MacPyMOL in command line mode with "-c -q" option. While directly logged in to the computer, it works. But if I ssh into the computer (even with X11 forwarding enabled), it fails with some errors about connecting to WindowServer  And I can tell it actually tried to launch the GUI very briefly, then returned to the command line to process the scripts. Is this right? Can I run it remotely on another computer just from pure command line. 
>> 
>> Thanks. 
>> 
>> CY


-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi CY -

If you're using the -c flag, you shouldn't need a windowing system at all.  The following works for me between a MacBook Air and an iMac, both running 10.9.5, with MacPyMOL 1.7.6.0 installed on the iMac.

### begin shell ###
(macbook-air)~ › ssh jared@imac
Password:
Last login: Fri May 29 10:37:12 2015 from macbook-air
(imac)~ › /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -cqkd "fetch 3opl, async=0; save tmp.png"
PyMOL>fetch 3opl, async=0; save tmp.png
HEADER    HYDROLASE                               01-SEP-10   3OPL
TITLE     ESBL R164H MUTANT SHV-1 BETA-LACTAMASE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: BETA-LACTAMASE SHV-1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: PIT-2;
COMPND   5 EC: 3.5.2.6;
COMPND   6 ENGINEERED: YES;
COMPND   7 MUTATION: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 4 symmetry operators.
 CmdLoad: "./3opl.pdb" loaded as "3opl".
 Ray: render time: 0.99 sec. = 3622.2 frames/hour (0.99 sec. accum.).
 ScenePNG: wrote 640x480 pixel image to file "tmp.png".
(imac)~ › exit
logout
Connection to imac closed.
(macbook-air)~ ›
### end shell ###

The file ~/tmp.png is created on the iMac.  I also used -k to prevent PyMOL from reading my ~/.pymolrc; and -d to pass the string of PyMOL commands.  If you're running a .pml script, you don't need to include -d, just the path to the script (which must be on the remote machine).  As you noted, when it runs I see the MacPyMOL application icon pop into the Dock on the iMac and then disappear as soon as the script finishes.

Hope that helps.

Cheers,
Jared

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






On May 28, 2015, at 11:28 AM, Yu Chen <ch...@um...<mailto:ch...@um...>> wrote:

Hello,

I am trying to run MacPyMOL in command line mode with "-c -q" option. While directly logged in to the computer, it works. But if I ssh into the computer (even with X11 forwarding enabled), it fails with some errors about connecting to WindowServer  And I can tell it actually tried to launch the GUI very briefly, then returned to the command line to process the scripts. Is this right? Can I run it remotely on another computer just from pure command line.

Thanks.

CY
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Hi Justin,

the logo that Brenton is referring to isn't included in the Open-Source repo or tarballs. It's only used with Mobile PyMOL and Incentive PyMOL.

Cheers,
  Thomas

On 28 May 2015, at 14:16, Justin Lecher <j.l...@fz...> wrote:

> On 28/05/15 19:26, Thomas Holder wrote:
>> Hi Brenton,
>> 
>> the logo is currently not available under any license, it's a trademark of Schrödinger. This means you can't upload it on Wikimedia Commons.
>> 
>> Cheers,
>>  Thomas
>> 
> 
> Hi Thomas,
> 
> That brings up an interesting question about the usage in distro
> packages. At least Fedora and Gentoo are using it separately from the
> svn repo.
> 
> Cheers,
> Justin

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

On 28/05/15 19:26, Thomas Holder wrote:
> Hi Brenton,
> 
> the logo is currently not available under any license, it's a trademark of Schrödinger. This means you can't upload it on Wikimedia Commons.
> 
> Cheers,
>   Thomas
> 

Hi Thomas,

That brings up an interesting question about the usage in distro
packages. At least Fedora and Gentoo are using it separately from the
svn repo.

Cheers,
Justin

Hi Brenton,

the logo is currently not available under any license, it's a trademark of Schrödinger. This means you can't upload it on Wikimedia Commons.

Cheers,
  Thomas

On 28 May 2015, at 08:32, Brenton Horne <bre...@ym...> wrote:

> Hi, 
> 
> I would like to know the legal licensing of PyMOL's logo (i.e., this one), as I would like to upload it to Wikimedia Commons. 
> 
> Thanks for your time,
> Brenton

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello,

I am trying to run MacPyMOL in command line mode with "-c -q" option. While
directly logged in to the computer, it works. But if I ssh into the
computer (even with X11 forwarding enabled), it fails with some errors
about connecting to WindowServer  And I can tell it actually tried to
launch the GUI very briefly, then returned to the command line to process
the scripts. Is this right? Can I run it remotely on another computer just
from pure command line.

Thanks.

CY

Hi Vaheh,

I can't reproduce the font color problem. What operating system do you use and what kind of graphics card? Do you set any settings (e.g. in your pymolrc)? How do you change the background color (menu, command, setting)?

I can reproduce the non-instant appearing of the sequence viewer when enabling it from the upper menu. We'll fix that. As a workaround: If you use the "S" button in the lower right corner, the sequence shows instantly.

Cheers,
  Thomas

On 28 May 2015, at 08:55, Oganesyan, Vaheh <Oga...@Me...> wrote:

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

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Thomas,

You're absolutely right. I had completely forgotten the find_pairs
function!  Thanks for the clarification.

Cheers,
  Osvaldo.


On Thu, May 28, 2015 at 10:17 AM, Thomas Holder <
tho...@sc...> wrote:

> Hi Osvaldo,
>
> your solution can be simplified if you use cmd.find_pairs:
>
> http://pymolwiki.org/index.php/find_pairs
>
> Cheers,
>   Thomas
>
> On 28 May 2015, at 09:06, Osvaldo Martin <alo...@gm...> wrote:
>
> > Hi Tobias,
> >
> > One possible solution will be to run the following code.
> >
> > import pymol
> > from pymol import cmd, stored
> >
> > stored.pd = []
> > stored.pairs = []
> >
> > cmd.iterate('name pd', 'stored.pd.append(index)')
> >
> > for i in stored.pd:
> >     cmd.iterate('name si within 2.5 of index %s' % i,
> 'stored.pairs.append((%s, index))' % i)
> >
> > print stored.pairs
> >
> >
> > If you run the above code you will obtain a list of tuples, each tuple
> contains the indexes of the pairs Pd-Si atoms (fulfilling the "within 2.5
> A" criteria).  Then you should iterate over "stored.pairs"  to create the
> bonds between the atoms in each pair. Something like this:
> >
> > for pair in stored.pairs:
> >     cmd.bond('index %s' % pair[0], 'index %s' % pair[1])
> >
> >
> > Cheers,
> > Osvaldo.
> >
> > On Thu, May 28, 2015 at 7:37 AM, Tobias Martin <ma...@ch...>
> wrote:
> > I want to create bonds between e.g. all Pd atoms and all
> > Si atoms, but only within a specified cutoff radius.
> >
> >      bond (n. pd), (n. si) within 2.5 of (n. pd)
> >
> > creates all possible bonds between all Pd atoms and all Si
> > atoms near enough to any Pd atom. This yields a weired
> > structure with very long, unwanted bonds.
> > I tried to iterate over the first selection, to draw only
> > bonds between an Pd atom and Si atoms which are within
> > range to that Pd atom like
> >
> >    iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
> > ID)
> >
> > but get an syntax error. Is it possible to create bonds
> > within an iteration?
> >
> > Best regards,
> > tmartin
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Osvaldo,

your solution can be simplified if you use cmd.find_pairs:

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

Cheers,
  Thomas

On 28 May 2015, at 09:06, Osvaldo Martin <alo...@gm...> wrote:

> Hi Tobias,
> 
> One possible solution will be to run the following code.
> 
> import pymol
> from pymol import cmd, stored
> 
> stored.pd = []
> stored.pairs = []
> 
> cmd.iterate('name pd', 'stored.pd.append(index)')
> 
> for i in stored.pd: 
>     cmd.iterate('name si within 2.5 of index %s' % i, 'stored.pairs.append((%s, index))' % i)
>     
> print stored.pairs
> 
> 
> If you run the above code you will obtain a list of tuples, each tuple contains the indexes of the pairs Pd-Si atoms (fulfilling the "within 2.5 A" criteria).  Then you should iterate over "stored.pairs"  to create the bonds between the atoms in each pair. Something like this:
> 
> for pair in stored.pairs:
>     cmd.bond('index %s' % pair[0], 'index %s' % pair[1])
> 
> 
> Cheers,
> Osvaldo.
> 
> On Thu, May 28, 2015 at 7:37 AM, Tobias Martin <ma...@ch...> wrote:
> I want to create bonds between e.g. all Pd atoms and all
> Si atoms, but only within a specified cutoff radius.
> 
>      bond (n. pd), (n. si) within 2.5 of (n. pd)
> 
> creates all possible bonds between all Pd atoms and all Si
> atoms near enough to any Pd atom. This yields a weired
> structure with very long, unwanted bonds.
> I tried to iterate over the first selection, to draw only
> bonds between an Pd atom and Si atoms which are within
> range to that Pd atom like
> 
>    iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
> ID)
> 
> but get an syntax error. Is it possible to create bonds
> within an iteration?
> 
> Best regards,
> tmartin

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear PyMOL developers,

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

Thank you.
Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com

To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by 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 Tobias,

One possible solution will be to run the following code.

import pymol
from pymol import cmd, stored

stored.pd = []
stored.pairs = []

cmd.iterate('name pd', 'stored.pd.append(index)')

for i in stored.pd:
    cmd.iterate('name si within 2.5 of index %s' % i,
'stored.pairs.append((%s, index))' % i)

print stored.pairs


If you run the above code you will obtain a list of tuples, each tuple
contains the indexes of the pairs Pd-Si atoms (fulfilling the "within 2.5
A" criteria).  Then you should iterate over "stored.pairs"  to create the
bonds between the atoms in each pair. Something like this:

for pair in stored.pairs:
    cmd.bond('index %s' % pair[0], 'index %s' % pair[1])


Cheers,
Osvaldo.

On Thu, May 28, 2015 at 7:37 AM, Tobias Martin <ma...@ch...>
wrote:

> I want to create bonds between e.g. all Pd atoms and all
> Si atoms, but only within a specified cutoff radius.
>
>      bond (n. pd), (n. si) within 2.5 of (n. pd)
>
> creates all possible bonds between all Pd atoms and all Si
> atoms near enough to any Pd atom. This yields a weired
> structure with very long, unwanted bonds.
> I tried to iterate over the first selection, to draw only
> bonds between an Pd atom and Si atoms which are within
> range to that Pd atom like
>
>    iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
> ID)
>
> but get an syntax error. Is it possible to create bonds
> within an iteration?
>
> Best regards,
> tmartin
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi,

I would like to know the legal licensing of PyMOL's logo (i.e., this one 
<)," rel="nofollow">https://a.fsdn.com/allura/p/pymol/icon>), as I would like to upload it 
to Wikimedia Commons.

Thanks for your time,
Brenton

I want to create bonds between e.g. all Pd atoms and all 
Si atoms, but only within a specified cutoff radius.

     bond (n. pd), (n. si) within 2.5 of (n. pd)

creates all possible bonds between all Pd atoms and all Si 
atoms near enough to any Pd atom. This yields a weired 
structure with very long, unwanted bonds.
I tried to iterate over the first selection, to draw only 
bonds between an Pd atom and Si atoms which are within 
range to that Pd atom like

   iterate (n. pd), bond id ID, (n. si) within 2.5 of (id 
ID)

but get an syntax error. Is it possible to create bonds 
within an iteration?

Best regards,
tmartin

Hi Stéphane,

You could use four pseudoatoms A,B,C,D and have bonds between A/B and C/D.
Then you show them as sticks with A/B in red and C/D in white and let B+C
move from position A to position D.

Alternatively, you can use CGO.

Cheers,

Tsjerk

On Wed, May 27, 2015 at 3:30 PM, ABEL Stephane 175950 <Ste...@ce...>
wrote:

> Hello Pymol users
>
> I want to add a time bar in movie  done with pymol.  Is it possible with a
> pymol script ? If not do you know an alternative (except VMD)?
>
> Thanks in advance
>
> Stéphane
>
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hello Pymol users

I want to add a time bar in movie  done with pymol.  Is it possible with a pymol script ? If not do you know an alternative (except VMD)?

Thanks in advance

Stéphane

Hi Yeping Sun,

In such cases, I usually use light colors with little contrast (white,
wheat, grey, pastel) for the surroundings (on a white background) and
bright, contrasting colors (chartreuse, orange, hotpink, marine) for what
you want to highlight. In addition, you may want to play around with
transparency.

Cheers,

Tsjerk

On Thu, May 21, 2015 at 3:02 AM, sunyeping <sun...@al...> wrote:

>
> Dear all,
>
> In order to emphasize local interactions of several residues within a
> protein, I want to highlight these studied residues but make other residues
> vague and being as background. The setting "set fog, on" doesn't help much
> because the constrast between the studied residues and other residues is
> not strong. Could you help me with this problem? With many thanks.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
>
>
> ------------------------------------------------------------------------------
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> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
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> _______________________________________________
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> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Smith,

The colors are interpolated linearly from the minimum to the maximum value.
'spectrum' allows specifying the extreme values, which is handy when you
need a symmetric scale. If you color green_yellow_blue, you get a green to
yellow gradient from min to (min+max)/2 and a yellow to blue gradient from
there to max. With more colors you'll get more of those intervals.

Hope it helps,

Tsjerk
On May 24, 2015 08:12, "Smith Liu" <smi...@16...> wrote:

> Dear All,
>
> in the pymol default color based on b-factor spectrum, will you please
> tell me how pymol determines the specific color based on the b-factor leve?
> For example, in which scope of b-factors the protein part would be in red
> and in which scope of b-factors the protein part would be in green, yellow
> and blue?
>
> Smith
>
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> 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,
 
in the pymol default color based on b-factor spectrum, will you please tell me how pymol determines the specific color based on the b-factor leve? For example, in which scope of b-factors the protein part would be in red and in which scope of b-factors the protein part would be in green, yellow and blue?
 
Smith

Thank you all for your comments and suggestions .


Regards


On Fri, May 22, 2015 at 1:51 PM, Andreas Warnecke <
4nd...@gm...> wrote:

> Hej,
>
> Just a minor amendment:
>
> the line
>
> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
>
> will treat heteroatoms etc. as part of the area calculation and may thus
> affect the calculation of available surface area.
>
> To ignore heteroatams, remove them before, or change the line to:
>
> for obj in objectlist: cmd.get_area(selection='%s and not hetatm'%obj,
> load_b=1)
>
> In the latter case the area will not be calculated for the heteroatoms (b
> will be b-factor still), but also they will not be considered when
> calculating area for the other atoms.
>
> It is also possible to run both lines sequentually, but usually one
> doesn't care for the heteroatoms.
>
> This is just to avoid potential influences by surrounding waters, or other
> stuff.
>
> Cheers,
>
> Andreas
>
>
>
> On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke <
> 4nd...@gm...> wrote:
>
>> Hej,
>>
>> depends on what you want, single atoms or residues. You can output the
>> available surface are for every atom and then decide which ones are
>> accessible based on your cutoff stringency.
>> Here is some code that will print the info in PyMOL, alternatively you
>> could modify it to print to a file instead, but copy-paste to EXCEL works
>> fine.
>>
>> # Object list
>> objectlist=cmd.get_object_list()
>>
>> # Calculate area:
>> python
>> cmd.set('dot_solvent',1)
>> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
>> # this writes the area into the b-factor field
>> python end
>>
>> # print info
>> print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
>> cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
>>
>> Then, in EXCEL you can use the data (sort/filter) to figure out which
>> atoms are most exposed, or above a set threshold.
>>
>> Hope this is useful,
>>
>> Andreas
>>
>>
>> On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
>> vin...@sc...> wrote:
>>
>>> Hi All
>>>
>>> I have a task in hand where need your suggestions and comments
>>>
>>> Task is to print list of solvent exposed surface amino acids or protein
>>> surface amino acids .
>>>
>>> By searching I had found this script
>>> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>>>
>>> which select the residues on the surface but I dont know
>>>
>>> how to print the residues names as an output ?
>>>
>>> Thanks in advance ...
>>>
>>> --
>>> Please feel free to call me or mail me
>>>
>>> Thanks and Regards
>>>
>>> Vinod.D M.Pharm.
>>> Jr. Applications Scientist
>>> Mobile no:+91-9900090044
>>>
>>> http://www.schrodinger.com/
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> One dashboard for servers and applications across Physical-Virtual-Cloud
>>> Widest out-of-the-box monitoring support with 50+ applications
>>> Performance metrics, stats and reports that give you Actionable Insights
>>> Deep dive visibility with transaction tracing using APM Insight.
>>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>


-- 
Please feel free to call me or mail me

Thanks and Regards

Vinod.D M.Pharm.
Junior Applications Scientist
Mobile no:+91-9900090044

http://www.schrodinger.com/

Hej,

Just a minor amendment:

the line

for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)

will treat heteroatoms etc. as part of the area calculation and may thus
affect the calculation of available surface area.

To ignore heteroatams, remove them before, or change the line to:

for obj in objectlist: cmd.get_area(selection='%s and not hetatm'%obj,
load_b=1)

In the latter case the area will not be calculated for the heteroatoms (b
will be b-factor still), but also they will not be considered when
calculating area for the other atoms.

It is also possible to run both lines sequentually, but usually one doesn't
care for the heteroatoms.

This is just to avoid potential influences by surrounding waters, or other
stuff.

Cheers,

Andreas



On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke <
4nd...@gm...> wrote:

> Hej,
>
> depends on what you want, single atoms or residues. You can output the
> available surface are for every atom and then decide which ones are
> accessible based on your cutoff stringency.
> Here is some code that will print the info in PyMOL, alternatively you
> could modify it to print to a file instead, but copy-paste to EXCEL works
> fine.
>
> # Object list
> objectlist=cmd.get_object_list()
>
> # Calculate area:
> python
> cmd.set('dot_solvent',1)
> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
> # this writes the area into the b-factor field
> python end
>
> # print info
> print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
> cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
>
> Then, in EXCEL you can use the data (sort/filter) to figure out which
> atoms are most exposed, or above a set threshold.
>
> Hope this is useful,
>
> Andreas
>
>
> On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
> vin...@sc...> wrote:
>
>> Hi All
>>
>> I have a task in hand where need your suggestions and comments
>>
>> Task is to print list of solvent exposed surface amino acids or protein
>> surface amino acids .
>>
>> By searching I had found this script
>> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>>
>> which select the residues on the surface but I dont know
>>
>> how to print the residues names as an output ?
>>
>> Thanks in advance ...
>>
>> --
>> Please feel free to call me or mail me
>>
>> Thanks and Regards
>>
>> Vinod.D M.Pharm.
>> Jr. Applications Scientist
>> Mobile no:+91-9900090044
>>
>> http://www.schrodinger.com/
>>
>>
>>
>> ------------------------------------------------------------------------------
>> One dashboard for servers and applications across Physical-Virtual-Cloud
>> Widest out-of-the-box monitoring support with 50+ applications
>> Performance metrics, stats and reports that give you Actionable Insights
>> Deep dive visibility with transaction tracing using APM Insight.
>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Hej,

depends on what you want, single atoms or residues. You can output the
available surface are for every atom and then decide which ones are
accessible based on your cutoff stringency.
Here is some code that will print the info in PyMOL, alternatively you
could modify it to print to a file instead, but copy-paste to EXCEL works
fine.

# Object list
objectlist=cmd.get_object_list()

# Calculate area:
python
cmd.set('dot_solvent',1)
for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
# this writes the area into the b-factor field
python end

# print info
print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')

Then, in EXCEL you can use the data (sort/filter) to figure out which atoms
are most exposed, or above a set threshold.

Hope this is useful,

Andreas


On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
vin...@sc...> wrote:

> Hi All
>
> I have a task in hand where need your suggestions and comments
>
> Task is to print list of solvent exposed surface amino acids or protein
> surface amino acids .
>
> By searching I had found this script
> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>
> which select the residues on the surface but I dont know
>
> how to print the residues names as an output ?
>
> Thanks in advance ...
>
> --
> Please feel free to call me or mail me
>
> Thanks and Regards
>
> Vinod.D M.Pharm.
> Jr. Applications Scientist
> Mobile no:+91-9900090044
>
> http://www.schrodinger.com/
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Vinod

The exposed residues are stored in the selection “exposed_res_02”. You can
iterate <" rel="nofollow">http://www.pymolwiki.org/index.php/Iterate> this selection to get
several properties like the residues names, for example the command:

iterate exposed_res_02, resn

will return the name of the residues, and the command

iterate exposed_res_02, resn, resi

will return the name and the residue number.

Cheers,
Osvaldo.

On Thu, May 21, 2015 at 7:03 AM, Vinod Devaraji <
vin...@sc...> wrote:

Hi All
>
> I have a task in hand where need your suggestions and comments
>
> Task is to print list of solvent exposed surface amino acids or protein
> surface amino acids .
>
> By searching I had found this script
> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>
> which select the residues on the surface but I dont know
>
> how to print the residues names as an output ?
>
> Thanks in advance ...
>
> --
> Please feel free to call me or mail me
>
> Thanks and Regards
>
> Vinod.D M.Pharm.
> Jr. Applications Scientist
> Mobile no:+91-9900090044
>
> http://www.schrodinger.com/
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
​

Hi All

I have a task in hand where need your suggestions and comments

Task is to print list of solvent exposed surface amino acids or protein
surface amino acids .

By searching I had found this script
http://www.pymolwiki.org/index.php/FindSurfaceResidues

which select the residues on the surface but I dont know

how to print the residues names as an output ?

Thanks in advance ...

-- 
Please feel free to call me or mail me

Thanks and Regards

Vinod.D M.Pharm.
Jr. Applications Scientist
Mobile no:+91-9900090044

http://www.schrodinger.com/

Dear all,In order to emphasize local interactions of several residues within a protein, I want to highlight these studied residues but make other residues vague and being as background. The setting "set fog, on" doesn't help much because the constrast between the studied residues and other residues is not strong. Could you help me with this problem? With many thanks.Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences