Re: [PyMOL] Multiple molecules

[Folmer Fredslund]

Hi João,



On 2017-06-10 15:57, João Oliveira Jr. wrote:
I wont ask "why not", but once I just import the molecules to another 
software/app I think I'd loose the scale size... Some molecules would 
have biger secondary orders compared to other... or not?


But... In the picture you provide as an example, you already have a 
difference in the size of the secondary structure elements, so I did not 
think it mattered.



Aldo what's the big deal regarding this Ray traced option?


Here is information about ray tracing:
https://pymolwiki.org/index.php/Ray

Best regards,
Folmer



Regards!!


Em sáb, 10 de jun de 2017 às 10:48, Folmer Fredslund 
<folm...@gmail.com <mailto:folm...@gmail.com>> escreveu:


Hi João,

Yes and no.

You can not (or only with a lot of to me unnecessary tweaks) make
something like that in PyMOL.

What you should do (IMHO) is to make a ray traced figure of each
of the molecules you want and then use
a program like inkscape to import the ray traced molecules and add
the text, which would then give you a new figure in a format of
your desire.

I hope this helps,
Folmer




On 2017-06-10 13:59, João Oliveira Jr. wrote:

Hi again guys

So I'm a areacher and I downloaded the Educational version. I'd
like doing an slide exactly like the attached imagem.

Is that possible?



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Re: [PyMOL] Segmentation fault

[Folmer Fredslund]

Hi João,

On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 
and "--use-msgpackc=no" I get a working pymol with revision 4170.


Have you tried creating a new user and test pymol from that account? 
That should help you identify if it is solely a problem with your own 
account.


HTH,
Folmer

On 2017-03-28 03:15, João M. Damas wrote:
Nobody experiencing the same issues? Any tips on what I may be doing 
wrong on the installation?


João

On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas > wrote:


Dear all,

I started experiencing segmentation fault on a pymol that I had
installed through the omnia channel on conda.

Then, I decided to install from scratch using this recipe:
https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN


Still getting the segmentation fault, so maybe something changed
in my system and it's conflicting with?

The segmentation fault is not on launching PyMOL, but rather when
I do stuff: loading a PDB file, building a fragment. Like this:

```
./pymol: line 3: 28505 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
"$@"
```

Curiously, when I load a 1.740 session (.pse file I had saved), it
works (no segmentation fault), I can even perform commands like
select and stuff, and they work. If I load a more recent 1.803
session, it also seg faults:

```
 Executive: Loading version 1.803 session...
./pymol: line 3: 29221 Segmentation fault  "/usr/bin/python2.7"
"/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py"
"$@"
```

Any clues? Am I doing something wrong?

Thanks,
João

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Re: [PyMOL] Video in Ubuntu Linux

[Folmer Fredslund]

Dear Ioannis,



On 2016-07-08 09:04, Ioannis Michalopoulos wrote:
> Dear PyMOL users,
>
> I use Kubuntu 14.04. I compiled PyMOL, following some instructions on the web.
> This produced the directory:
>
> /opt/pymol-svn/
>
> and a symbolic link to pymol executable:
>
> /usr/bin/pymol -> /opt/pymol-svn/pymol*
>
> PyMOL works fine. Nevertheless, when I try:
>
> File > Save Movie As > MPEG...
>
> I get the following error message:
>
> MPEG encoder missing.
> The FreeMOL add-ons may not be installed
>
> I downloaded the source code for mpeg_encode (freemol-mpeg_encode.tar.gz)
> from:
>
> http://www.bioinformatics.org/cgi-bin/viewvc.cgi/freemol/trunk/src/mpeg_encode/?view=tar
>
> and I did the following:
>
> tar zxvf freemol-mpeg_encode.tar.gz
> cd mpeg_encode
> ./configure
> make
> sudo make install
>
> This created the following file:
>
> /bin/mpeg_encode.exe
>
> That means that mpeg_encode.exe is in the PATH (it runs from any directory).
> mpeg_encode.exe seems to work. Unfortunately, when I try to produce a movie in
> pymol, I get the same error message. What have I done wrong?

I hope it is very simple.
You need to include an environment variable $FREEEMOL pointing at the 
directory where
freemol is installed

If you are using bash that would be
export FREEMOL=/your/bath/to/freemol/
where the mpeg_encode.exe file is in 
/your/bath/to/freemol/bin/mpeg_encode.exe

Hope this helps!

Folmer


> Thank you in advance.
>
> Best Regards,
>
> Ioannis


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Re: [PyMOL] Testing if a .pml script is run in command line mode

[Folmer Fredslund]

Dear list,

Seems like I was able to find it myself by searching for "scene" in the
code on github.

The magic name is  "get_scene_list", which perhaps was not such a strange
name afterall

So, now I have put together a small script, to take all scenes in a pml
script and render them by running PyMOL on the command line like this:
pymol -c script.pml -r ray_scenes.py

Thanks to Jesper Karlsen (off-list) for pushing a bit further with this and
Tsjerk for introducing me to "invocation._argv"

Best regards,
Folmer


2016-02-01 15:19 GMT+01:00 Folmer Fredslund <folm...@gmail.com>:

> Dear list,
>
> Moving a bit further with this, I have been trying to find an easy way to
> iterate through the list of scene names. Or to get them somehow.
> I don't seem to be able to find any information about this and thought
> someone probably already knew.
>
> Thanks in advance!
>
> Folmer
>
> 2016-01-27 14:07 GMT+01:00 Folmer Fredslund <folm...@gmail.com>:
>
>> Dear Tsjerk,
>>
>> Thanks! simply including
>> if '-c' in invocation._argv
>> in the script works fine for me,
>>
>> Best,
>> Folmer
>>
>> 2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>>
>>> Hey Folmer,
>>>
>>> You can check if '-c' not in invocation._argv
>>> Of course, you'd also need to check combinations, so it would be
>>> matching -.*c.* on the elements in _argv.
>>>
>>> There probably is a way to check for the GUI directly though.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <folm...@gmail.com>
>>> wrote:
>>>
>>>> Hi there,
>>>>
>>>> I was wondering if there is a way to check if a .pml is being run in
>>>> command line mode (pymol -c), i.e. without the GUI.
>>>>
>>>> The reason I'm asking, is because I am making some scripts for figures,
>>>> and save the representations as scenes. It would be nice to both be able
>>>> to view them (running the .pml normally) and also make raytraced png's
>>>> when the .pml is being run in commandline mode.
>>>>
>>>> Best regards,
>>>> Folmer Fredslund
>>>>
>>>>
>>>> --
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>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>>
>>
>>
>> --
>> Folmer Fredslund
>>
>
>
>
> --
> Folmer Fredslund
>



-- 
Folmer Fredslund
#!/usr/bin/python
# Run a pymol script with scenes like this:
# pymol -c your.pml -r thisscript.py
# and a png for every scene will be generated


from pymol import cmd
resolution = 500

pymol_flags = pymol.invocation._argv[1]
print "PyMOL flags: %s"%(pymol_flags)
if pymol_flags.startswith( '-' ):
if "c" in pymol_flags:  
for scene in cmd.get_scene_list():
cmd.scene(key=scene, action='recall', animate=0)
print "This is scene %s"%(scene)
cmd.png(scene+".png", resolution, ray=1, dpi=300)

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Re: [PyMOL] Testing if a .pml script is run in command line mode

[Folmer Fredslund]

Dear list,

Moving a bit further with this, I have been trying to find an easy way to
iterate through the list of scene names. Or to get them somehow.
I don't seem to be able to find any information about this and thought
someone probably already knew.

Thanks in advance!

Folmer

2016-01-27 14:07 GMT+01:00 Folmer Fredslund <folm...@gmail.com>:

> Dear Tsjerk,
>
> Thanks! simply including
> if '-c' in invocation._argv
> in the script works fine for me,
>
> Best,
> Folmer
>
> 2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>
>> Hey Folmer,
>>
>> You can check if '-c' not in invocation._argv
>> Of course, you'd also need to check combinations, so it would be matching
>> -.*c.* on the elements in _argv.
>>
>> There probably is a way to check for the GUI directly though.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <folm...@gmail.com>
>> wrote:
>>
>>> Hi there,
>>>
>>> I was wondering if there is a way to check if a .pml is being run in
>>> command line mode (pymol -c), i.e. without the GUI.
>>>
>>> The reason I'm asking, is because I am making some scripts for figures,
>>> and save the representations as scenes. It would be nice to both be able
>>> to view them (running the .pml normally) and also make raytraced png's
>>> when the .pml is being run in commandline mode.
>>>
>>> Best regards,
>>> Folmer Fredslund
>>>
>>>
>>> --
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>
>
> --
> Folmer Fredslund
>



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[PyMOL] Testing if a .pml script is run in command line mode

[Folmer Fredslund]

Hi there,

I was wondering if there is a way to check if a .pml is being run in
command line mode (pymol -c), i.e. without the GUI.

The reason I'm asking, is because I am making some scripts for figures,
and save the representations as scenes. It would be nice to both be able
to view them (running the .pml normally) and also make raytraced png's
when the .pml is being run in commandline mode.

Best regards,
Folmer Fredslund

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Re: [PyMOL] Testing if a .pml script is run in command line mode

[Folmer Fredslund]

Dear Tsjerk,

Thanks! simply including
if '-c' in invocation._argv
in the script works fine for me,

Best,
Folmer

2016-01-27 12:43 GMT+01:00 Tsjerk Wassenaar <tsje...@gmail.com>:

> Hey Folmer,
>
> You can check if '-c' not in invocation._argv
> Of course, you'd also need to check combinations, so it would be matching
> -.*c.* on the elements in _argv.
>
> There probably is a way to check for the GUI directly though.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Jan 27, 2016 at 11:49 AM, Folmer Fredslund <folm...@gmail.com>
> wrote:
>
>> Hi there,
>>
>> I was wondering if there is a way to check if a .pml is being run in
>> command line mode (pymol -c), i.e. without the GUI.
>>
>> The reason I'm asking, is because I am making some scripts for figures,
>> and save the representations as scenes. It would be nice to both be able
>> to view them (running the .pml normally) and also make raytraced png's
>> when the .pml is being run in commandline mode.
>>
>> Best regards,
>> Folmer Fredslund
>>
>>
>> --
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


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Re: [PyMOL] color based on residue sequence

[Folmer Fredslund]

Hi Smith,

Have you tried reading in the wiki?

This page on advanced coloring (
http://pymolwiki.org/index.php/Advanced_Coloring) might help you to color
in a number of ways.
Your specific request could be handled by the util.chainbow command, which
is also available in the color menu of each object.

Best regards,
Folmer

2015-12-05 9:54 GMT+01:00 Smith Liu <smith_liu...@163.com>:

> Dear All,
>
> Is any way by pymol we color the protein based on residue sequence, for
> example from red starting resi 1 gradually to blue at residue 1000?
>
> Smith
>
>
>
>
>
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Re: [PyMOL] How to forbid merging of files?

[Folmer Fredslund]

Hi Alsa,

In the line where you save the file, you need to specify a selection,
otherwise, everything will be saved
Look at http://www.pymolwiki.org/index.php/Save#PYMOL_API

So instead of
cmd.save(filenameN + '.mol')
you want something like
cmd.save(filenameN + '.mol', filename)

I haven't tested this myself though.

Hope this helps
Folmer


2015-06-06 11:53 GMT+02:00 AE alsalisb...@yahoo.com:

 Good day,

 I have several thousands of files, which I upload using the loop:

 myDir = ‘/dirWithFiles'
 for filename in os.listdir(myDir):
 cmd.load (filename)
 filenameN = os.path.splitext(filename)[0]
 cmd.save(filenameN + '.mol')
 cmd.disable(filename)

 I am trying to save them one by one in a different (.mol) format. However,
 the files are saved together, i.e.: first file opened contains only
 molecule from the first file; second: first + second; third: first + second
 + third etc. But I want firstFile.readableFormat to be converted into
 firstFile.mol, secondFile.readableFormat - secondFile.mol etc, without any
 addition of other files. How can I do that?

 Thank you,

 Best Regards,

 Alsa

 Sorry I have sent it already, accidentally forgot to finish the question
 in subject(

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Re: [PyMOL] sticks do not connect to the backbone

[Folmer Fredslund]

Hi Yeping,

You can also try
set cartoon_side_chain_helper, on

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

Regards,
Folmer

2015-05-18 10:23 GMT+02:00 sunyeping sunyep...@aliyun.com:


 Dear all,


 I find that when I show the protein as cartoon representation in pymol,
 and select some residues to show as sticks, then the sticks do not connect
 to the backbone shown by the cartoon but looks as floating over the
 backbone. How to make the sticks connect to the backbone?


 With many thanks.

 Yeping Sun

 Institute of Microbiology, Chinese Academy of Sciences




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Re: [PyMOL] Is Ball Stick models of molecules possible?

[Folmer Fredslund]

Hi Rajib  Yuktimmana,

For the question about ball  stick see this page on the wiki:

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


HTH,
Folmer


2015-04-23 7:41 GMT+02:00 bkpsusmitaa bkpsusmi...@gmail.com:

 Hi!

 So far we have been able to make only stick models for molecules.

 We now wish to build both solid (based on electronic clouds) and Ball
  stick models.

 Can we have several molecules of identical types to build crystal
 structures, amorphous structures or fluide models, as the cases could
 be for specific molecules?

 Eager for your inputs.

 Rajib  Yuktimmana


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Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead of .pdbs

[Folmer Fredslund]

Hi,

For the version in Ubuntu 14.04 (1.7.0.0) it also defaults to downloading
the structure factors in cif format, instead of the model coordinates, so
I'm not sure this is the right way to do it, or perhaps something changed
between 1.7.0.0 and 1.7.4

Best regards,
Folmer

2015-03-20 10:26 GMT+01:00 Lukáš Pravda xpra...@ncbr.muni.cz:

 Which version of PyMOL do you have? Mine is 1.7.4 and it is working just
 fine. So in case you have and older version( 1.3 I guess) it might not
 work properly.



 Lukas



 *From:* Brenton Horne [mailto:brentonho...@ymail.com]
 *Sent:* Friday, March 20, 2015 12:02 AM
 *To:* Lukáš Pravda
 *Subject:* Re: [PyMOL] Fetching PDBs; how to load .cifs provided instead
 of .pdbs



 Thanks for ya help but I'm afraid this isn't working. See it saves the
 fetched file as .sf format which it then fails to recognize.


 PyMOLfetch 4V7Y, type = cif
  please wait ...
 PyMOLas cartoon
  CmdLoad: .\4v7y.sf loaded as 4V7Y.



 On 19/03/2015 9:31 PM, Lukáš Pravda wrote:

 Hi Brenton,



 fetch 4v7y, type=cif



 is the command you are looking for



 All the best



 Lukas Pravda

 ---

 CEITEC - Central European Institute of Technology

 Masaryk University

 Brno, Czech Republic

 ---



 *From:* Brenton Horne [mailto:brentonho...@ymail.com
 brentonho...@ymail.com]
 *Sent:* Thursday, March 19, 2015 4:55 AM
 *To:* pymol-users@lists.sourceforge.net
 *Subject:* [PyMOL] Fetching PDBs; how to load .cifs provided instead of
 .pdbs



 Hi,

 I have noticed that for some PDBs wwPDB doesn't contain PDB files (e.g.,
 4V7Y http://www.rcsb.org/pdb/explore/explore.do?structureId=4V7Y), but
 rather they have mmCIF files instead and I was wondering if it was possible
 to get the fetch command to fetch these mmCIFs instead of PDBs. Now to be
 clear, I do understand how to load mmCIFs that I have downloaded manually
 from wwPDB by going to File-Open... but I'd like to know how to get
 PyMOL to fetch these files from wwPDB and load them.

 Thanks for your time,
 Brenton




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Re: [PyMOL] Selecting specific ligands for colouring

[Folmer Fredslund]

Hi Brenton,

It seems 2HYY only has that one (type of) ligand present?
so:

fetch 2hyy
as cartoon
show sticks, organic
color black, elem c and organic
remove not chain a

gives me a cartoon representation of the protein, with a stick
representation of the ligand. There are 4 copies of the complex in the
asymmetric unit and they have chain ID's A-D, so the last command removes
all atoms except the ones in chain a.

I am personally more comfortable with this kind of selections, instead of
the 2hhy/something/something/something

In case you want to keep all molecules, but just select on of the ligands,
you could do something like:

select ligandA, organic and chain a and resname STI


Hope this helps,
Folmer




2015-01-06 9:40 GMT+01:00 Brenton Horne brentonho...@ymail.com:

  Hi,

 I know I must be getting annoying, although I must say this mailing list
 and its users have been very helpful for me so thank you all. My question
 this time is how do I select specific ligands? Like I am using PDB ID 2HYY
 and I'd like to set the imatinib (STI600) ligand as the only visible
 ligand, plus I'd like to colour it according to the CPK scheme, except with
 carbons coloured black. Now I've tried:

 select 2hyy/A/STI

 based on the Selection Algebra
 http://pymolwiki.org/index.php/Selection_Algebra page on PyMOL Wiki but
 this returned the result:

 Selector: selection sele defined with 0 atoms.


 ps. is there are any PDF document showing complete up-to-date command-line
 syntax for PyMOL because I think this will really help me. PyMOL Wiki I
 find generally only gives a snippet of the command-line syntax for a given
 topic. Plus I generally find the really general format of the syntax (e.g.,

 show reprentation [,object]

 ) with the square brackets PyMOL sometimes shows is confusing to me,
 unless it's accompanied by an example of how that code appears for a
 specific example.

 Thanks for your time,
 Brenton


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Re: [PyMOL] Is it possible to move different subunits independently using Pymol

[Folmer Fredslund]

Hi Cacau,

You can move objects independently of each other, but not selections inside
objects AFAIK.

So, you would need to *extract* or *create* new objects and then manipulate
them with the editing mode.

Best regards,
Folmer

2014-11-17 9:57 GMT+01:00 Cacau Centurion cacaucenturi...@gmail.com:

 Hi all,

 I am wondering if it is possible to move different subunits independently
 with Pymol. Can anyone let me know about it?

 Yours,
 Cacau


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Re: [PyMOL] PyMOL performance improvement

[Folmer Fredslund]

Dear Annalisa,

Perhaps you should consider installing the nvidia driver instead of using
nouveau?

Venlig hilsen
Folmer Fredslund
Den 07/11/2014 04.07 skrev Annalisa Arcella annalisa.arce...@gmail.com:

 Hi All,
 I have installed PyMol by terminal

 sudo apt-get install pymol

 on my Ubuntu14.04 but it is very slow.
 Please can you tell me if it can be supported by my PC?

 Memory 7.7 GiB
 Processor Intel Core i5CPU 650@ 3.20GHz X 4
 Graphics Gallium 0.4 on NV86
 OS-Type 64-bit

 And here is what is written on PyMOL window when I open it





















 *PyMOL(TM) Molecular Graphics System, Version 1.7.0.0. Copyright (c)
 Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D.
 PyMOL is user-supported open-source software.  Although some versions  are
 freely available, PyMOL is not in the public domain.  If PyMOL is helpful
 in your work or study, then please volunteer   support for our ongoing
 efforts to create open and affordable scientific  software by purchasing a
 PyMOL Maintenance and/or Support subscription.  More information can be
 found at http://www.pymol.org http://www.pymol.org.  Enter help for a
 list of commands.  Enter help command-name for information on a
 specific command. Hit ESC anytime to toggle between text and
 graphics.  Detected OpenGL version 2.0 or greater. Shaders
 available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR:
 nouveau GL_RENDERER: Gallium 0.4 on NV86 GL_VERSION:  3.0 Mesa
 10.1.3 Detected 4 CPU cores.  Enabled multithreaded rendering.*

 ​

 --
 *Annalisa*

 What gets us into trouble
 is not what we don't know

 it's what we know for sure
 that just ain't so
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Re: [PyMOL] naming of chain id

[Folmer Fredslund]

Hi Yeping Sun,

Did you solve your problem?

According to http://www.wwpdb.org/procedure.html#toc_4

What is the maximum number of chain IDs in a file?

Up to 62 chains can be included in the PDB entry. Upper case letters and
numbers (0-9) should be used first for chain IDs. Lower case letters should
be used only after all upper letters and numbers have been used. Symbols
should never be used for chain IDs.

you can use numbers and also small letters in the PDB file format.


I don't know if PyMOL will let you do this, though.

Regards,

Folmer

2014-09-02 10:41 GMT+02:00 sunyeping sunyep...@aliyun.com:

 I have a protein which contains 32 chains. By using A-Z can only name 26
 chains. Can I use expression containing two character such as A1, AB, etc.
 to as chain id? Will this change the format of the pdb files?

 Yeping Sun

 Institute of Microbiology, Chinese Academy of Sciences



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Re: [PyMOL] Coloring of helices

[Folmer Fredslund]

Hi Markus,

As Andreas already mentioned, the cartoon color is taken from the color of
the CA atoms. So you could just color those differently and that should be
reflected in the cartoon colors.

But I think a better option is to use the cartoon_color command.
http://www.pymolwiki.org/index.php/Cartoon_color

I've just tried it on 1.4.1, and expect any recent PyMOL's to behave the
same.

Hope this helps,
Folmer


2014-08-22 0:33 GMT+02:00 Markus Heller mhel...@cdrd.ca:

 Hi all,

 I'm stuck.  I'm trying to create a figure where I show a helix bundle,
 with select side chains shown as sticks.  I would like the helices to be
 green, and the side chains in different colors.  Easy enough, *but* the
 carbon color of the side chains supersedes the green color of the helices.

 I tried to duplicate the object and show sticks for one objects and
 helices for the other, which works in terms of color, *but* now the
 cartoon_side_chain_helper doesn't work, since I'm displaying sticks and
 helices from 2 different objects.

 How do I go about this?

 Thanks and Cheers
 Markus

 PS: Here's my attempt:

 # reset everything
 delete all

 # white background
 bg_color white

 # show valences
 set valence, 1

 # show valences inside rings, 0 = centered, 1 = inside
 set valence_mode, 1

 # antialias
 set antialias = 1

 # don't show backbone for cartoons
 set cartoon_side_chain_helper, on

 # keep standard helix, strand, loop representations
 # other options: cartoon loop, cartoon rect,
 # cartoon oval , cartoon tube
 cartoon automatic

 # Molscript-like edges for helices
 set cartoon_fancy_helices = 1

 # color inside of helices gray
 set cartoon_highlight_color, gray

 # load the PDB file

 load example.pdb, EXA

 # duplicate protein
 copy EXA_dup, EXA

 # hide everything
 hide everything

 # select protein
 select prot, polymer

 # show cartoon ribbon
 show cartoon, EXA

 # select helices
 select heli, (ss h and EXA)
 select heli_dup, (ss h and EXA_dup)

 # color everything limon
 color limon

 # select residue of interest
 select V27, (resi 27 and EXA)
 select S31, (resi 31 and EXA)
 select A34, (resi 34 and EXA)
 select H37, (resi 37 and EXA)
 select W41, (resi 41 and EXA)

 # show sticks for ROIs
 show sticks, (V27 or S31 or A34 or H37 or W41)

 # color ROIs
 color atomic, (V27 or S31 or A34 or H37 or W41)
 color yellow, (name C* and V27)
 color orange, (name C* and S31)
 color cyan, (name C* and A34)
 color magenta, (name C* and H37)
 color purple, (name C* and W41)

 # color helices properly
 show cartoon, EXA_dup
 color limon, EXA_dup

 # deselect all to avoid little pink squares
 deselect

 --
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[PyMOL] Text in main windows missing with bg_color = white

[Folmer Fredslund]

Hi all,

I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
(reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
after startup).

When the bg_color is set to white (also gray, it seems) the text in the
main window of PyMOL is missing (revealed when pressing ESC).

The text looks just fine if bg_color is black.

Does anyone know if this is a feature or a bug?

Best regards,
Folmer

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Re: [PyMOL] Text in main windows missing with bg_color = white

[Folmer Fredslund]

Hi Thomas,



2014-06-04 18:02 GMT+02:00 Thomas Holder thomas.hol...@schrodinger.com:

 Hi Folmer,

  I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
 (reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
 after startup).

 looks like you should do a clean rebuild (remove the build directory).


Yes, that changed the version number.


  When the bg_color is set to white (also gray, it seems) the text in the
 main window of PyMOL is missing (revealed when pressing ESC).
 
  The text looks just fine if bg_color is black.
 
  Does anyone know if this is a feature or a bug?

 it's not a feature, for sure. We'll fix that.


OK, sounds great!


 Cheers,
   Thomas

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger, Inc.




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Re: [PyMOL] Pseudo AxPyMol

[Folmer Fredslund]

Hi Jordan,

I don't know if this helps you, but you can start pymol in presentation
mode (by saving a session with scenes and then edit the name to psw
instead of pse). Then you will immediately go full-screen and hitting
space (or the clicker I presume) will let you move to the next scene.
This might not be fancy enough, but I thought I'd mention it.

One other thing you could do is to save the files in the movie (instead of
making a movie directly) and then make small movies from the output png's.

Hope this helps,
Folmer



2014-03-04 23:41 GMT+01:00 Jordan Willis jwillis0...@gmail.com:

 I'm using powerpoint for mac, so I don't have the luxury of Axpymol (any
 plans for OSX?)

 I wanted to make a movie that iterates through scenes of a PyMol session
 and pauses there until I hit the next button on powerpoint. My workaround
 was to simply make a movie that went trough all scenes and break them up
 into separate movies. When I hit next on the clicker for powerpoint, it
 would make that movie appear on the slide and it would be appear to be a
 continuation of the last movie.

 I was wondering if there is a way to render movies by frame. For instance
 only tell PyMol to render frames 1-30. Then in another movie 31-60 etc.
 Perhaps the simplest way would be to dump every frame as a separate .png,
 and reconstruct manually.

 Any thoughts on this? How to make it easier, or does this seem like the
 easiest way.

 Jordan

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Re: [PyMOL] Pymol 1.3 and 1.6 compatability?

[Folmer Fredslund]

Hi Lapolla,

The PyMOL source is available here:
http://sourceforge.net/projects/pymol/

Hope this helps,
Folmer


2014/1/14 Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu

 I thought that 1.7 was not free--that you had to pay for it.  Not true? If
 1.7 is free, could you give me a link? Thank you.
 
 From: Engin Özkan [eoz...@stanford.edu]
 Sent: Tuesday, January 14, 2014 3:10 PM
 To: pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Pymol 1.3 and 1.6 compatability?

 While you are updating, you might as well update to the very recently
 released version, 1.7.

 Engin


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Re: [PyMOL] rotate cell

[Folmer Fredslund]

Dear Chandan,

I think you want to use the move command  (
http://pymolwiki.org/index.php/Move) which moves the camera around the
molecule, instead of the rotate command (
http://pymolwiki.org/index.php/Rotate) which alters the coordinates of the
object you are looking at.

Hope this helps
Folmer



2013/11/12 Chandan Choudhury iitd...@gmail.com

 Dear PyMOL users,

 I want to rotate/revolve the loaded structure. The cell parameter should
 also rotate.
 I am aware of rotate command.
 eg. rotate X, 90.

 But when I view the cell. The rotation does not happen here.

 My purpose is to generated a snapshot showing the boundaries.
 How can this be acheived?

 Chandan

 --
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 NCL, Pune
 INDIA


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Re: [PyMOL] commands history

[Folmer Fredslund]

Dear Chandan,

The command log_open will start writing a log file of events happening.

If you want a specific name for the logfile you write log_open myfile.pml

In that file the commands you type will be saved, as well as actions from
menus (not sure how many, but I think most of them).

Hope this helps.
Best regards,
Folmer


2013/11/11 Chandan Choudhury iitd...@gmail.com


 Dear PyMOL users,

 I was just wandering to know that does PyMOL saves the history of the
 commands typed?

 If so, please let me know how can it be done.

 Chandan


 --
 Chandan kumar Choudhury
 NCL, Pune
 INDIA


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Re: [PyMOL] Making selections separately among 2 or more proteins loaded into PyMOL

[Folmer Fredslund]

Hi Anasuya

You must remember to also but in the name of the protein you. You were
almost there!


2013/8/8 Anasuya Dighe anas...@mbu.iisc.ernet.in

 Hello PyMOL users,

 Say, I have three pdb files loaded onto PyMOL. Lets assume that each of
 the pdb
 file has 3 chains, i.e A,B,C in them.

 If I want to select residues 1,5,6,7 in chain A of Protein_1, residues
 4,8,9,12
 in chain B of Protein_2 and residues 1,5,12,43 in chain A of Protein_3.

 I know the command to select residues, i.e select name1, resi 1+5+6+7 and
 chain
 A , but when i execute this command, residues 15 of chainA of the
 Protein_1 and
 Protein_3, are selected.

 How do I specify that the selection has to be at the chain A in Protein_1 ?
 I tried loading the files one by one and doing this, but when I come to the
 third pdb file and execute the select command, I am running in to the same
 problem,i.e residues 1 and 5 of protein_1 are also getting selected.


You need to also specify the molecule:

select name1, Protein_1 and resi 1+5+6+7 and chain A



 How do i avoid this ?  Some additional syntax required ?
 Also, once this is done, how to align these selections spanning 3 different
 chains among 3 separate proteins ?
 Will the align command suffice ?



I'm not sure, but I don't think the align command will work on just those
selections (too few atoms).

I think pair_fit is better to use
http://www.pymolwiki.org/index.php/Pair_fit

Hope this helps!

mvh
Folmer



 Please let me know.

 Thanks  Regards,

 Anasuya Dighe
 Molecular Biophysics Unit Annexe,
 Indian Institute of Science,
 Bangalore - 560012
 INDIA


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Re: [PyMOL] pymol windows gone

[Folmer Fredslund]

Hi,

If you have a problem with PyMOL, I think it would be nice to include more
information.

For instance, the version of PyMOL you are using?
The operating system?
Has the problem happened several times?
As much information about the problem as possible.


With the information you provide I'm not sure that anyone can help you.

Best regards,
Folmer


2013/3/21 lina lina.lastn...@gmail.com

 Hi,

 Surprisingly the pymol menu windows was gone, only the pymol viewer,

 any clues?

 Thanks,


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Re: [PyMOL] symmetry operation to generate the whole virus particle

[Folmer Fredslund]

Hi Yeping,

Searching for pymol biomt gives this page on the pymol wiki:

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

Should have all the information you need.

Best regards,
Folmer



2013/2/28 yp sun sunyep...@yahoo.com.cn

 Dear pymol users:

 Usually pymol can show only one chain when you open a pdb file of virus
 particles (such as 2buk,1sva, etc.). I am trying to create the whole virus
 particle and I know it may need applying symmetry operations. And these
 symmetry operation has been given in the pdb files. For example, the follow
 is the symmetry operation of 2buk:

 REMARK
 350
 REMARK 350 GENERATING THE
 BIOMOLECULE
 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
 KNOWN
 REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
 THE
 REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
 TRANSFORMATIONS
 REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
 AND
 REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
 GIVEN.
 REMARK
 350

 But I don't understand how to do symmetry operations. Can pymol do these
 or other software is needed? Please help.

 Yeping Sun
 CAS Key Laboratory of Pathogenic Microbiology  Immunology
 INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
 NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china


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Re: [PyMOL] Write vector graphics of session

[Folmer Fredslund]

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Re: [PyMOL] How to analyze and calculate tetramer interaction area and complexation energy

[Folmer Fredslund]

Dear Jun,

I would recommend you to have a look at the PISA webserver and the output
it will provide you.

Best regards,
Folmer

link: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html


2012/11/13 Jun Huang huan0...@umn.edu

 hello, everyone:
 I am a new user. I am analyzing the tetramer interfaces of SABP2
 protein(pdb code: 1y7i). I download the SABP2 protein structure(pdb code:
 1y7i) from pdb database, but the structure is dimer.could you tell me how
 to analyze  SABP2 tetramer interface and calculate interaction area and
 complexation energy.
  with best regards
  Jun Huang


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Re: [PyMOL] electron density map

[Folmer Fredslund]

Dear Amna (?),


2012/11/12 amna khan amnakhan...@gmail.com

 i have docked ligand with protein and final docked protein containing
 ligand conformation have been generated into one file. Now for this
 docked ligand-protein structure i want to calculate the electron dennsity
 map by pymol.



If I understand correctly, what you are doing does not make any sense (I am
a protein crystallographer...)

To the best of my knowledge, what you are trying to do is not possible.

With best intentions,

Folmer





 On Sun, Nov 11, 2012 at 5:22 PM, Folmer Fredslund folm...@gmail.comwrote:

 Dear Amna (?),


 2012/11/11 amna khan amnakhan...@gmail.com

 hi,

 i want to calculate the electron density maps for my docked protein from
 autodock4.2, when i load. fld.maps file generated by autodock and my docked
 protein at same time , no maps are generated.



 1. electron density maps are calculated from experimental data and model
 phases. No computer program will ever give you any (real) electron density.
 I think you are confusing the terms here.

 2. Are you trying to dock a ligand, or dock two proteins together?  There
 is a very nice plugin (http://www.pymolwiki.org/index.php/Autodock_plugin)
 by Daniel Seeliger. I would use that.

 Hope this helps

 Folmer Fredslund








 please help

 regards


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Re: [PyMOL] electron density map

[Folmer Fredslund]

Dear Amna (?),


2012/11/11 amna khan amnakhan...@gmail.com

 hi,

 i want to calculate the electron density maps for my docked protein from
 autodock4.2, when i load. fld.maps file generated by autodock and my docked
 protein at same time , no maps are generated.



1. electron density maps are calculated from experimental data and model
phases. No computer program will ever give you any (real) electron density.
I think you are confusing the terms here.

2. Are you trying to dock a ligand, or dock two proteins together?  There
is a very nice plugin (http://www.pymolwiki.org/index.php/Autodock_plugin)
by Daniel Seeliger. I would use that.

Hope this helps

Folmer Fredslund








 please help

 regards


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Re: [PyMOL] Getting surface residues

[Folmer Fredslund]

Hi Troels,

I've been using

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

at some point. Seems to work well enough.

Otherwise you could go through the PISA server at
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

But I don't remember how exactly I would get the surface residues out from
that.

mvh
Folmer

2012/10/31 Troels Emtekær Linnet tlin...@gmail.com

 Hi Pymolers.

 How would you get a list of surface residues the fastest way?

 Like:
  [3-10], [14-18]

 I have a rough structure from crystallography, and have made
 a trypsin digest and mass spec analysis.

 And I see fragments which have been post-trans modified.

 Now I am interested in matching if those fragments are surface exposed or
 internal.

 What tools does pymol have to find out if the residues are surface exposed?
 Or is there another easy tool?

 Best
 Troels Emtekær Linnet
 Ved kløvermarken 9, 1.th
 2300 København S
 Mobil: +45 60210234



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Re: [PyMOL] Select crystal waters inside protein

[Folmer Fredslund]

Hi Martin,


2012/10/4 Martin Hediger ma@bluewin.ch

 Dear PyMOL Users
 I'm trying to remove water molecules from a crystal structure which are
 on the crystal surface while preserving the ones within the crystal
 interior.

 What I do is:

 select waters, resn HOH
 # cmd.select(waters, (waters extend 1), enable=1)
 get_area waters, load_b=1
 remove waters and b20

 This only works partially because of some waters, only the oxygen atom
 is removed, while of others only one of the hydrogens is removed (some
 waters are completely removed which is good). It does not make a
 difference if I include the commented command above.


You might want to read up on the selection algebra of PyMOL (
http://www.pymolwiki.org/index.php/Selection_Algebra) which is quite
powerfull.

You can use the by residue selection to select the entire residue that
fits you description, so in your case

remove byres waters and b20

Will remove every residues within your selection waters, where at least one
atom has a b factor of more than 20. (and of course now you have altered
the b factor according to the calculated surface area)



Also, what does load_b=1 mean?


http://www.pymolwiki.org/index.php/Get_Area
It is explained in the last example (3)
load_b=1 will put the value of the surface area into the b factor column.


Hope that helps!

Best regards,
Folmer




 Further feedback would be greatly appreciated.
 Martin





 On 26.04.12 14:46, Thomas Holder wrote:
  Hi Martin  James,
 
  is it just a coincident that you both ask almost the same question?
 
  You could remove all water atoms with few protein contacts or with a
  small surface area. For example:
 
  remove solvent beyond 3.5 of polymer
  set dot_solvent
  get_area solvent, load_b=1
  remove solvent and b  20
 
  Hope that helps.
 
  Cheers,
Thomas
 
  On 04/26/2012 10:55 AM, James Starlight wrote:
  Another question- I have my protein.pdb with some inserted crystall
  waters within protein interiour as well as water surrounded of my
  protein. I want to remove only sorrounding water but prevent internal
  water ( wich could be functional relevant ).
 
  How I could to select such surrounded water ( e.g via some cutoff
  radius relative my protein etc) wich I'd like to remove further ?
 
  On 04/25/2012 05:34 PM, Martin Hediger wrote:
  In a crystal structure, there are usually a number of relevant crystal
  waters, as well as water molecules on the surface. In our approach, we
  model the protein structure within a dielectric continuum, so surface
  water molecules are not required (to save computer time). However,
  waters in the interior should remain in our model. How could we discard
  the surface waters while keeping the internal waters?
 



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Re: [PyMOL] Saving setting in PyMol

[Folmer Fredslund]

Hi James

Check out the information about how to load custom settings and functions:
http://www.pymolwiki.org/index.php/Pymolrc

Hope this helps,
Folmer


2012/8/16 James Starlight jmsstarli...@gmail.com:
 Dear PyMol users!


 I wounder to know about possible way to save settings of the PyMol
 after LogOut from it.

 E.g I've defined some basic settings like fetch_host and fetch_patch
 for uploading of new pdb files as well as set new background colour.
 Also I've changed some advanced settings - e.g I defined to unchange
 atom order in the processed pdb by the below commands
 set retain_order,1  set pdb_retain_ids,1


 After exiting from PyMol and starting of the new session I must to
 define this settings each time again. Is there any way to save this
 parameters for each new pymol session ?

 JAmes

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Re: [PyMOL] Messed up structures in movie

[Folmer Fredslund]

Hi Ritu,

Could you elaborate on some of the ligand structures get completely messed
up when viewed as sticks or lines?

To get the best possible answer a few more details would help.

Best regards,
Folmer

2012/5/23 Rituparna Sengupta rsengu...@wisc.edu

 Hi,

 Just observed something weird. When I try loading protein -ligand
 complexes as frames of a movie (same protein but different ligands for
 different frames), some of the ligand structures get completely messed up
 when viewed as sticks or lines. Right now I'm using spheres instead, but
 wondering if there's a way to work around the problem and still view the
 ligands as sticks/lines.


 Thanks,
 Ritu


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Re: [PyMOL] Messed up structures in movie

[Folmer Fredslund]

Hi again Ritu,

This does seem odd. I have no idea what might be wrong, but could you
provide an example pdb, or a png of the output you see?

I would personally try to strip all extra information from the ligand pdb
(so only ATOM and HETATM records is included) and then try loading that pdb.

Best regards,
Folmer

2012/5/23 Rituparna Sengupta rsengu...@wisc.edu

 Hi,

 Sorry about the lack of description in the previous post.
 The chemicals show incorrect bond connections. Some of the rings go
 missing. In all, the structure changes and just by looking at it, its
 possible to tell that the structure is not right. I didn't see much details
 though, except that the atom connections seem to be wrong.


 Thanks,
 Ritu

 On 05/23/12, Folmer Fredslund
  wrote:
  Hi Ritu,
 
  Could you elaborate on some of the ligand structures get completely
 messed up when viewed as sticks or lines?
 
  To get the best possible answer a few more details would help.
 
  Best regards,
  Folmer
 
  2012/5/23 Rituparna Sengupta PyMOL-users@lists.sourceforge.net 
 rsengu...@wisc.edu') target=1rsengu...@wisc.edu
 
   Hi,
  
   Just observed something weird. When I try loading protein -ligand
 complexes as frames of a movie (same protein but different ligands for
 different frames), some of the ligand structures get completely messed up
 when viewed as sticks or lines. Right now I#39;m using spheres instead,
 but wondering if there#39;s a way to work around the problem and still
 view the ligands as sticks/lines.
  
  
   Thanks,
   Ritu
  
  
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Re: [PyMOL] creating PDB structure

[Folmer Fredslund]

On 11/23/2011 01:18 PM, James Starlight wrote:
 Thanks Thomas!

 Those scripts works fine. Could you tell me if there any way to install
 all of those scripts as the pymol plugins ( that I need not to load this
 scripts every time when I sttart pymol de novo )?


 James


Hi James

Jason Vertrees has previously responded to a similar question:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09579.html

This is the essence of the email:
Put the following code (after editing the /path/to/dir, obviously) in 
your .pymolrc
--
python

# make a list of all your directories w/scripts

known_directories = [ /path/to/dir1, /path/to/dir2, ... ]

import glob

for p in known_directories:
 for f in glob.glob(p+/*.py):
cmd.do(run  + f)

python end
---

(see here http://www.pymolwiki.org/index.php/Launching_PyMOL for an 
explanation of the .pymolrc file)


Hope this helps

Best regards,
Folmer




 2011/11/23 James Starlight jmsstarli...@gmail.com
 mailto:jmsstarli...@gmail.com

 Thanks thomas

 Those scripts works fine. Could you tell me if there any way to
 install all of those scripts as the pymol plugins ( that I need not
 to load this scripts every time when I sttart pymol de novo )?


 James


 2011/11/23 Thomas Holder spel...@users.sourceforge.net
 mailto:spel...@users.sourceforge.net

 Hi James,

 check this PyMOLWiki page: http://pymolwiki.org/index.__php/Fab
 http://pymolwiki.org/index.php/Fab

 However, the fab command does not take user defined phi/psi
 angles, only 4 predefined conformations (ss argument). User
 defined phi/psi can be handled by these scripts:

 http://pymolwiki.org/index.__php/CreateSecondaryStructure
 http://pymolwiki.org/index.php/CreateSecondaryStructure
 http://pldserver1.biochem.__queensu.ca/~rlc/work/pymol/#__model
 http://pldserver1.biochem.queensu.ca/%7Erlc/work/pymol/#model

 Cheers,
   Thomas

 James Starlight wrote, On 11/23/11 11:43:

 Dear PyMol Users!

 I wounder to know about possible ways of creation of the
 peptide structures via PyMol Builder module. In particular I
 need create a linear structure of my protein ( with fixed
 phi and psi angles) for futher folding molecular dynamics
 simulation of that peptide. But in builder module I found
 only helix and sheet conformations for each aa. residue. How
 I can specify desired values for both torsion angles ?

 Also I'd like to know is there any module for pymol wich
 could be used for obtaining linear unfolded structure for
 the defined sequence or folded protein ( in pdb) ?

 Thanks,


 James


 --
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 Spemannstr. 35
 D-72076 Tübingen





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Re: [PyMOL] How to label a cartoon representation?

[Folmer Fredslund]

Dear Petro,

Text labels in PyMOL (http://pymolwiki.org/index.php/Label) are displayed
per atom, so the usual way is to make a pseudoatom (
http://pymolwiki.org/index.php/Pseudoatom) for each helix label you want to
make.

Using selections this can be pretty straight forward.

Let's say you have your coloured helices as selections you could do
something like:

zoom helix1
pseudoatom labelhelix1
label labelhelix1, Helix 1

The position of the label can be changes using the edit mode  (see e.g.
http://pymolwiki.org/index.php/MovieSchool_3#Mouse_Modes)

Hope this helps

Best regards,
Folmer Fredslund


2011/10/30 Piter_ x.pi...@gmail.com

 Hi all.
 I have a protein structure in cartoon representation. It has 5 helices
 and iconnecting loops. I have colored 3 of the helices in to different
 color. now i want to add text label to them. How can I do it?
 Thanks.
 Petro.


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Re: [PyMOL] SURFACE MODEL

[Folmer Fredslund]

Dear Spyros,

Do you know about the PyMOL wiki (http://pymolwiki.org/)?

Take a look here: http://pymolwiki.org/index.php/Color
for an explanation about colors.
In the default representation
Green: Carbon
Blue: Nitrogen
Red: Oxygen
Yellow: sulfur

For coloring eg.
color gray
will color everything gray. This is done on the command-line.
You can also use the gui (top right there is a multicolored square
with the letter C, for color) and select many different colors. This
can be done for all or individually for each object/pdb you load.

Hope this helps!

Best regards,
Folmer Fredslund

2011/7/17 Spyros Charonis s.charo...@gmail.com:
 Hello PyMOLers,
 A quick question on the surface model, is there anywhere where I can learn
 how molecules are color-coded. The default scheme has green, red, and bits
 of yellow (I know the accessible to solvents surface is what is shown, but
 I'm not sure what red, green, and yellow bits mean)? Also, is there a way I
 can turn the whole thing gray (monochrome) so that I can color in parts I
 want to examine with my own coloring method?
 Spyros
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Re: [PyMOL] Spectrumany bug?

[Folmer Fredslund]

Dear Tassos

2011/4/5 Anastassis Perrakis a.perra...@nki.nl:
 Hi -

 I am trying to use the script by Thomas Holder, Spectrumany

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


Very nice that you link to the program you use, but possibly someone
is going to ask about the PyMOL version ;-)

 When I import the script (run) I get:

 PyMOLrun sp.pml
 Traceback (most recent call last):
   File /Applications/MacPyMOL.app/pymol/modules/pymol/parser.py,
 line 332, in parse

 parsing
 .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
   File /Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py,
 line 455, in run_file
     execfile(file,global_ns,local_ns)
   File sp.pml, line 81
      col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list)
                                                    ^
  SyntaxError: invalid syntax

 ==

 any help?

I'm on ubuntu, and the script (freshly downloaded from the wiki) works
fine for my in both PyMOL version 1.2r2 and version 1.4 (compiled
today).

One thought was to maybe rename your sp.pml to sp.py as this is
generally what is expected for a script I think. (at least version 1.4
suggested for me to use @sp.pml instead of run).

Hope this helps!

Best regards,
Folmer




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Re: [PyMOL] using pymol from python script

[Folmer Fredslund]

Dear John

2011/2/17 John Russo lamaro...@gmail.com:
 Hi,
 I'm sorry for making such beginner's questions but searching the manual,
 google
 or the wiki didn't help me.


You're welcome to ask here.

 I know how to extend pymol by writing python functions (through the
 extend command).
 But is it possible to do the opposite? I want to write a script that
 loads a molecule, does something
 to it and then displays the pymol window or outputs a png file. I want
 to this without having to
 enter commands in the pymol command line, since I need to put these
 operations in a script,
 without interactive control on pymol.

 Example. I want to write a script examply.py with which I can do

 ./examply.py mymolecule.xyz

 And for output I want to get mymolecule.png or the pymol window with all
 the operations
 already done.


I saw Tsjerks comment, ( and now yours since I write too slow) but was
wondering maybe what you need is more simple.
Do require to load PyMOL from a python script?

If not, then simply put the commands you need into a text file with
the .pml extension and PyMOL will recognize this when you run it.

An example file (example.pml)

load mymolecule.xyz
zoom residue 45-60
png mymolecule.png


Then do like this
pymol -c example.pml

And you get mymolecule.png

Best regards,

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Re: [PyMOL] Newbie question

[Folmer Fredslund]

Dear Bryan,

Curiously the escape key will switch back for you. It's been this way
forever I think.

When asking questions please specify some details on your version of
PyMOL. In my version (1.2) the figure in the main window does not
disappear when invoking the help command.

Hope this helps!

Best regards,
Folmer Fredslund

2010/10/29 Prince, D Bryan dbryan.pri...@astrazeneca.com:
 Dear PyMOL users:



 I have been working my way through a tutorial on how to use PyMOL, and
 working primarily from the command line. Being somewhat schooled in UNIX, I
 ran into a problem and typed help show on the command line. I got the
 information much like I would have from a UNIX terminal, but I was not able
 to figure out how to return to the model I had been working on. I randomly
 tried to hide all and show all, but nothing happened. Is there a way to get
 back to the figure after invoking help on the command line?



 Many thanks,



 Bryan

 

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Re: [PyMOL] print quality pictures

[Folmer Fredslund]

Dear Vivek,

On 15 July 2010 05:33, Vivek Ranjan vran...@gmail.com wrote:
 Hello,
 Once I get a high quality picture from pymol, I want to put some labels,
 combine a few of them together, add some arrows and texts, etc. Any
 suggestions on what is a good way to do that so that I don't lose resolution
 ? I generally crop the pictures in gimp to get rid of the white space
 around, then insert them in a powerpoint and resize them to fit a few
 together on one slide, then add texts, labels, arrows, etc. Save the slide
 in as a jpg and then crop it again. But I believe that even though I starts
 with a high resolution pictures created by pymol, I end up with not so good
 picture due to the procedure I described above.


You could take a look at inkscape (www.inkscape.org). It will
certainly be able to do what you want, and you can export the result
into many different formats.

Best regards,
Folmer Fredslund




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Re: [PyMOL] sequence conservation alignment onto structure

[Folmer Fredslund]

Dear Humayun,


On 4 June 2010 13:30, humayun scherrif hum@gmail.com wrote:
 Dear All,
 Is there any way of color coding sequence conservation of a protein onto
 structure by using multiple sequence alignment and structure in pymol ?


It might be possible to do this in PyMOL, but I would strongly advise
you to have a look at ALINE:
http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/

Here you can color the alignment and export the colors to a PyMOL script.

This is at least one way to do it.

Best regards,
Folmer Fredslund




 Thanks in advance

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 Tel (Lab) : +82-62-970-2549
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Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids

[Folmer Fredslund]

Dear Carsten,

On 17 May 2010 14:39, Carsten Siebenhaar csie...@gwdg.de wrote:
 Hello, I'm new to this board.
 I came across a certain problem with the mutagenesis tool. I got a pdb-file 
 with amino acids that are partly displayed as 2 rotamers (so one amino acid 
 displayed in two different ways in the Viewer).
 Usually, the mutagenesis tool works fine, but if you try to mutate this amino 
 acid it won't accept it, but will just mention in the external GUI that it 
 selected the corresponding atoms:
You clicked /11//A/HIS`509/CD2`A
  Selector: selection sele defined with 20 atoms.
 PyMol keeps on asking me to pick a residue.

 Is there a way to easily avoid this problem or could this be considered a 
 real bug?
 Thanks a lot!
 Carsten


Do you want to retain the double conformations? If not, then you could
use PyMOL to delete the alternate conformations thus, just retaining
one of them.

# select  remove all non A altlocs
remove not (alt ''+A)
# reset the PDB information
alter all, alt=''

taken from:
http://pymolwiki.org/index.php/Property_Selectors#Alternate_Locations


I hope this helps.
Folmer Fredslund




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Re: [PyMOL] echoing command line history

[Folmer Fredslund]

Dear Tsjerk,


On 18 March 2010 10:08, Tsjerk Wassenaar tsje...@gmail.com wrote:
 Hi Jason, e.a.

 I would really like to be able to echo my session command line history
 to a file. I'm not sure whether I just missed something, or that it's
 not in yet. If the latter is the case, I'd like to put it forward as a
 feature request. Otherwise, I'd be eager to be enlightened. I found
 something about logging, but it didn't seem to produce a file, or it
 hid it very well. Also, that seems to echo results from commands,
 while I would like to have just the commands I entered. And I did
 search the mailing list :)


Perhaps you are looking for the log_open and log_close commands?
After opening PyMOL you simply type

log_open myfile.txt

And every following command will be written to the file myfile.txt.
And you can close the log again with log_close.

I am not sure if this is what you found earlier on, but this has
worked nicely for me everytime I've used it.
You don't mention what OS you are using, but the pwd command will give
you your current path (at least on linux) and it should be relatively
easy to find the output file afterwards.

Best regards,
Folmer Fredslund



 Thanks in advance,

 Tsjerk

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Re: [PyMOL] how to run the script file in pymol

[Folmer Fredslund]

Hi John,

Please be aware that there is a difference between a python script
that allows you to define some functionality you can use in PyMOL
(usually with a .py ending), and a script that will read coordinates
and do some PyMOL stuff (which I usually apply a .pml ending).

So, what I think is happening is that you have a python script that
defines a function in PyMOL. But you don't use the function afterwards
to actually make something appear on the screen.

Alternatively you have a script with proper PyMOL commands, but that
kind of scripts you need to run by typing @myscript.pml on the
command line. Don't know how to do that from the GUI.

I think that http://www.pymolwiki.org/index.php/LoadDir should give
you an idea of what I am talking about.

Hope this helps.

Regards,
Folmer

On 6 February 2010 09:59, Jhon Thomas jhon1.tho...@gmail.com wrote:
 Hello all

 I am novice to the crystallography and i have a very little idea of the
 programming and scripting. I would like to run some python script which is
 already available on the pymol wiki.Whenevr i run the script file the
 image never appreas. This is the way i following the path.

 1). copy the script in file with extension.py for example. draw_line.py.
 2). Then i go in the File drop down in pymol GUI and select the run
 option.
 3). select the file which i want to run. for example. draw_line.py

 The image of line never appears on the screen. pymol doesnot show any syntax
 or any kind of error. Where i am making a mistake or any thing which is not
 being done.or any other way to run the script. I am using the pymol version
 0.99rc 6. I will appreciate the help.

 Thanks in advance

 john


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Re: [PyMOL] Regarding Object Find

[Folmer Fredslund]

Dear Suneel Kumar,



2009/10/26 Suneel Kumar Bommisetty suneel.bommise...@gvkbio.com:
 Dear All,



 I am looking for script for “object find” In pymol. I have a sd file
 contains 20 molecules. I have loaded into pymol. If I want visualize next
 molecule, I need to press Play or forward or disply – sequence function. Is
 there any script to/load/select/highlight specific molecule from one object?



 Please reply back



I don't think you need a script to do this.
Look into this link
http://pymolwiki.org/index.php/States
and I think you will understand.

Best regards,
Folmer Fredslund

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Re: [PyMOL] Viewport dimensions query

[Folmer Fredslund]

Hi Carsten,

Is this what you are looking for?
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05888.html

Best regards,
Folmer Fredslund

2009/9/24 Schubert, Carsten [PRDUS] cschu...@its.jnj.com:
 Hi,

 Does anyone know how to  get a hold of the viewport dimensions from within a
 script? I vaguely remember some posts about this subject, but could not find
 anything in my archive.

 Thanks

     Carsten

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[PyMOL] Getting ranges from selections

[Folmer Fredslund]

Dear all,

For several reasons I have been printing the residue numbers from
selections. This could be just the loops, or interface residues
defined with the script from Jason Vertrees.

I use iterate for this and it works well enough, however I would like
to be able to make:

1. a non-redundant list (e.g. residue 12 will only appear once)
2. adjacent numbers into ranges (e.g. residues 1, 2, 4, 5, 6, 10, 11,
12 would become 1:2, 4:6, 10:12 or something similar)

Any ideas on how to do this best? Ideally this should of course be
possible from within PyMOL, but any kind of script that will work on
your normal linux distribution would make me happy.

Best regards,

Folmer Fredslund

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Re: [PyMOL] Label coordinates

[Folmer Fredslund]

Dear Warran,

Thanks for the swift reply.

In the meantime I will workaround it by creating a new molecule with
the labeled atoms and move the atoms. This works more or less the way
I entended.


Best regards,
Folmer



2009/7/9 Warren DeLano war...@delsci.com:
 Folmer,

 Sorry no, this is still a to do item.

 Cheers,
 Warren

 -Original Message-
 From: Folmer Fredslund [mailto:folm...@gmail.com]
 Sent: Thursday, July 09, 2009 6:33 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Label coordinates

 Dear all,

 Is there a way to get the coordinates for manually shifted labels?
 What I want to do is to include the label positions in my script
 instead of moving the labels each time I update my figure.

 Thanks in advance,

 Folmer Fredslund


 
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[PyMOL] Label coordinates

[Folmer Fredslund]

Dear all,

Is there a way to get the coordinates for manually shifted labels?
What I want to do is to include the label positions in my script
instead of moving the labels each time I update my figure.

Thanks in advance,

Folmer Fredslund

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Re: [PyMOL] surface area calculation

[Folmer Fredslund]

Dear Luisa,



2009/4/21 Maria Luisa Rodrigues mlrodrig...@igc.gulbenkian.pt:
 Dear all,

 Is there any PyMOL command to calculate surface areas?
 Many thanks,



Did you try to search for information yourself first?

Anyways, the pymolwiki.org is always a good place to go and then you
would have found something like this:
http://pymolwiki.org/index.php/Get_Area

I hope this is what you are looking for?

Best regards,
Folmer Fredslund

Re: [PyMOL] Saving figures for publication

[Folmer Fredslund]

Dear Abhinav

2009/3/13 Abhinav Kumar abhin...@slac.stanford.edu:
 Hi,

 I need to make figures in tiff format with at least 600 dpi resolution
 as required by the journal. The default resolution in Pymol figures is
 72. Is there a simple way to increase the resolution (and save it in
 tiff format)?
 Alternatively, I can 'convert' from png to tiff afterwards


I don't think anything changed so the only possibility is png format.
The command is very well documented in the wiki:
http://www.pymolwiki.org/index.php/Cmd_png

Or within pymol (help png).

Please, DO read the manual.

Best regards,
Folmer




 --
 Thanks
 Abhinav

Re: [PyMOL] Newbie Questions: Sequence Bar breaks vs gaps? Residue NAG? HOH?

[Folmer Fredslund]

Hi Massimo

2008/10/13 Massimo Heitor massimohei...@gmail.com:
 I am looking at the residue sequence for a protein that I'm studying for a
 class and I have a few questions.
 I understand the regular amino acid codes (CYS, ARG, LEU, etc...).
 What is NAG? I see one sequence NAG NAG NAG NAG (resisting off-topic joke)

If you have access to wikipedia a quick search would indicate that you
might be looking at N-Acetylglucosamine
(http://en.wikipedia.org/wiki/N-Acetylglucosamine).

 What is HOH? I see about 107 HOH elements in a row. They are all colored
 red. What is that?

Ok, I'm going to ask a question. What molecule has to H atoms and one O?

 On the sequence number bar, I see one break represented as //, and one gap
 in the numbering. 130-133 is NAG NAG NAG NAG, and 140-246 is all HOH, but
 there is seemingly nothing at positions 134-139. Why is that? What is the
 difference between a // break and a numbering sequence gap?

I don't use the sequence bar myself so I'll have to pass an that question.

 Thanks!

Hope this helps!

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Re: [PyMOL] Electron density map in pymol

[Folmer Fredslund]

2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
 Hello all pymol users

 I am new to pymol and trying to open a .xplor map file in pymol to get the
 electron density map of publication grade.
 The command i write for pymol to open the file and show electron density
 map  is -

 1) I convert ccp4 .map file into the .xplor file through mapman.

 # mymap.xplor loaded as  mymap loaded as state 0.
 2) Then i load the .xplor map file into pymol and write the following
 commands-

 isomesh map, mymap.xplor, 2.0, site, carve=1.6

 isomesh: map or brick object mymap.xplor not found.


I have to load the map first!

Example:

load mymap.xplor, themap
isomesh themapobject, themap, 2.0, site, carve=1.6







 What could be the problem? can any one give suggestion to solve it?

 Thanks in advance

 Jhon

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Re: [PyMOL] Electron density map in pymol

[Folmer Fredslund]

2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
 hello Mr. Fredslund

 I tried the way you have written but it is not working--

 map file name - test_map.xplor
 load test_map.xplor

 isomeah map, test_map.xplor, 2.0, site, carve=1.6

 Is this is the correct of writing the command

Dear Mr. Thomas

Ok, some basic PyMOL knowledge:

whenever you load something to PyMOL it is given a name.

load test_map.xplor, test_map

Now PyMOL knows that the map is henceforth called test_map

Therefore you should write
 isomesh mapobject, test_map, 2.0, site, carve=1.6

btw it is also possible to use a ccp4 map; simply rename the file to
end with ccp4 instead of map

example:

mv test_map.map test_map.ccp4

use test_map.ccp4 instead of the xplor map. (this might prove to be
slower though)

furthermore I would suggest you read the pymol wiki
(http://www.pymolwiki.org/index.php/Load)

or when using PyMOL try the help function:

help load
help isomesh
help color

hope this helps



 On Fri, Sep 26, 2008 at 5:42 PM, Folmer Fredslund folm...@gmail.com wrote:

 2008/9/26 Jhon Thomas jhon1.tho...@gmail.com:
  Hello all pymol users
 
  I am new to pymol and trying to open a .xplor map file in pymol to get
  the
  electron density map of publication grade.
  The command i write for pymol to open the file and show electron density
  map  is -
 
  1) I convert ccp4 .map file into the .xplor file through mapman.
 
  # mymap.xplor loaded as  mymap loaded as state 0.
  2) Then i load the .xplor map file into pymol and write the following
  commands-
 
  isomesh map, mymap.xplor, 2.0, site, carve=1.6
 
  isomesh: map or brick object mymap.xplor not found.
 

 I have to load the map first!

 Example:

 load mymap.xplor, themap
 isomesh themapobject, themap, 2.0, site, carve=1.6






 
  What could be the problem? can any one give suggestion to solve it?
 
  Thanks in advance
 
  Jhon
 
 
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