pymol-users Mailing List for PyMOL Molecular Graphics System

Hi HJ,

this should help:

PyMOL> set cylinder_shader_ff_workaround

Cheers,
  Thomas

On 26 Dec 2013, at 04:11, HJ Lee <hoj...@gm...> wrote:

> For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the cylindrical helices in cartoon presentation. It just presents helices as an empty space when the cylindrical helices option is ON . Regular helix representation works well. 
> 
> That would be really great if anyone could give me a clue how to fix it. 
> 
> Many thanks
> 
> HJ

For some reasons, PyMOL (1.6.0.0, windows 64 bits) doesn't show the cylindrical helices in cartoon presentation. It just presents helices as an empty space when the cylindrical helices option is ON . Regular helix representation works well. 

That would be really great if anyone could give me a clue how to fix it. 

Many thanks

HJ

How about,

color measure01, red
color measure02, yellow
etc.

Roger Rowlett
On Dec 24, 2013 8:51 AM, "Li Xue" <me....@gm...> wrote:

> Hello all,
>
> Is it possible that I could use *different* colors for the dashes for the
> distance measurements?
>
> I know I can use "set dash_color, red" to set all distance dashes into
> red.
>
> Many thanks.
>
> Li
>
> --
> Xue, Li
> Post-doctoral Research Associate
> College of Information Sciences and Technology
> Penn State University
> Email: me....@gm...
> Web site: http://www.cs.iastate.edu/~lixue/
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello all,

Is it possible that I could use *different* colors for the dashes for the
distance measurements?

I know I can use "set dash_color, red" to set all distance dashes into red.

Many thanks.

Li

-- 
Xue, Li
Post-doctoral Research Associate
College of Information Sciences and Technology
Penn State University
Email: me....@gm...
Web site: http://www.cs.iastate.edu/~lixue/

Hi Ahmet,

On 22 Dec 2013, at 12:17, Ahmet yıldırım wrote:
> Pymol show them as a sticks but they are very similar. How can I color each residue with different colors?

if you have incentive PyMOL 1.6, you can use the spectrum command to color by residue type:

PyMOL> spectrum resn

With older versions or with open-source, you have to do this manually:

PyMOL> color blue, resn ALA
PyMOL> color red, resn GLY
PyMOL> color yellow, resn CYS
PyMOL> ...

There are scripts on the web for that, for example Robert Campbell has one:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Hope that helps.

Cheers,
  Thomas

On 22 Dec 2013, at 12:17, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear Thomas,
> 
> I did as you said "PyMOL> set use_shaders, 0". The problem is solved. Thanks.
> But I have a small problem.
> I typed:  
> select resi resi 15-18
> show sticks, sele
> 
> Pymol show them as a sticks but they are very similar. How can I color each residue with different colors?
> 
> Thanks in advance
> 
> 2013/12/22 Thomas Holder
> Hi Ahmet,
> 
> could be a shader problem (missing support by your graphics driver). Try:
> 
> PyMOL> set cylinder_shader_ff_workaround
> (see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround )
> 
> or:
> 
> PyMOL> set use_shaders, 0
> 
> Cheers,
>   Thomas
> 
> On 22 Dec 2013, at 00:39, Ahmet yıldırım wrote:
> 
> > Dear users,
> >
> > I want to show the residue 15 as a stick in xxxx.pdb.
> > pymol-->file-->Open-->xxxx.pdb
> > PyMOL> hide everything, all
> > PyMOL> select active, resi 15
> > PyMOL> show sticks, resi 15
> >
> > Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
> > Where did I mistake?
> >
> > Thanks in advance
> >
> > --
> > Ahmet Yıldırım
> -- 
> Ahmet Yıldırım

this works for me when testing using PDB ID code 4GRV (and others).  Can you test this PDB ID with your setup to see if it works?  The unknown variable here is your pdb file, possibly something is odd about it or something might be wrong with PyMOL as Thomas has indicated.  If PDB ID code 4GRV works ok for you, then the problem is probably your pdb file.


Cheers,
Nick


________________________________________
From: Ahmet yıldırım [ahm...@gm...]
Sent: Sunday, December 22, 2013 12:39 AM
To: pym...@li...
Subject: [PyMOL] sticks

Dear users,

I want to show the residue 15 as a stick in xxxx.pdb.
pymol-->file-->Open-->xxxx.pdb
PyMOL> hide everything, all
PyMOL> select active, resi 15
PyMOL> show sticks, resi 15

Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
Where did I mistake?

Thanks in advance

--
Ahmet Yıldırım

Hello all,

I installed pymol from source to my mac. At first I can invoke pymol from
terminal without any problem. But after a few days, if I invoke pymol from
terminal the Tcl/Tk GUI does not show up any more.

Does anyone know about it? Thanks.

Li

-- 
Xue, Li
Post-doctoral Research Associate
College of Information Sciences and Technology
Penn State University
Email: me....@gm...
Web site: http://www.cs.iastate.edu/~lixue/

Hi Ahmet,

could be a shader problem (missing support by your graphics driver). Try:

PyMOL> set cylinder_shader_ff_workaround
(see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround )

or:

PyMOL> set use_shaders, 0

Cheers,
  Thomas

On 22 Dec 2013, at 00:39, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear users,
> 
> I want to show the residue 15 as a stick in xxxx.pdb.
> pymol-->file-->Open-->xxxx.pdb
> PyMOL> hide everything, all
> PyMOL> select active, resi 15
> PyMOL> show sticks, resi 15
> 
> Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
> Where did I mistake?
> 
> Thanks in advance
> 
> -- 
> Ahmet Yıldırım

Dear users,

I want to show the residue 15 as a stick in xxxx.pdb.
pymol-->file-->Open-->xxxx.pdb
PyMOL> hide everything, all
PyMOL> select active, resi 15
PyMOL> show sticks, resi 15

Unfortunately, pymol doesnt show it as a stick. Please see image
https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
Where did I mistake?

Thanks in advance

-- 
Ahmet Yıldırım

I finally figured out the problem while trying to kluge a workaround. I
thought I'd mention the solution for the archive trawlers benefit. The
group command was unnecessary and when removed the script behaved
perfectly.

Thanks for all your time and help,
Katherine


On Thu, Dec 19, 2013 at 7:34 AM, Katherine Sippel <
kat...@gm...> wrote:

> Sorry if I was unclear. Currently I've got a functioning script that looks
> for a specific set of interactions in 3D space for each ligand in a pdb. If
> this interaction exists it gets passed along to a solvent accessible
> surface area %cutoff to eliminate ligands that are sitting on bulk solvent.
> I need to distinguish between genuine solvent exposed ligands and those
> that are sitting on a biological interface that isn't represented in the
> crystallographic ASU. Loading as a multiplex=1 or grouping alone is
> insufficient for program to recognize and account for the other molecules
> and include them in the calculations, hence the create command.
>
> Basically I need a way to load the .pdb1 files as the full biological
> assembly. I need it recognize if it is a multimer (I was using count_states
> if loop as that recognition mechanism). If it recognizes that it is a
> multimer it needs to then pass the multimer into the group/create loop. If
> it is a monomer it needs to proceed through the rest of the script. This is
> a PDB datamining thing so it needs to be broad enough to account for any
> possible oligomer. If there is another way for the program to recognize
> that there are multimers present that would be great. Count_states was the
> only criteria I managed to fish out of the wiki/bb archives.
>
> Thanks for the advice,
> Katherine
>
>
> On Thu, Dec 19, 2013 at 12:20 AM, Tsjerk Wassenaar <ts...@gm...>wrote:
>
>> Hi Katherine,
>>
>> You explain some of how you want to do it, but you don't explain what
>> you're trying to do. What is the objective? It may well be that there's an
>> easier way. As a sidenote, create can also make an object with multiple
>> states. Check the help.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>> On Wed, Dec 18, 2013 at 10:57 PM, Katherine Sippel <
>> kat...@gm...> wrote:
>>
>>> Hi all,
>>>
>>> I'm trying to load biological assemblies into my script. From old
>>> bulletin board messages I figured out that multiplex=1 would output the
>>> biological assembly as different states and objects. I worked out that
>>> cmd.group() would give a single object with multiple states. Then
>>> cmd.create() would make one object with one state. Unfortunately if you
>>> group a monomer with one state it gives you a selection of 0 atoms. There
>>> is a whole bunch of arithmetic on the back end of the script crashes with a
>>> divide by zero error for the monomeric ones. I thought I'd be smart and use
>>> count_states to build a conditional loop but I don't think I"m using it
>>> correctly because it isn't passing the multiple states into the loop.
>>>
>>> Is there some requirement that I'm missing or not seeing here?
>>>
>>> This might be easier to explain if I snip from scripts...
>>>
>>> #Outputs the monomers correctly but doesn't account for the biological
>>> assembly so I get false negatives
>>>
>>> cmd.set("all_states", 1)
>>> for file in glob("*.pdb1"):
>>>     cmd.load(file,'prot')
>>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>>
>>> #Outputs the multimers correctly but gives a divide by zero error for
>>> the monomers
>>>
>>> cmd.set("all_states", 1)
>>> for file in glob("*.pdb1"):
>>>     cmd.load(file,'prot', multiplex =1)
>>>     cmd.group('ens', 'prot'+'*')
>>>     cmd.create('BA', 'ens')
>>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>>
>>> #Outputs the monomers correctly but doesn't pass multimers into the
>>> conditional loop. I've also tried moving the cmd.group() before the if
>>> loop. That didn't work either.
>>>
>>> cmd.set("all_states", 1)
>>> for file in glob("*.pdb1"):
>>>     cmd.load(file,'prot', multiplex=1)
>>>     if cmd.count_states('prot') > 1:
>>>         cmd.group('ens', 'prot')
>>>         cmd.create('BA', 'ens')
>>>         cmd.delete('ens')
>>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>>
>>> Any help would be appreciated. I swear this is the last time I'll bother
>>> you. Thanks again.
>>> Katherine
>>>
>>>
>>>
>>> --
>>> "Nil illegitimo carborundum"* - *Didactylos
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Rapidly troubleshoot problems before they affect your business. Most IT
>>> organizations don't have a clear picture of how application performance
>>> affects their revenue. With AppDynamics, you get 100% visibility into
>>> your
>>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>>> AppDynamics Pro!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> 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.
>>
>>
>
>
> --
> "Nil illegitimo carborundum"* - *Didactylos
>



-- 
"Nil illegitimo carborundum"* - *Didactylos

Sorry if I was unclear. Currently I've got a functioning script that looks
for a specific set of interactions in 3D space for each ligand in a pdb. If
this interaction exists it gets passed along to a solvent accessible
surface area %cutoff to eliminate ligands that are sitting on bulk solvent.
I need to distinguish between genuine solvent exposed ligands and those
that are sitting on a biological interface that isn't represented in the
crystallographic ASU. Loading as a multiplex=1 or grouping alone is
insufficient for program to recognize and account for the other molecules
and include them in the calculations, hence the create command.

Basically I need a way to load the .pdb1 files as the full biological
assembly. I need it recognize if it is a multimer (I was using count_states
if loop as that recognition mechanism). If it recognizes that it is a
multimer it needs to then pass the multimer into the group/create loop. If
it is a monomer it needs to proceed through the rest of the script. This is
a PDB datamining thing so it needs to be broad enough to account for any
possible oligomer. If there is another way for the program to recognize
that there are multimers present that would be great. Count_states was the
only criteria I managed to fish out of the wiki/bb archives.

Thanks for the advice,
Katherine


On Thu, Dec 19, 2013 at 12:20 AM, Tsjerk Wassenaar <ts...@gm...>wrote:

> Hi Katherine,
>
> You explain some of how you want to do it, but you don't explain what
> you're trying to do. What is the objective? It may well be that there's an
> easier way. As a sidenote, create can also make an object with multiple
> states. Check the help.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Dec 18, 2013 at 10:57 PM, Katherine Sippel <
> kat...@gm...> wrote:
>
>> Hi all,
>>
>> I'm trying to load biological assemblies into my script. From old
>> bulletin board messages I figured out that multiplex=1 would output the
>> biological assembly as different states and objects. I worked out that
>> cmd.group() would give a single object with multiple states. Then
>> cmd.create() would make one object with one state. Unfortunately if you
>> group a monomer with one state it gives you a selection of 0 atoms. There
>> is a whole bunch of arithmetic on the back end of the script crashes with a
>> divide by zero error for the monomeric ones. I thought I'd be smart and use
>> count_states to build a conditional loop but I don't think I"m using it
>> correctly because it isn't passing the multiple states into the loop.
>>
>> Is there some requirement that I'm missing or not seeing here?
>>
>> This might be easier to explain if I snip from scripts...
>>
>> #Outputs the monomers correctly but doesn't account for the biological
>> assembly so I get false negatives
>>
>> cmd.set("all_states", 1)
>> for file in glob("*.pdb1"):
>>     cmd.load(file,'prot')
>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>
>> #Outputs the multimers correctly but gives a divide by zero error for
>> the monomers
>>
>> cmd.set("all_states", 1)
>> for file in glob("*.pdb1"):
>>     cmd.load(file,'prot', multiplex =1)
>>     cmd.group('ens', 'prot'+'*')
>>     cmd.create('BA', 'ens')
>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>
>> #Outputs the monomers correctly but doesn't pass multimers into the
>> conditional loop. I've also tried moving the cmd.group() before the if
>> loop. That didn't work either.
>>
>> cmd.set("all_states", 1)
>> for file in glob("*.pdb1"):
>>     cmd.load(file,'prot', multiplex=1)
>>     if cmd.count_states('prot') > 1:
>>         cmd.group('ens', 'prot')
>>         cmd.create('BA', 'ens')
>>         cmd.delete('ens')
>>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>>
>> Any help would be appreciated. I swear this is the last time I'll bother
>> you. Thanks again.
>> Katherine
>>
>>
>>
>> --
>> "Nil illegitimo carborundum"* - *Didactylos
>>
>>
>> ------------------------------------------------------------------------------
>> Rapidly troubleshoot problems before they affect your business. Most IT
>> organizations don't have a clear picture of how application performance
>> affects their revenue. With AppDynamics, you get 100% visibility into your
>> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
>> Pro!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>> _______________________________________________
>> 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.
>
>


-- 
"Nil illegitimo carborundum"* - *Didactylos

Hi Katherine,

You explain some of how you want to do it, but you don't explain what
you're trying to do. What is the objective? It may well be that there's an
easier way. As a sidenote, create can also make an object with multiple
states. Check the help.

Hope it helps,

Tsjerk


On Wed, Dec 18, 2013 at 10:57 PM, Katherine Sippel <
kat...@gm...> wrote:

> Hi all,
>
> I'm trying to load biological assemblies into my script. From old
> bulletin board messages I figured out that multiplex=1 would output the
> biological assembly as different states and objects. I worked out that
> cmd.group() would give a single object with multiple states. Then
> cmd.create() would make one object with one state. Unfortunately if you
> group a monomer with one state it gives you a selection of 0 atoms. There
> is a whole bunch of arithmetic on the back end of the script crashes with a
> divide by zero error for the monomeric ones. I thought I'd be smart and use
> count_states to build a conditional loop but I don't think I"m using it
> correctly because it isn't passing the multiple states into the loop.
>
> Is there some requirement that I'm missing or not seeing here?
>
> This might be easier to explain if I snip from scripts...
>
> #Outputs the monomers correctly but doesn't account for the biological
> assembly so I get false negatives
>
> cmd.set("all_states", 1)
> for file in glob("*.pdb1"):
>     cmd.load(file,'prot')
>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>
> #Outputs the multimers correctly but gives a divide by zero error for the
> monomers
>
> cmd.set("all_states", 1)
> for file in glob("*.pdb1"):
>     cmd.load(file,'prot', multiplex =1)
>     cmd.group('ens', 'prot'+'*')
>     cmd.create('BA', 'ens')
>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>
> #Outputs the monomers correctly but doesn't pass multimers into the
> conditional loop. I've also tried moving the cmd.group() before the if
> loop. That didn't work either.
>
> cmd.set("all_states", 1)
> for file in glob("*.pdb1"):
>     cmd.load(file,'prot', multiplex=1)
>     if cmd.count_states('prot') > 1:
>         cmd.group('ens', 'prot')
>         cmd.create('BA', 'ens')
>         cmd.delete('ens')
>     cmd.select('allLigands', "het and (not resn HOH)") etc.
>
> Any help would be appreciated. I swear this is the last time I'll bother
> you. Thanks again.
> Katherine
>
>
>
> --
> "Nil illegitimo carborundum"* - *Didactylos
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> _______________________________________________
> 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.

Hi all,

I'm trying to load biological assemblies into my script. From old bulletin
board messages I figured out that multiplex=1 would output the biological
assembly as different states and objects. I worked out that cmd.group()
would give a single object with multiple states. Then cmd.create() would
make one object with one state. Unfortunately if you group a monomer with
one state it gives you a selection of 0 atoms. There is a whole bunch of
arithmetic on the back end of the script crashes with a divide by zero
error for the monomeric ones. I thought I'd be smart and use count_states
to build a conditional loop but I don't think I"m using it correctly
because it isn't passing the multiple states into the loop.

Is there some requirement that I'm missing or not seeing here?

This might be easier to explain if I snip from scripts...

#Outputs the monomers correctly but doesn't account for the biological
assembly so I get false negatives

cmd.set("all_states", 1)
for file in glob("*.pdb1"):
    cmd.load(file,'prot')
    cmd.select('allLigands', "het and (not resn HOH)") etc.

#Outputs the multimers correctly but gives a divide by zero error for the
monomers

cmd.set("all_states", 1)
for file in glob("*.pdb1"):
    cmd.load(file,'prot', multiplex =1)
    cmd.group('ens', 'prot'+'*')
    cmd.create('BA', 'ens')
    cmd.select('allLigands', "het and (not resn HOH)") etc.

#Outputs the monomers correctly but doesn't pass multimers into the
conditional loop. I've also tried moving the cmd.group() before the if
loop. That didn't work either.

cmd.set("all_states", 1)
for file in glob("*.pdb1"):
    cmd.load(file,'prot', multiplex=1)
    if cmd.count_states('prot') > 1:
        cmd.group('ens', 'prot')
        cmd.create('BA', 'ens')
        cmd.delete('ens')
    cmd.select('allLigands', "het and (not resn HOH)") etc.

Any help would be appreciated. I swear this is the last time I'll bother
you. Thanks again.
Katherine



-- 
"Nil illegitimo carborundum"* - *Didactylos

Hi Katherine,

PyMOL can do what you want. I've done this exact task before.

Here's the idea. If you have a PDB with multiple ligands and you use,

  select allLigands, organic and myProtein

you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do is extract each ligand,
molecule by molecule, from the allLigands selection using selection
algebra until myLigands is empty. It's done like this:

# create a selection containing the atoms of all ligands

select allLigands, organic and myProtein

# create a selection to use later as we iterate across
# all ligands, this will hold individual ligands we extract
# from allLigands

select current_ligand, none

# enter a Python block so we can use Python while-loop
# and other Python syntax

python

# loop until allLigands is not empty

while cmd.count_atoms("myLigands") > 0:

  # copy the first ligand selection, by molecule, into
  # the, "current_ligand"

  cmd.select("current_ligand", "bm. first allLigands")

  # do something with "current_ligand", like finding all ligands
  # without waters nearby

  if cmd.count_atoms("solvent within 5 of current_ligand") == 0:

    print "This is an interesting ligand."

  # now remove current_ligand from allLigands
  # and loop again

  cmd.select("allLigands", "allLigands and not current_ligand")

python end

Good luck!

Cheers,

-- Jason


On Fri, Dec 13, 2013 at 4:58 PM, Katherine Sippel
<kat...@gm...> wrote:
> Hi Carsten,
>
> Thanks for the help. I've tried variants of that selection and it works
> great if there is only one ligand. Unfortunately it breaks down when there
> are multiple ligands and they don't all fit the criteria. I'm surveying
> almost half the PDB so these are all different proteins with different
> binding sites and ligands. I was hoping for a way to get pymol to recognize
> each individual ligand automatically by grouping common resids within the
> non-solvent hetatm selection. Using the %s %(resi) seems to require an
> explicit input.
>
> I might be able to extract an explicit chain/resi designation for each file
> from the het portion of the pdb header, though I'm not sure how to automate
> this. I suppose it's back to the script repository for me.
>
> Cheers,
> Katherine
>
>
> On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS]
> <CSC...@it...> wrote:
>>
>> Katherine,
>>
>>
>>
>> not sure if that is what you are looking for but you can select for
>> non-polymer residues with:
>>
>>
>>
>> select lig, prot and organic
>>
>>
>>
>> That will select any non polymer (protein and R(D)NA) residues present in
>> the pdb. You then would need to break the selection further into the
>> individual constituents, by either chain Id and resid.
>>
>>
>>
>> Hope this helps a bit.
>>
>>
>>
>> Carsten
>>
>>
>>
>> From: Katherine Sippel [mailto:kat...@gm...]
>> Sent: Friday, December 13, 2013 10:28 AM
>> To: pym...@li...
>> Subject: [PyMOL] Selection algebra issue
>>
>>
>>
>> Hi all,
>>
>> I'm trying to write a script to data mine the pdb. I'm want to look at the
>> ligands in a pdb file and fish out those that meet a certain criteria. I've
>> got a script that can look at the ligands all at once but I need to assess
>> each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
>> define them individually. I've tried variations on "%s' % (resi)" and
>> "bymolec" but I can't seem to figure out how to get them parsed separately
>> without specifying a number. I've also tried using index to create a tuples
>> list and iterating from that but I keep hitting the same issue. I've
>> attached a couple of the attempted scripts so you can laugh at my google
>> derived python skills.
>>
>> I've been trying to figure this out for a week now and I'm completely
>> stumped. If anyone could nudge me in the right direction, even if it's some
>> Pymolwiki article I missed, I would appreciate it immensely.
>>
>> Thanks for your time,
>> Katherine
>>
>>
>> --
>>
>> "Nil illegitimo carborundum" - Didactylos
>
>
>
>
> --
> "Nil illegitimo carborundum" - Didactylos
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
> Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Carsten,

Thanks for the help. I've tried variants of that selection and it works
great if there is only one ligand. Unfortunately it breaks down when there
are multiple ligands and they don't all fit the criteria. I'm surveying
almost half the PDB so these are all different proteins with different
binding sites and ligands. I was hoping for a way to get pymol to recognize
each individual ligand automatically by grouping common resids within the
non-solvent hetatm selection. Using the %s %(resi) seems to require an
explicit input.

I might be able to extract an explicit chain/resi designation for each file
from the het portion of the pdb header, though I'm not sure how to automate
this. I suppose it's back to the script repository for me.

Cheers,
Katherine


On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS] <
CSC...@it...> wrote:

>  Katherine,
>
>
>
> not sure if that is what you are looking for but you can select for
> non-polymer residues with:
>
>
>
> select lig, prot and organic
>
>
>
> That will select any non polymer (protein and R(D)NA) residues present in
> the pdb. You then would need to break the selection further into the
> individual constituents, by either chain Id and resid.
>
>
>
> Hope this helps a bit.
>
>
>
> Carsten
>
>
>
> *From:* Katherine Sippel [mailto:kat...@gm...]
> *Sent:* Friday, December 13, 2013 10:28 AM
> *To:* pym...@li...
> *Subject:* [PyMOL] Selection algebra issue
>
>
>
> Hi all,
>
> I'm trying to write a script to data mine the pdb. I'm want to look at the
> ligands in a pdb file and fish out those that meet a certain criteria. I've
> got a script that can look at the ligands all at once but I need to assess
> each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
> define them individually. I've tried variations on "%s' % (resi)" and
> "bymolec" but I can't seem to figure out how to get them parsed separately
> without specifying a number. I've also tried using index to create a tuples
> list and iterating from that but I keep hitting the same issue. I've
> attached a couple of the attempted scripts so you can laugh at my google
> derived python skills.
>
> I've been trying to figure this out for a week now and I'm completely
> stumped. If anyone could nudge me in the right direction, even if it's some
> Pymolwiki article I missed, I would appreciate it immensely.
>
> Thanks for your time,
> Katherine
>
>
> --
>
> "Nil illegitimo carborundum"* - *Didactylos
>



-- 
"Nil illegitimo carborundum"* - *Didactylos

Katherine,

not sure if that is what you are looking for but you can select for non-polymer residues with:

select lig, prot and organic

That will select any non polymer (protein and R(D)NA) residues present in the pdb. You then would need to break the selection further into the individual constituents, by either chain Id and resid.

Hope this helps a bit.

Carsten

From: Katherine Sippel [mailto:kat...@gm...]
Sent: Friday, December 13, 2013 10:28 AM
To: pym...@li...
Subject: [PyMOL] Selection algebra issue

Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the ligands in a pdb file and fish out those that meet a certain criteria. I've got a script that can look at the ligands all at once but I need to assess each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to define them individually. I've tried variations on "%s' % (resi)" and "bymolec" but I can't seem to figure out how to get them parsed separately without specifying a number. I've also tried using index to create a tuples list and iterating from that but I keep hitting the same issue. I've attached a couple of the attempted scripts so you can laugh at my google derived python skills.
I've been trying to figure this out for a week now and I'm completely stumped. If anyone could nudge me in the right direction, even if it's some Pymolwiki article I missed, I would appreciate it immensely.
Thanks for your time,
Katherine

--
"Nil illegitimo carborundum" - Didactylos

Hi all,

I'm trying to write a script to data mine the pdb. I'm want to look at the
ligands in a pdb file and fish out those that meet a certain criteria. I've
got a script that can look at the ligands all at once but I need to assess
each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
define them individually. I've tried variations on "%s' % (resi)" and
"bymolec" but I can't seem to figure out how to get them parsed separately
without specifying a number. I've also tried using index to create a tuples
list and iterating from that but I keep hitting the same issue. I've
attached a couple of the attempted scripts so you can laugh at my google
derived python skills.

I've been trying to figure this out for a week now and I'm completely
stumped. If anyone could nudge me in the right direction, even if it's some
Pymolwiki article I missed, I would appreciate it immensely.

Thanks for your time,
Katherine

-- 
"Nil illegitimo carborundum"* - *Didactylos

Hi,

to get the angle between 4 atoms, use get_dihedral. For angle between 3 atoms (lines intersect) use get_angle.

http://pymolwiki.org/index.php/Get_Angle
http://pymolwiki.org/index.php/Get_Dihedral

Cheers,
  Thomas

PS: it's nice to give your name in an email to a list like this one

On 12 Dec 2013, at 18:24, rainfieldcn wrote:
> Hi All,
> I want to measure the angle between two lines in pymol.
> So I made two pseudoatoms on each line and want to define two vectors
> then measure the angle.
> How can I define this vector?
> Thanks!

Hi All,
I want to measure the angle between two lines in pymol.
So I made two pseudoatoms on each line and want to define two vectors
then measure the angle.
How can I define this vector?
Thanks!

Hi
thanks Pete, but I tried to install it with python 2.6.8 (the one I 
found on the net) and it still doesn't work (for any pymol version)...
I eventually reinstalled a very old version (0.99) which is the only one 
working for now

-- 
Edith Gincel
===========================================================
Universite Paris Descartes
UFR des Sciences Pharmaceutiques et Biologiques
UMR 8015 CNRS
Laboratoire de cristallographie et RMN biologiques
4, avenue de l'Observatoire    75270 PARIS Cedex 06
Tel: 33 (0) 1 53 73 96 87    Fax: 33 (0) 1 43 26 69 18
email : edi...@pa...
===========================================================


Le 10/12/2013 18:32, Pete Meyer a écrit :
> Hi,
>
> It sounds like you should check the version of python you're using to 
> try to build pymol.
>
> I've been able to build pymol 1.4.1 using python 2.6.4 (and pmw 1.3.2) 
> on several linux distributions (although I haven't tried on Centos 
> 5.10) and OS X.
>
> Hope this helps,
>
> Pete
>
> Edith Gincel wrote:
>> Dear all
>>
>> I am working on Centos 5.10, kernel 2.6.18-371.1.2.el5
>>
>> I was using pymol 1.3r2, and it worked perfectly
>> I installed a second screen (useful for NMR) on my computer, and 
>> since then, I have problems with pymol
>>
>> I first had to update my kernel, which is now the one I wrote on the 
>> top of my post.
>> but then, I couldn't launch pymol, I always got a "segmentation 
>> fault" and that was it....
>> I couln't find any reason for that
>>
>> So, I decided to install a new version of pymol.
>> I tried the 1.6.0.0 one,
>> "python setup.py build install"
>> Traceback (most recent call last):
>>    File "setup.py", line 142, in ?
>>      import create_shadertext
>>    File "/home/edith/logiciels/pymol/create_shadertext.py", line 8
>>      with open(os.path.join(shaderdir, inputfile)) as f:
>>              ^
>> SyntaxError: invalid syntax
>>
>> So I tried the 1.5 version, no more success (with other errors) .... 
>> neither any of the former versions could be installed (unless the 
>> 1.3r2 which doesn't work at all)
>>
>>
>> Does someone have any idea?
>>
>> thank you very much
>>
>>
>>
>
>

angstrom

J
On Dec 12, 2013, at 3:41 AM, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear users, 
> 
> What is the unit of RMSD in pymol? Nanometer or angstrom?
> 
> PyMOL>align structure1 & n. ca, structure2 & n. ca
> 
> -- 
> Ahmet Yıldırım
> 
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT 
> organizations don't have a clear picture of how application performance 
> affects their revenue. With AppDynamics, you get 100% visibility into your 
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk_______________________________________________
> 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 users,

What is the unit of RMSD in pymol? Nanometer or angstrom?

PyMOL>align structure1 & n. ca, structure2 & n. ca

-- 
Ahmet Yıldırım

Hi Yeping,

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

PyMOL>spectrum b, blue_white_red, byres=1

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

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

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

Hope that helps.

Cheers,
  Thomas

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

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

Hi,

It sounds like you should check the version of python you're using to 
try to build pymol.

I've been able to build pymol 1.4.1 using python 2.6.4 (and pmw 1.3.2) 
on several linux distributions (although I haven't tried on Centos 5.10) 
and OS X.

Hope this helps,

Pete

Edith Gincel wrote:
> Dear all
> 
> I am working on Centos 5.10, kernel 2.6.18-371.1.2.el5
> 
> I was using pymol 1.3r2, and it worked perfectly
> I installed a second screen (useful for NMR) on my computer, and since 
> then, I have problems with pymol
> 
> I first had to update my kernel, which is now the one I wrote on the top 
> of my post.
> but then, I couldn't launch pymol, I always got a "segmentation fault" 
> and that was it....
> I couln't find any reason for that
> 
> So, I decided to install a new version of pymol.
> I tried the 1.6.0.0 one,
> "python setup.py build install"
> Traceback (most recent call last):
>    File "setup.py", line 142, in ?
>      import create_shadertext
>    File "/home/edith/logiciels/pymol/create_shadertext.py", line 8
>      with open(os.path.join(shaderdir, inputfile)) as f:
>              ^
> SyntaxError: invalid syntax
> 
> So I tried the 1.5 version, no more success (with other errors) .... 
> neither any of the former versions could be installed (unless the 1.3r2 
> which doesn't work at all)
> 
> 
> Does someone have any idea?
> 
> thank you very much
> 
> 
> 

Dear all

I am working on Centos 5.10, kernel 2.6.18-371.1.2.el5

I was using pymol 1.3r2, and it worked perfectly
I installed a second screen (useful for NMR) on my computer, and since 
then, I have problems with pymol

I first had to update my kernel, which is now the one I wrote on the top 
of my post.
but then, I couldn't launch pymol, I always got a "segmentation fault" 
and that was it....
I couln't find any reason for that

So, I decided to install a new version of pymol.
I tried the 1.6.0.0 one,
"python setup.py build install"
Traceback (most recent call last):
   File "setup.py", line 142, in ?
     import create_shadertext
   File "/home/edith/logiciels/pymol/create_shadertext.py", line 8
     with open(os.path.join(shaderdir, inputfile)) as f:
             ^
SyntaxError: invalid syntax

So I tried the 1.5 version, no more success (with other errors) .... 
neither any of the former versions could be installed (unless the 1.3r2 
which doesn't work at all)


Does someone have any idea?

thank you very much



-- 
Edith Gincel
==========================================================
Universite Paris Descartes - UFR des Sciences Pharmaceutiques et 
Biologiques
UMR 8015 CNRS - Laboratoire de cristallographie et RMN biologiques
4, avenue de l'Observatoire 75270 PARIS Cedex 06
Tel: 33 (0) 1 53 73 96 87 Fax: 33 (0) 1 43 26 69 18
email : edi...@pa...
==========================================================