Re: [PyMOL] Multi-snapshot superimposition

2019-06-27 Thread James Starlight
update:

for the realisation I have tried to use sep_state script with python version

so I modified sep_state adding superimposition
# pymol_save.py#
from pymol import cmd
import glob
import re

def save_sep(prefix=''):
  obj_list = cmd.get_names("public_objects")
  if obj_list:
for i in range(len(obj_list)):
  obj_name = "%s%s.pdb" % (prefix, obj_list[i])
  cmd.save(obj_name, obj_list[i])
  print "Saving %s" %  obj_name
  else:
print "No objects found"

cmd.extra_fit('name CA', '*', 'super')
cmd.extend('save_sep', save_sep)


and use it with my pdbs
pymol ${output}/*.pdb -ckqr pymol_save.py > ${output}/!temp/rmsf_fit.log

it align ensemble but did not save the resulted pdbs in separate
files. Finally, the same happenes when I open it in Pymol GUI
pymol-2.2.0 *.pdb pymol_save.py
remarkably when I use in this GUI session just a command 'save_sep' it
saves the files within the same directory (Which is ok!)
however cmd.extend('prefix', save_sep)does not work :(

чт, 27 июн. 2019 г. в 11:48, James Starlight :
>
> Dear Pymol users!
>
> I have a folder with many pdb files. I would like to use pymol in
> no-gui mode in order to i)load all pdb within the pymol; ii)
> superimpose each pdb agains the first (top) pdb; iii) save sperimposed
> pdbs into the new folder under the SAME names of pdbs.
>
> Here is model of my script, which should be modified according to the
> indicated commentaries (mostly on the step of saving results).
>
> ${pymol} -c -d "
>   from pymol import cmd
>   # we open at once all pdbs which have "B-factors" suffix in its name!
>   cmd.load('${output}/!temp/B-factors*')
>   # it do almost what I want in terms of the superimposition, however
> not all snapshots are aligned properly
>   cmd.extra_fit('name CA', '*', 'super')
>  # here the most tricky part that should be modified since I need to
> save snapshots using some command keeping its original names!
>   cmd.save('output' + '.pdb')
>   "
>
> so the task is that I would like to use it in one command rather then
> to put inside the loop (e.g. opening 2 snapshots for each time to make
> mobile, reference superimposition, which is more easy way).
>
> Thank you in advance!
> James


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[PyMOL] Multi-snapshot superimposition

2019-06-27 Thread James Starlight
Dear Pymol users!

I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.

Here is model of my script, which should be modified according to the
indicated commentaries (mostly on the step of saving results).

${pymol} -c -d "
  from pymol import cmd
  # we open at once all pdbs which have "B-factors" suffix in its name!
  cmd.load('${output}/!temp/B-factors*')
  # it do almost what I want in terms of the superimposition, however
not all snapshots are aligned properly
  cmd.extra_fit('name CA', '*', 'super')
 # here the most tricky part that should be modified since I need to
save snapshots using some command keeping its original names!
  cmd.save('output' + '.pdb')
  "

so the task is that I would like to use it in one command rather then
to put inside the loop (e.g. opening 2 snapshots for each time to make
mobile, reference superimposition, which is more easy way).

Thank you in advance!
James


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Re: [PyMOL] set transparency for selected elements of secondary structure

2019-06-26 Thread James Starlight
OK, with latest pymol

this works fine
set cartoon_transparency, 0.5, object

this does not work
set cartoon_transparency, 0.5, ss H+S

how I can select for example all of the objects in the current session
+ ss H+S ?

ср, 26 июн. 2019 г. в 11:13, Thomas Holder :
>
> Hi James and Ali,
>
> Are you using PyMOL 2.3 yet?
>
> "As of PyMOL version 2.3, cartoon transparency is now an atom-level setting."
>
> https://pymolwiki.org/index.php/Cartoon_transparency
>
> Cheers,
>   Thomas
>
> > On Jun 26, 2019, at 10:26 AM, Ali Kusay  wrote:
> >
> > Hi James,
> >
> > I am not sure what the exact cause of your issue is but I think if you make 
> > a selection first then apply the transparency to the selection that should 
> > work, i.e.:
> >
> > sele ss H+S
> > set cartoon_transparency, 0.5, sele
> >
> > Something to do with selection based transparency settings not enabling 
> > newer ones to be made
> >
> > Cheers,
> >
> > Ali
> >
> > On 26/6/19, 6:18 pm, "James Starlight"  wrote:
> >
> >Dear pymol users!
> >
> >I am trying to set transparency based on the secondary structure using
> >pymol selection algebra
> >
> ># set transparency to all helix and sheets but not loops
> >set cartoon_transparency, 0.5, ss H+S
> >
> >which produce the following output
> >PyMOL>set cartoon_transparency, 0.5, ss H+S
> > Setting: cartoon_transparency set for 144 atoms in object 
> > "0190_before_minim".
> >
> >but actually do nothing in terms of visualization.
> >
> >Could you suggest me how it would be possible to fix it?
> >
> >Thanks in advance!
> >
> >
> >___
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> >
> >
> >
> > ___
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> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>


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[PyMOL] set transparency for selected elements of secondary structure

2019-06-26 Thread James Starlight
Dear pymol users!

I am trying to set transparency based on the secondary structure using
pymol selection algebra

# set transparency to all helix and sheets but not loops
set cartoon_transparency, 0.5, ss H+S

which produce the following output
PyMOL>set cartoon_transparency, 0.5, ss H+S
 Setting: cartoon_transparency set for 144 atoms in object "0190_before_minim".

but actually do nothing in terms of visualization.

Could you suggest me how it would be possible to fix it?

Thanks in advance!


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Re: [PyMOL] PDB post-processing and TER records

2019-06-26 Thread James Starlight
Awesome, thanks so much Jared for your usefull suggestions!

all the best

james

вт, 25 июн. 2019 г. в 22:00, Jared Sampson :
>
> Hi James - Glad you got it working.
>
> > chains_array = ["A", "B"]
>
> If you want a list of chains without having to hard-code them, try the 
> `get_chains` command.
>
> ```
> chains_array = cmd.get_chains()
> ```
>
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
>
> Alternatively, if you want to remove all the chain IDs (which it appears you 
> might), you don't need a list of chains at all, and can just do:
>
> ```
> alter all, chain=''
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On June 25, 2019 at 11:48:32 AM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> I have got it, it works now!
> in my example the double quotes were not escaped in pymol script :-)
>
> the only (more python-oriented) question, would it be possible to
> indicate chains_array for all letters A-Z (e.g. using some python
> regex, rather just for A and B, chains_array = ["A", "B"], like in my
> example?
>
>
> вт, 25 июн. 2019 г. в 17:22, James Starlight :
> >
> > I actually tried to do like that still defining chains_array = ["A",
> > "B"] inside of pymol script and use external bash loop to loop over
> > pdbs
> > but it does not works ;(
> >
> > #!/bin/bash
> > # this script rename chains in pdb to "empty" chain
> > home=$(pwd)
> > pdb_folder=$home/pdbs
> > output=$home/output
> > rm -r $output
> > mkdir $output
> >
> > #pymol -cQkd "
> > for pdb in "${pdb_folder}"/*.pdb ; do
> > pdb_name2=$(basename "${pdb}")
> > pdb_name="${pdb_name2/pdb}"
> > pymol -c -d "
> > from pymol import cmd
> > chains_array = ["A", "B"]
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
> > cmd.set('pdb_use_ter_records', 1)
> > cmd.set('retain_order', 1)
> > cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
> > " > $output/pymol_${pdb_name}.log
> > done
> >
> > вт, 25 июн. 2019 г. в 16:58, James Starlight :
> > >
> > > yes, actually it is better because we avoid looping!
> > > and how it would be possible to use array provided in the externall shell?
> > >
> > > #!/bin/bash
> > > pdb="final.pdb"
> > > output=$(pwd)
> > >
> > > # array given in bash
> > > chains_array=('A' 'B')
> > >
> > > # chains are cutted by pymol
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> > > cmd.set('pdb_use_ter_records', 1)
> > > cmd.set('retain_order', 1)
> > > cmd.save('output_without'+"".join($chains_array) + '.pdb')
> > > "
> > >
> > > вт, 25 июн. 2019 г. в 16:47, Thomas Holder 
> > > :
> > > >
> > > > If you want to rename multiple chains at once, make a selection like 
> > > > (chain A+B+C). This list selection syntax is documented here: 
> > > > https://pymolwiki.org/index.php/Property_Selectors
> > > >
> > > > cmd.load(pdb)
> > > > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > > > cmd.save('output.pdb')
> > > >
> > > > Cheers,
> > > > Thomas
> > > >
> > > >
> > > > > On Jun 25, 2019, at 4:14 PM, James Starlight  
> > > > > wrote:
> > > > >
> > > > > thanks so much Thomas, for this example!
> > > > >
> > > > > Actually, your python script does exactly what my bash script -
> > > > > produces number of pdbs for each of the renamed chain.
> > > > > I would like rather to produce at the end ONE pdb with all chains
> > > > > renamed to empty chain...
> > > > > I guess I need to save the result outside of the loop something like 
> > > > > this
> > > > >
> > > > >  hop hey lalaley #
> > > > > from pymol import cmd
> > > > > pdb = "Ev_complex_model_final.pdb"
> > > > > chains_array = ["A", "B"] # add more chains in case of more complex 
> > > > > pdb
> > > > >
> > > > > # loop over chains to rename it
> > > > > for chain in chains_array:
> > > > > cmd.load(pdb)
> > > > > cmd.alter('chain ' + chain, 'chain=""')
> > > > > cmd.delete('*')
> > > > > ##
> > > > >
> > > > > # save output as pdb
> > > > > # I need to add something in the name of output indicating how much
> > > > > chains have been renamed
> > > > > # like output_withoutAB.pdb
> > > > > cmd.save('output_' + '.pdb')
> > > > >
> > > > > thanks in advance for help!
> > > >
> > > > --
> > > > Thomas Holder
> > > > PyMOL Principal Developer
> > > > Schrödinger, Inc.
> > > >
>
>
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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
I have got it, it works now!
in my example the double quotes were not escaped in pymol script :-)

the only (more python-oriented) question, would it be possible to
indicate chains_array for all letters A-Z (e.g. using some python
regex, rather just for A and B, chains_array = ["A", "B"], like in my
example?


вт, 25 июн. 2019 г. в 17:22, James Starlight :
>
> I actually tried to do like that still defining chains_array = ["A",
> "B"] inside of pymol script and use external bash loop to loop over
> pdbs
> but it does not works ;(
>
> #!/bin/bash
> # this script rename chains in pdb to "empty" chain
> home=$(pwd)
> pdb_folder=$home/pdbs
> output=$home/output
> rm -r $output
> mkdir $output
>
> #pymol -cQkd "
> for pdb in "${pdb_folder}"/*.pdb ; do
>   pdb_name2=$(basename "${pdb}")
>   pdb_name="${pdb_name2/pdb}"
> pymol -c -d "
> from pymol import cmd
> chains_array = ["A", "B"]
> cmd.load('${pdb}')
> cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
> " > $output/pymol_${pdb_name}.log
> done
>
> вт, 25 июн. 2019 г. в 16:58, James Starlight :
> >
> > yes, actually it is better because we avoid looping!
> > and how it would be possible to use array provided in the externall shell?
> >
> > #!/bin/bash
> > pdb="final.pdb"
> > output=$(pwd)
> >
> > # array given in bash
> > chains_array=('A' 'B')
> >
> > # chains are cutted by pymol
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> > cmd.set('pdb_use_ter_records', 1)
> > cmd.set('retain_order', 1)
> > cmd.save('output_without'+"".join($chains_array) + '.pdb')
> > "
> >
> > вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
> > >
> > > If you want to rename multiple chains at once, make a selection like 
> > > (chain A+B+C). This list selection syntax is documented here: 
> > > https://pymolwiki.org/index.php/Property_Selectors
> > >
> > > cmd.load(pdb)
> > > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > > cmd.save('output.pdb')
> > >
> > > Cheers,
> > >   Thomas
> > >
> > >
> > > > On Jun 25, 2019, at 4:14 PM, James Starlight  
> > > > wrote:
> > > >
> > > > thanks so much Thomas, for this example!
> > > >
> > > > Actually, your python script does exactly what my bash script -
> > > > produces number of pdbs for each of the renamed chain.
> > > > I would like rather to produce at the end ONE pdb with all chains
> > > > renamed to empty chain...
> > > > I guess I need to save the result outside of the loop something like 
> > > > this
> > > >
> > > >  hop hey lalaley #
> > > > from pymol import cmd
> > > > pdb = "Ev_complex_model_final.pdb"
> > > > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> > > >
> > > > # loop over chains to rename it
> > > > for chain in chains_array:
> > > >cmd.load(pdb)
> > > >cmd.alter('chain ' + chain, 'chain=""')
> > > >cmd.delete('*')
> > > > ##
> > > >
> > > > # save output as pdb
> > > > # I need to add something in the name of output indicating how much
> > > > chains have been renamed
> > > > # like output_withoutAB.pdb
> > > > cmd.save('output_'  + '.pdb')
> > > >
> > > > thanks in advance for help!
> > >
> > > --
> > > Thomas Holder
> > > PyMOL Principal Developer
> > > Schrödinger, Inc.
> > >


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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
I actually tried to do like that still defining chains_array = ["A",
"B"] inside of pymol script and use external bash loop to loop over
pdbs
but it does not works ;(

#!/bin/bash
# this script rename chains in pdb to "empty" chain
home=$(pwd)
pdb_folder=$home/pdbs
output=$home/output
rm -r $output
mkdir $output

#pymol -cQkd "
for pdb in "${pdb_folder}"/*.pdb ; do
  pdb_name2=$(basename "${pdb}")
  pdb_name="${pdb_name2/pdb}"
pymol -c -d "
from pymol import cmd
chains_array = ["A", "B"]
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join(chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('${output}/output_without'+"".join(chains_array) + '.pdb')
" > $output/pymol_${pdb_name}.log
done

вт, 25 июн. 2019 г. в 16:58, James Starlight :
>
> yes, actually it is better because we avoid looping!
> and how it would be possible to use array provided in the externall shell?
>
> #!/bin/bash
> pdb="final.pdb"
> output=$(pwd)
>
> # array given in bash
> chains_array=('A' 'B')
>
> # chains are cutted by pymol
> pymol -c -d "
> cmd.load('${pdb}')
> cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> cmd.save('output_without'+"".join($chains_array) + '.pdb')
> "
>
> вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
> >
> > If you want to rename multiple chains at once, make a selection like (chain 
> > A+B+C). This list selection syntax is documented here: 
> > https://pymolwiki.org/index.php/Property_Selectors
> >
> > cmd.load(pdb)
> > cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> > cmd.save('output.pdb')
> >
> > Cheers,
> >   Thomas
> >
> >
> > > On Jun 25, 2019, at 4:14 PM, James Starlight  
> > > wrote:
> > >
> > > thanks so much Thomas, for this example!
> > >
> > > Actually, your python script does exactly what my bash script -
> > > produces number of pdbs for each of the renamed chain.
> > > I would like rather to produce at the end ONE pdb with all chains
> > > renamed to empty chain...
> > > I guess I need to save the result outside of the loop something like this
> > >
> > >  hop hey lalaley #
> > > from pymol import cmd
> > > pdb = "Ev_complex_model_final.pdb"
> > > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> > >
> > > # loop over chains to rename it
> > > for chain in chains_array:
> > >cmd.load(pdb)
> > >cmd.alter('chain ' + chain, 'chain=""')
> > >cmd.delete('*')
> > > ##
> > >
> > > # save output as pdb
> > > # I need to add something in the name of output indicating how much
> > > chains have been renamed
> > > # like output_withoutAB.pdb
> > > cmd.save('output_'  + '.pdb')
> > >
> > > thanks in advance for help!
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >


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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
yes, actually it is better because we avoid looping!
and how it would be possible to use array provided in the externall shell?

#!/bin/bash
pdb="final.pdb"
output=$(pwd)

# array given in bash
chains_array=('A' 'B')

# chains are cutted by pymol
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('chain ' + '+'.join($chains_array), 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join($chains_array) + '.pdb')
"

вт, 25 июн. 2019 г. в 16:47, Thomas Holder :
>
> If you want to rename multiple chains at once, make a selection like (chain 
> A+B+C). This list selection syntax is documented here: 
> https://pymolwiki.org/index.php/Property_Selectors
>
> cmd.load(pdb)
> cmd.alter('chain ' + '+'.join(chains_array), 'chain=""')
> cmd.save('output.pdb')
>
> Cheers,
>   Thomas
>
>
> > On Jun 25, 2019, at 4:14 PM, James Starlight  wrote:
> >
> > thanks so much Thomas, for this example!
> >
> > Actually, your python script does exactly what my bash script -
> > produces number of pdbs for each of the renamed chain.
> > I would like rather to produce at the end ONE pdb with all chains
> > renamed to empty chain...
> > I guess I need to save the result outside of the loop something like this
> >
> >  hop hey lalaley #
> > from pymol import cmd
> > pdb = "Ev_complex_model_final.pdb"
> > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> >
> > # loop over chains to rename it
> > for chain in chains_array:
> >cmd.load(pdb)
> >cmd.alter('chain ' + chain, 'chain=""')
> >cmd.delete('*')
> > ##
> >
> > # save output as pdb
> > # I need to add something in the name of output indicating how much
> > chains have been renamed
> > # like output_withoutAB.pdb
> > cmd.save('output_'  + '.pdb')
> >
> > thanks in advance for help!
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>


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Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
in python version I have got it

# to be run with PyMOL:
#pymol -ckqr pymol_cut_off.py
 cut_off.py #
from pymol import cmd
pdb = "final.pdb"
chains_array = ["A", "B"] # two chains will be cuted

for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')


cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
cmd.save('output_without'+"".join(chains_array) + '.pdb')

now the question would it be possible to do the same but in my bash script?

вт, 25 июн. 2019 г. в 16:20, James Starlight :
>
> OK Lorenzo, thank you !
>
> As an alternative question, would it be possible to put that loop
> while renaming of the chains in the processed PBD within the bash
> loop?
>
> Here is an idea
>
> #!/bin/bash
> # this script rename chains in pdb to "empty" chain
> pdb="my.pdb"
> output=$(pwd)
>
> # chain array is provided in a shell array
> chains=('A' 'B')
>
> # create several pdbs without individual chains
> #pymol -cQkd "
> pymol -c -d "
> # I need to add loop within PYMOL over the elements of external arrays
> for chains
> # mb for i in chains:
> cmd.load('${pdb}')
> cmd.alter('(chain $i)', 'chain=\"\"')
> cmd.set('pdb_use_ter_records', 1)
> cmd.set('retain_order', 1)
> # close the loop and save final output as 1 pdb
> cmd.save('${output}/output_withoutAB.pdb','all')
> "
>
> вт, 25 июн. 2019 г. в 16:14, James Starlight :
> >
> > thanks so much Thomas, for this example!
> >
> > Actually, your python script does exactly what my bash script -
> > produces number of pdbs for each of the renamed chain.
> > I would like rather to produce at the end ONE pdb with all chains
> > renamed to empty chain...
> > I guess I need to save the result outside of the loop something like this
> >
> >  hop hey lalaley #
> > from pymol import cmd
> > pdb = "Ev_complex_model_final.pdb"
> > chains_array = ["A", "B"] # add more chains in case of more complex pdb
> >
> > # loop over chains to rename it
> > for chain in chains_array:
> > cmd.load(pdb)
> > cmd.alter('chain ' + chain, 'chain=""')
> > cmd.delete('*')
> > ##
> >
> > # save output as pdb
> > # I need to add something in the name of output indicating how much
> > chains have been renamed
> > # like output_withoutAB.pdb
> > cmd.save('output_'  + '.pdb')
> >
> > thanks in advance for help!
> >
> > вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
> > >
> > > > generally if I integrate a pymol silent script inside my
> > > > bash script, I do not need to use cmd.* syntax, right?
> > >
> > > Correct. The -d argument takes PyMOL commands, like a .pml script. Python 
> > > syntax is optional.
> > >
> > > Python syntax (cmd.*) is necessary and most useful if you write a Python 
> > > script (.py extension) and run that with PyMOL. You could write your 
> > > multi-chains loop as a Python script:
> > >
> > >  example.py ##
> > > from pymol import cmd
> > > pdb = "my.pdb"
> > > chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
> > >
> > > for chain in chains_array:
> > > cmd.load(pdb)
> > > cmd.alter('chain ' + chain, 'chain=""')
> > > cmd.save('output_' + chain + '.pdb')
> > > cmd.delete('*')
> > > ##
> > >
> > > Then run it with PyMOL:
> > > pymol -ckqr example.py
> > >
> > > See also:
> > > https://pymolwiki.org/index.php/Launching_From_a_Script
> > > https://pymolwiki.org/index.php/Python_Integration
> > >
> > > Cheers,
> > >   Thomas
> > >
> > > > On Jun 25, 2019, at 3:08 PM, James Starlight  
> > > > wrote:
> > > >
> > > > one extra programming question:
> > > >
> > > > imagine now in my pdb I have severals chain which I would like to
> > > > rename to blank chain.
> > > >
> > > > I can do it simply like this
> > > > # a case for 3 chains to be renamed
> > > >
> > > > #!/bin/bash
> > > > pdb="my.pdb"
> > > > output=$(pwd)
> > > > pymol -c -d "
> > > > cmd.load('${pdb}')
> > > >

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
OK Lorenzo, thank you !

As an alternative question, would it be possible to put that loop
while renaming of the chains in the processed PBD within the bash
loop?

Here is an idea

#!/bin/bash
# this script rename chains in pdb to "empty" chain
pdb="my.pdb"
output=$(pwd)

# chain array is provided in a shell array
chains=('A' 'B')

# create several pdbs without individual chains
#pymol -cQkd "
pymol -c -d "
# I need to add loop within PYMOL over the elements of external arrays
for chains
# mb for i in chains:
cmd.load('${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.set('pdb_use_ter_records', 1)
cmd.set('retain_order', 1)
# close the loop and save final output as 1 pdb
cmd.save('${output}/output_withoutAB.pdb','all')
"

вт, 25 июн. 2019 г. в 16:14, James Starlight :
>
> thanks so much Thomas, for this example!
>
> Actually, your python script does exactly what my bash script -
> produces number of pdbs for each of the renamed chain.
> I would like rather to produce at the end ONE pdb with all chains
> renamed to empty chain...
> I guess I need to save the result outside of the loop something like this
>
>  hop hey lalaley #
> from pymol import cmd
> pdb = "Ev_complex_model_final.pdb"
> chains_array = ["A", "B"] # add more chains in case of more complex pdb
>
> # loop over chains to rename it
> for chain in chains_array:
> cmd.load(pdb)
> cmd.alter('chain ' + chain, 'chain=""')
> cmd.delete('*')
> ##
>
> # save output as pdb
> # I need to add something in the name of output indicating how much
> chains have been renamed
> # like output_withoutAB.pdb
> cmd.save('output_'  + '.pdb')
>
> thanks in advance for help!
>
> вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
> >
> > > generally if I integrate a pymol silent script inside my
> > > bash script, I do not need to use cmd.* syntax, right?
> >
> > Correct. The -d argument takes PyMOL commands, like a .pml script. Python 
> > syntax is optional.
> >
> > Python syntax (cmd.*) is necessary and most useful if you write a Python 
> > script (.py extension) and run that with PyMOL. You could write your 
> > multi-chains loop as a Python script:
> >
> >  example.py ##
> > from pymol import cmd
> > pdb = "my.pdb"
> > chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
> >
> > for chain in chains_array:
> > cmd.load(pdb)
> > cmd.alter('chain ' + chain, 'chain=""')
> > cmd.save('output_' + chain + '.pdb')
> > cmd.delete('*')
> > ##
> >
> > Then run it with PyMOL:
> > pymol -ckqr example.py
> >
> > See also:
> > https://pymolwiki.org/index.php/Launching_From_a_Script
> > https://pymolwiki.org/index.php/Python_Integration
> >
> > Cheers,
> >   Thomas
> >
> > > On Jun 25, 2019, at 3:08 PM, James Starlight  
> > > wrote:
> > >
> > > one extra programming question:
> > >
> > > imagine now in my pdb I have severals chain which I would like to
> > > rename to blank chain.
> > >
> > > I can do it simply like this
> > > # a case for 3 chains to be renamed
> > >
> > > #!/bin/bash
> > > pdb="my.pdb"
> > > output=$(pwd)
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('(chain A)', 'chain=\"\"')
> > > cmd.alter('(chain B)', 'chain=\"\"')
> > > cmd.alter('(chain C)', 'chain=\"\"')
> > > cmd.save('${output}/output.pdb','all')
> > > "
> > >
> > > or for multi-chain protein I can alternatively create external loop,
> > > thus running pymol 3 times iteratively (which is not good realization)
> > > providin array info from external shell session
> > >
> > > # this example save 7 different pdbs renaming one chain in each of them
> > > #!/bin/bash
> > > pdb="my.pdb"
> > > output=$(pwd)
> > > chains_arrays=( A B C D E F G )
> > >
> > > for i in "$chains_array[@]}"; do
> > > pymol -c -d "
> > > cmd.load('${pdb}')
> > > cmd.alter('(chain $i)', 'chain=\"\"')
> > > cmd.save('${output}/output_$i.pdb','all')
> > > "
> > > done
> > >
> > > would it be possible rather to make an array and loop inside the pymol
> > > to ren

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
thanks so much Thomas, for this example!

Actually, your python script does exactly what my bash script -
produces number of pdbs for each of the renamed chain.
I would like rather to produce at the end ONE pdb with all chains
renamed to empty chain...
I guess I need to save the result outside of the loop something like this

 hop hey lalaley #
from pymol import cmd
pdb = "Ev_complex_model_final.pdb"
chains_array = ["A", "B"] # add more chains in case of more complex pdb

# loop over chains to rename it
for chain in chains_array:
cmd.load(pdb)
cmd.alter('chain ' + chain, 'chain=""')
cmd.delete('*')
##

# save output as pdb
# I need to add something in the name of output indicating how much
chains have been renamed
# like output_withoutAB.pdb
cmd.save('output_'  + '.pdb')

thanks in advance for help!

вт, 25 июн. 2019 г. в 16:03, Thomas Holder :
>
> > generally if I integrate a pymol silent script inside my
> > bash script, I do not need to use cmd.* syntax, right?
>
> Correct. The -d argument takes PyMOL commands, like a .pml script. Python 
> syntax is optional.
>
> Python syntax (cmd.*) is necessary and most useful if you write a Python 
> script (.py extension) and run that with PyMOL. You could write your 
> multi-chains loop as a Python script:
>
>  example.py ##
> from pymol import cmd
> pdb = "my.pdb"
> chains_arrays = ["A", "B", "C", "D", "E", "F", "G"]
>
> for chain in chains_array:
> cmd.load(pdb)
> cmd.alter('chain ' + chain, 'chain=""')
> cmd.save('output_' + chain + '.pdb')
> cmd.delete('*')
> ##
>
> Then run it with PyMOL:
> pymol -ckqr example.py
>
> See also:
> https://pymolwiki.org/index.php/Launching_From_a_Script
> https://pymolwiki.org/index.php/Python_Integration
>
> Cheers,
>   Thomas
>
> > On Jun 25, 2019, at 3:08 PM, James Starlight  wrote:
> >
> > one extra programming question:
> >
> > imagine now in my pdb I have severals chain which I would like to
> > rename to blank chain.
> >
> > I can do it simply like this
> > # a case for 3 chains to be renamed
> >
> > #!/bin/bash
> > pdb="my.pdb"
> > output=$(pwd)
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('(chain A)', 'chain=\"\"')
> > cmd.alter('(chain B)', 'chain=\"\"')
> > cmd.alter('(chain C)', 'chain=\"\"')
> > cmd.save('${output}/output.pdb','all')
> > "
> >
> > or for multi-chain protein I can alternatively create external loop,
> > thus running pymol 3 times iteratively (which is not good realization)
> > providin array info from external shell session
> >
> > # this example save 7 different pdbs renaming one chain in each of them
> > #!/bin/bash
> > pdb="my.pdb"
> > output=$(pwd)
> > chains_arrays=( A B C D E F G )
> >
> > for i in "$chains_array[@]}"; do
> > pymol -c -d "
> > cmd.load('${pdb}')
> > cmd.alter('(chain $i)', 'chain=\"\"')
> > cmd.save('${output}/output_$i.pdb','all')
> > "
> > done
> >
> > would it be possible rather to make an array and loop inside the pymol
> > to rename all chains into the blank chain during one execution of
> > pymol?
> >
> > Thanks in advance!
> >
> > вт, 25 июн. 2019 г. в 14:50, James Starlight :
> >>
> >> I have got the idea!
> >> thank you so much Thomas!
> >> One question: generally if I integrate a pymol silent script inside my
> >> bash script, I do not need to use cmd.* syntax, right?  In what cases
> >> cmd.* sytax might be usefull?
> >>
> >> Thank you again!
> >>
> >> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
> >>>
> >>>
> >>>> On Jun 25, 2019, at 11:48 AM, James Starlight  
> >>>> wrote:
> >>>>
> >>>> so what I need is just to update my pymol, keep using the same command?
> >>>
> >>> Yes
> >>>
> >>>> P.S.would the following integration of the code into bash script be
> >>>> usefull to remove chains in no gui mode?
> >>>>
> >>>> pymol -cQkd "
> >>>> from pymol import cmd
> >>>> fetch $pdb, type=pdb, tmp
> >>>> cmd.alter('(chain A)',chain='')
> >>>> "
> >>>> I am not sure wh

Re: [PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
one extra programming question:

imagine now in my pdb I have severals chain which I would like to
rename to blank chain.

I can do it simply like this
# a case for 3 chains to be renamed

#!/bin/bash
pdb="my.pdb"
output=$(pwd)
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('(chain A)', 'chain=\"\"')
cmd.alter('(chain B)', 'chain=\"\"')
cmd.alter('(chain C)', 'chain=\"\"')
cmd.save('${output}/output.pdb','all')
"

or for multi-chain protein I can alternatively create external loop,
thus running pymol 3 times iteratively (which is not good realization)
providin array info from external shell session

# this example save 7 different pdbs renaming one chain in each of them
#!/bin/bash
pdb="my.pdb"
output=$(pwd)
chains_arrays=( A B C D E F G )

for i in "$chains_array[@]}"; do
pymol -c -d "
cmd.load('${pdb}')
cmd.alter('(chain $i)', 'chain=\"\"')
cmd.save('${output}/output_$i.pdb','all')
"
done

would it be possible rather to make an array and loop inside the pymol
to rename all chains into the blank chain during one execution of
pymol?

Thanks in advance!

вт, 25 июн. 2019 г. в 14:50, James Starlight :
>
> I have got the idea!
> thank you so much Thomas!
> One question: generally if I integrate a pymol silent script inside my
> bash script, I do not need to use cmd.* syntax, right?  In what cases
> cmd.* sytax might be usefull?
>
> Thank you again!
>
> вт, 25 июн. 2019 г. в 12:05, Thomas Holder :
> >
> >
> > > On Jun 25, 2019, at 11:48 AM, James Starlight  
> > > wrote:
> > >
> > > so what I need is just to update my pymol, keep using the same command?
> >
> > Yes
> >
> > > P.S.would the following integration of the code into bash script be
> > > usefull to remove chains in no gui mode?
> > >
> > > pymol -cQkd "
> > > from pymol import cmd
> > > fetch $pdb, type=pdb, tmp
> > > cmd.alter('(chain A)',chain='')
> > > "
> > > I am not sure whether I used here cmd.alter in correct way ..
> >
> >
> > With fetch, use "async=0" or use Python syntax. And keyword arguments 
> > (type=) must be after positional arguments (tmp).
> >
> > It's easier if you don't use Python syntax for alter, otherwise you'll need 
> > three levels of nested quotes, which gets ugly:
> >
> > pymol -cQkd "
> > fetch $pdb, tmp, type=pdb, async=0
> > alter (chain A), chain=''
> > "
> >
> > With Python syntax (note the ugly escaping of quotes):
> >
> > pymol -cQkd "
> > cmd.fetch('$pdb', 'tmp', type='pdb')
> > cmd.alter('(chain A)', 'chain=\"\"')
> > "
> >
> > Cheers,
> >   Thomas
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >


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[PyMOL] PDB post-processing and TER records

2019-06-25 Thread James Starlight
Dear Pymol Users!

I need to process input PDB via pymol (this time no need to do it via
no-gui mode!!) to remove chain id from PDB.

I am using alter command to do it with the following syntax
#rename chain A to phantom chain :-)
alter (chain A),chain=''

the problem that in my initial PDBs there are many TER records (e.g.
to separate protein from ligand etc), which should be keeped after
such post-processing in the form of original PDB (with chain A).

I have tried to do this before saving of the PDB
get pdb_use_ter_records

however, as the result, all the TER records were removed from the
processed pdb. How I could fix it?

Many thanks in advance!


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Re: [PyMOL] counting number of standard amino acids in PDB

2019-06-25 Thread James Starlight
Thank so much Jared!

So here is modified script:

#!/bin/bash
pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
LENGTH="$(pymol -cQ -d "
from pymol import cmd
load ${pdb}, tmp
sel = 'tmp and polymer'
print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
")"

echo $LENGTH

I guess it's a problem with the -cQ flag because without it your
script gives me the full output, while I echoes the variable:

PyMOL(TM) Molecular Graphics System, Version 1.7.2.1. 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;.
Enter "help" for a list of commands. Enter "help " for
information on a specific command. Hit ESC anytime to toggle between
text and graphics. Command mode. No graphics front end. Detected 20
CPU cores. Enabled multithreaded rendering. PyMOL> PyMOL>from pymol
import cmd PyMOL>load ./NpXynWT_apo_340K_MD_multi_0434.pdb, tmp
CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp".
PyMOL>sel = 'tmp and polymer' PyMOL>print(len(set([(i.chain, i.resi,
i.resn) for i in cmd.get_model(sel).atom]))) 219 PyMOL: normal program
termination.

however with -cQ it gives me nothing :-)

Hey Blaine,

your script is very usefull but it does not work in my case.
1) fetch command gives me an error (which is not the case of "load"
probably because I have outdated pymol).
2) I need to load pdbs inside of my shell script, meaning that I am
looping a folder by bash routine and use it then with pymol to measure
the length of PDB and save it as the variable (in bash!!), which is
expected to be used on the next step...

james

пн, 24 июн. 2019 г. в 18:53, Jared Sampson :
>
> Hi James -
>
> Try this, assigning to new variable LENGTH by using -Q flag to suppress other 
> output, and running in a subshell (untested, and assuming Bash):
>
> ```
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> LENGTH=$(pymol -cQ -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> ")
> ```
>
> Hopefully that works, or at least gives you an idea of how it might be done.
>
> Best,
> Jared
>
>
> On June 24, 2019 at 12:08:07 PM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
> pymol -c -d "
> from pymol import cmd
> load ${pdb}, tmp
> sel = 'tmp and polymer'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> "


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Re: [PyMOL] counting number of standard amino acids in PDB

2019-06-24 Thread James Starlight
hi Jared,
I have tried to use your script putting it into my test.sh script
I only changed the selection statement in sel = 'tmp and
polymer.protein' instead of sel = 'tmp and chain A and
polymer.protein'
since in my protein there is no chains assigned

pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
pymol -c -d "
from pymol import cmd
load ${pdb}, tmp
sel = 'tmp and polymer.protein'
print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
"

execution of that sh script gave me the following error


 PyMOL(TM) Molecular Graphics System, Version 1.7.2.1.
 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;.

Enter "help" for a list of commands.
Enter "help " for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Command mode. No graphics front end.
 Detected 20 CPU cores.  Enabled multithreaded rendering.
PyMOL>from pymol import cmd
PyMOL>load ./NpXynWT_apo_340K_MD_multi_0434.pdb, tmp
 CmdLoad: "./NpXynWT_apo_340K_MD_multi_0434.pdb" loaded as "tmp".
PyMOL>sel = 'tmp and polymer.protein'
PyMOL>print(len(set([(i.chain, i.resi, i.resn) for i in
cmd.get_model(sel).atom])))
Selector-Error: Invalid selection name "polymer.protein".
( tmp and polymer.protein )<--
 PyMOL: normal program termination.



пн, 24 июн. 2019 г. в 17:44, Jared Sampson :

>
> Hi James -
>
> You can give multiple commands by leaving the quote open as you did on the 
> first line (see Thomas' post from a day or two ago), but the `print` 
> statement, even though it is valid Python 2, will not work across line breaks 
> as written unless inside a `python` / `python end` block (also unless you are 
> using Python 2!).  I would suggest performing the print operation on a single 
> line.  You'll also need to load your model and specify the selection using 
> PyMOL selection syntax such that it includes only protein residues (e.g. 
> polymer.protein). For example, for my PyMOL running Python 3.7 (which 
> requires using the `print()` function, i.e. with parentheses), the following 
> command works:
>
> ```
> pymol -cQkd "
> from pymol import cmd
> load my_structure.pdb, tmp
> sel = 'tmp and chain A and polymer.protein'
> print(len(set([(i.chain, i.resi, i.resn) for i in cmd.get_model(sel).atom])))
> "
> ```
>
> Here I put in the -Q option which suppresses all of PyMOL's normal output, as 
> well as -k, which prevents it from loading the .pymolrc file (for speed, 
> mostly).  Also note the quotes in the `sel` variable assignment must be 
> single quotes to avoid closing the shell string.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
>
> On June 24, 2019 at 10:25:22 AM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> Thank you, Jared!
> how do you think would it be possible to run this command from no-gui pymol?
>
> pymol -c -d "
> from pymol import cmd
> print len( set( [(i.chain,i.resi,i.resn) for i in
> cmd.get_model(selection).atom] ) )
> "
>
> ?
>
> пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
> >
> > Hi James -
> >
> > Do any of the options from this previous BB discussion help?
> >
> > https://sourceforge.net/p/pymol/mailman/message/28466955/
> >
> > Cheers,
> > Jared
> >
> >
> > On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) 
> > wrote:
> >
> > Dear Pymol Users,
> >
> > that is not very related to pymol question but however probably it can
> > be solved via pymol as well ;-)
> >
> > I am looking for some script (e.g. via running in pymol no-gui), which
> > will count the number of standard amino acid residues in the given
> > PDB. E.g. for particular pdb consisted of 9 residues complexed with
> > part of the ligand I need to print the value of 9 (the end value of
> > 6th column before TER)
> >
> > ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N
> > ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C
> > ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C
> > ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O
> > ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C
> > ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C
> > ATOM 7 SD MET A 1 28.713

Re: [PyMOL] counting number of standard amino acids in PDB

2019-06-24 Thread James Starlight
i also tried more simple sollution directly from terminal but it
doesn't work also

pymol -c -d "
  from pymol import cmd
  cmd.load('my.pdb')
  cmd.count_atoms('n. CA')
  "

actually what I do need is to compute number of residues and store it
in a variable (inside of my shell script)

пн, 24 июн. 2019 г. в 16:25, James Starlight :
>
> Thank you, Jared!
> how do you think would it be possible to run this command from no-gui pymol?
>
> pymol -c -d "
>   from pymol import cmd
>   print len( set( [(i.chain,i.resi,i.resn) for i in
>   cmd.get_model(selection).atom] ) )
>   "
>
> ?
>
> пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
> >
> > Hi James -
> >
> > Do any of the options from this previous BB discussion help?
> >
> > https://sourceforge.net/p/pymol/mailman/message/28466955/
> >
> > Cheers,
> > Jared
> >
> >
> > On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) 
> > wrote:
> >
> > Dear Pymol Users,
> >
> > that is not very related to pymol question but however probably it can
> > be solved via pymol as well ;-)
> >
> > I am looking for some script (e.g. via running in pymol no-gui), which
> > will count the number of standard amino acid residues in the given
> > PDB. E.g. for particular pdb consisted of 9 residues complexed with
> > part of the ligand I need to print the value of 9 (the end value of
> > 6th column before TER)
> >
> > ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N
> > ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C
> > ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C
> > ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O
> > ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C
> > ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C
> > ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S
> > ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C
> > ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N
> > ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C
> > ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C
> > ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O
> > ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C
> > ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C
> > ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C
> > ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C
> > ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+
> > ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N
> > ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C
> > ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C
> > ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O
> > ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C
> > ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C
> > ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C
> > ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C
> > ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C
> > ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C
> > ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C
> > ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N
> > ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C
> > ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C
> > ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O
> > ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C
> > ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C
> > ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O
> > ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N
> > ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C
> > ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C
> > ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O
> > ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C
> > ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C
> > ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C
> > ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N
> > ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C
> > ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C
> > ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O
> > ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N
> > ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C
> > ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C
> > ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O
> > ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C
> > ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C
> > ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N
> > ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O
> > ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N
> > ATOM 56 CA GLY A 8 9.422 10.75

Re: [PyMOL] counting number of standard amino acids in PDB

2019-06-24 Thread James Starlight
Thank you, Jared!
how do you think would it be possible to run this command from no-gui pymol?

pymol -c -d "
  from pymol import cmd
  print len( set( [(i.chain,i.resi,i.resn) for i in
  cmd.get_model(selection).atom] ) )
  "

?

пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
>
> Hi James -
>
> Do any of the options from this previous BB discussion help?
>
> https://sourceforge.net/p/pymol/mailman/message/28466955/
>
> Cheers,
> Jared
>
>
> On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> Dear Pymol Users,
>
> that is not very related to pymol question but however probably it can
> be solved via pymol as well ;-)
>
> I am looking for some script (e.g. via running in pymol no-gui), which
> will count the number of standard amino acid residues in the given
> PDB. E.g. for particular pdb consisted of 9 residues complexed with
> part of the ligand I need to print the value of 9 (the end value of
> 6th column before TER)
>
> ATOM 1 N MET A 1 24.950 5.224 -5.601 1.00 30.01 N
> ATOM 2 CA MET A 1 24.822 3.740 -5.655 1.00 30.25 C
> ATOM 3 C MET A 1 23.719 3.091 -4.771 1.00 28.98 C
> ATOM 4 O MET A 1 23.417 1.937 -4.989 1.00 28.27 O
> ATOM 5 CB MET A 1 26.187 3.043 -5.448 1.00 31.03 C
> ATOM 6 CG MET A 1 26.869 3.182 -4.084 1.00 32.21 C
> ATOM 7 SD MET A 1 28.713 3.095 -4.227 1.00 34.63 S
> ATOM 8 CE MET A 1 29.205 3.597 -2.564 1.00 33.32 C
> ATOM 9 N LYS A 2 23.111 3.804 -3.818 1.00 27.78 N
> ATOM 10 CA LYS A 2 21.869 3.310 -3.188 1.00 27.21 C
> ATOM 11 C LYS A 2 20.671 4.237 -3.440 1.00 26.27 C
> ATOM 12 O LYS A 2 20.787 5.445 -3.300 1.00 25.96 O
> ATOM 13 CB LYS A 2 22.027 3.091 -1.684 1.00 27.32 C
> ATOM 14 CG LYS A 2 20.820 2.362 -1.065 1.00 27.75 C
> ATOM 15 CD LYS A 2 20.953 2.147 0.439 1.00 28.18 C
> ATOM 16 CE LYS A 2 19.928 1.130 0.938 1.00 29.30 C
> ATOM 17 NZ LYS A 2 20.083 0.809 2.386 1.00 30.36 N1+
> ATOM 18 N PHE A 3 19.528 3.658 -3.808 1.00 24.92 N
> ATOM 19 CA PHE A 3 18.306 4.421 -4.054 1.00 24.39 C
> ATOM 20 C PHE A 3 17.161 3.823 -3.246 1.00 24.12 C
> ATOM 21 O PHE A 3 16.991 2.597 -3.202 1.00 23.77 O
> ATOM 22 CB PHE A 3 17.940 4.222 -5.535 1.00 23.83 C
> ATOM 23 CG PHE A 3 19.003 4.968 -6.434 1.00 23.81 C
> ATOM 24 CD1 PHE A 3 19.132 6.337 -6.585 1.00 23.27 C
> ATOM 25 CD2 PHE A 3 19.876 4.135 -7.129 1.00 23.46 C
> ATOM 26 CE1 PHE A 3 20.110 6.868 -7.412 1.00 23.22 C
> ATOM 27 CE2 PHE A 3 20.862 4.660 -7.952 1.00 23.19 C
> ATOM 28 CZ PHE A 3 20.975 6.027 -8.102 1.00 23.07 C
> ATOM 29 N THR A 4 16.374 4.691 -2.624 1.00 23.47 N
> ATOM 30 CA THR A 4 15.326 4.278 -1.704 1.00 23.33 C
> ATOM 31 C THR A 4 13.946 4.720 -2.188 1.00 22.67 C
> ATOM 32 O THR A 4 13.779 5.810 -2.726 1.00 22.24 O
> ATOM 33 CB THR A 4 15.584 4.875 -0.295 1.00 23.52 C
> ATOM 34 CG2 THR A 4 14.441 4.560 0.650 1.00 23.80 C
> ATOM 35 OG1 THR A 4 16.798 4.328 0.245 1.00 23.98 O
> ATOM 36 N VAL A 5 12.955 3.866 -1.980 1.00 22.25 N
> ATOM 37 CA VAL A 5 11.577 4.216 -2.276 1.00 22.46 C
> ATOM 38 C VAL A 5 10.685 4.011 -1.038 1.00 22.44 C
> ATOM 39 O VAL A 5 10.951 3.145 -0.201 1.00 21.37 O
> ATOM 40 CB VAL A 5 11.033 3.456 -3.533 1.00 21.81 C
> ATOM 41 CG1 VAL A 5 11.786 3.902 -4.782 1.00 20.47 C
> ATOM 42 CG2 VAL A 5 11.127 1.940 -3.368 1.00 21.55 C
> ATOM 43 N GLY A 6 9.660 4.845 -0.908 1.00 23.27 N
> ATOM 44 CA GLY A 6 8.676 4.684 0.154 1.00 24.59 C
> ATOM 45 C GLY A 6 8.727 5.731 1.249 1.00 25.69 C
> ATOM 46 O GLY A 6 7.834 5.767 2.101 1.00 26.30 O
> ATOM 47 N ASN A 7 9.764 6.568 1.261 1.00 26.66 N
> ATOM 48 CA ASN A 7 9.775 7.728 2.155 1.00 27.39 C
> ATOM 49 C ASN A 7 10.165 9.028 1.436 1.00 27.80 C
> ATOM 50 O ASN A 7 11.263 9.569 1.622 1.00 28.37 O
> ATOM 51 CB ASN A 7 10.619 7.470 3.421 1.00 28.21 C
> ATOM 52 CG ASN A 7 12.089 7.278 3.127 1.00 29.85 C
> ATOM 53 ND2 ASN A 7 12.938 7.964 3.897 1.00 32.41 N
> ATOM 54 OD1 ASN A 7 12.466 6.525 2.229 1.00 32.61 O
> ATOM 55 N GLY A 8 9.232 9.521 0.622 1.00 27.41 N
> ATOM 56 CA GLY A 8 9.422 10.752 -0.139 1.00 27.40 C
> ATOM 57 C GLY A 8 9.309 10.498 -1.629 1.00 27.35 C
> ATOM 58 O GLY A 8 8.449 11.071 -2.303 1.00 27.93 O
> ATOM 59 N GLN A 9 10.178 9.630 -2.136 1.00 26.80 N
> ATOM 60 CA GLN A 9 10.215 9.294 -3.552 1.00 26.37 C
> ATOM 61 C GLN A 9 9.834 7.833 -3.736 1.00 25.75 C
> ATOM 62 O GLN A 9 10.308 6.970 -2.997 1.00 25.25 O
> ATOM 63 CB GLN A 9 11.622 9.522 -4.115 1.00 26.74 C
> ATOM 64 CG GLN A 9 12.197 10.924 -3.899 1.00 27.40 C
> ATOM 65 CD GLN A 9 11.327 12.028 -4.475 1.00 29.17 C
> ATOM 66 NE2 GLN A 9 10.896 11.863 -5.726 1.00 29.46 N
> ATOM 67 OE1 GLN A 9 11.048 13.025 -3.800 1.00 31.02 O
> TER
> ATOM 1719 C1 0XB B 220 6.613 3.931 -16.928 1.00 11.35 C
> ATOM 1720 C2 0XB B 220 7.042 5.128 -16.070 1.00 14.60 C
> ATOM 1721 O2 0XB B 220 6.3

[PyMOL] counting number of standard amino acids in PDB

2019-06-24 Thread James Starlight
Dear Pymol Users,

that is not very related to pymol question but however probably it can
be solved via pymol as well ;-)

I am looking for some script (e.g. via running in pymol no-gui), which
will count the number of standard amino acid residues in the given
PDB. E.g. for particular pdb consisted of 9 residues complexed with
part of the ligand I need to print the value of 9 (the end value of
6th column before TER)

ATOM  1  N   MET A   1  24.950   5.224  -5.601  1.00 30.01   N
ATOM  2  CA  MET A   1  24.822   3.740  -5.655  1.00 30.25   C
ATOM  3  C   MET A   1  23.719   3.091  -4.771  1.00 28.98   C
ATOM  4  O   MET A   1  23.417   1.937  -4.989  1.00 28.27   O
ATOM  5  CB  MET A   1  26.187   3.043  -5.448  1.00 31.03   C
ATOM  6  CG  MET A   1  26.869   3.182  -4.084  1.00 32.21   C
ATOM  7  SD  MET A   1  28.713   3.095  -4.227  1.00 34.63   S
ATOM  8  CE  MET A   1  29.205   3.597  -2.564  1.00 33.32   C
ATOM  9  N   LYS A   2  23.111   3.804  -3.818  1.00 27.78   N
ATOM 10  CA  LYS A   2  21.869   3.310  -3.188  1.00 27.21   C
ATOM 11  C   LYS A   2  20.671   4.237  -3.440  1.00 26.27   C
ATOM 12  O   LYS A   2  20.787   5.445  -3.300  1.00 25.96   O
ATOM 13  CB  LYS A   2  22.027   3.091  -1.684  1.00 27.32   C
ATOM 14  CG  LYS A   2  20.820   2.362  -1.065  1.00 27.75   C
ATOM 15  CD  LYS A   2  20.953   2.147   0.439  1.00 28.18   C
ATOM 16  CE  LYS A   2  19.928   1.130   0.938  1.00 29.30   C
ATOM 17  NZ  LYS A   2  20.083   0.809   2.386  1.00 30.36   N1+
ATOM 18  N   PHE A   3  19.528   3.658  -3.808  1.00 24.92   N
ATOM 19  CA  PHE A   3  18.306   4.421  -4.054  1.00 24.39   C
ATOM 20  C   PHE A   3  17.161   3.823  -3.246  1.00 24.12   C
ATOM 21  O   PHE A   3  16.991   2.597  -3.202  1.00 23.77   O
ATOM 22  CB  PHE A   3  17.940   4.222  -5.535  1.00 23.83   C
ATOM 23  CG  PHE A   3  19.003   4.968  -6.434  1.00 23.81   C
ATOM 24  CD1 PHE A   3  19.132   6.337  -6.585  1.00 23.27   C
ATOM 25  CD2 PHE A   3  19.876   4.135  -7.129  1.00 23.46   C
ATOM 26  CE1 PHE A   3  20.110   6.868  -7.412  1.00 23.22   C
ATOM 27  CE2 PHE A   3  20.862   4.660  -7.952  1.00 23.19   C
ATOM 28  CZ  PHE A   3  20.975   6.027  -8.102  1.00 23.07   C
ATOM 29  N   THR A   4  16.374   4.691  -2.624  1.00 23.47   N
ATOM 30  CA  THR A   4  15.326   4.278  -1.704  1.00 23.33   C
ATOM 31  C   THR A   4  13.946   4.720  -2.188  1.00 22.67   C
ATOM 32  O   THR A   4  13.779   5.810  -2.726  1.00 22.24   O
ATOM 33  CB  THR A   4  15.584   4.875  -0.295  1.00 23.52   C
ATOM 34  CG2 THR A   4  14.441   4.560   0.650  1.00 23.80   C
ATOM 35  OG1 THR A   4  16.798   4.328   0.245  1.00 23.98   O
ATOM 36  N   VAL A   5  12.955   3.866  -1.980  1.00 22.25   N
ATOM 37  CA  VAL A   5  11.577   4.216  -2.276  1.00 22.46   C
ATOM 38  C   VAL A   5  10.685   4.011  -1.038  1.00 22.44   C
ATOM 39  O   VAL A   5  10.951   3.145  -0.201  1.00 21.37   O
ATOM 40  CB  VAL A   5  11.033   3.456  -3.533  1.00 21.81   C
ATOM 41  CG1 VAL A   5  11.786   3.902  -4.782  1.00 20.47   C
ATOM 42  CG2 VAL A   5  11.127   1.940  -3.368  1.00 21.55   C
ATOM 43  N   GLY A   6   9.660   4.845  -0.908  1.00 23.27   N
ATOM 44  CA  GLY A   6   8.676   4.684   0.154  1.00 24.59   C
ATOM 45  C   GLY A   6   8.727   5.731   1.249  1.00 25.69   C
ATOM 46  O   GLY A   6   7.834   5.767   2.101  1.00 26.30   O
ATOM 47  N   ASN A   7   9.764   6.568   1.261  1.00 26.66   N
ATOM 48  CA  ASN A   7   9.775   7.728   2.155  1.00 27.39   C
ATOM 49  C   ASN A   7  10.165   9.028   1.436  1.00 27.80   C
ATOM 50  O   ASN A   7  11.263   9.569   1.622  1.00 28.37   O
ATOM 51  CB  ASN A   7  10.619   7.470   3.421  1.00 28.21   C
ATOM 52  CG  ASN A   7  12.089   7.278   3.127  1.00 29.85   C
ATOM 53  ND2 ASN A   7  12.938   7.964   3.897  1.00 32.41   N
ATOM 54  OD1 ASN A   7  12.466   6.525   2.229  1.00 32.61   O
ATOM 55  N   GLY A   8   9.232   9.521   0.622  1.00 27.41   N
ATOM 56  CA  GLY A   8   9.422  10.752  -0.139  1.00 27.40   C
ATOM 57  C   GLY A   8   9.309  10.498  -1.629  1.00 27.35   C
ATOM 58  O   GLY A   8   8.449  11.071  -2.303  1.00 27.93   

Re: [PyMOL] pymol in no-gui mode

2019-06-23 Thread James Starlight
thank you very much, Ali!
I only changed the quotes in your script because I have integrated it
to my shell script in order to use with the varibables:

  # run pymol to align the snapshots and save it to the session
  pymol -c -d "
  from pymol import cmd
  cmd.load('${sim}/${simulation}_after_minimization.pdb')
  cmd.load('${sim}/${simulation}_after_equilibration.pdb')
  cmd.remove('resn WAT')
  
cmd.super('${simulation}_after_equilibration*','${simulation}_after_minimization*')
  cmd.bg_color('white')
  cmd.save('${output}/!!!pymol_sessions/${simulation}_superimposed.pse')
  "

вс, 23 июн. 2019 г. в 12:05, Ali Kusay :
>
> Hi James,
>
> Just a follow up, I would still recommend you use the script in a file to do 
> this as it is less messy but it can be done:
>
> pymol -c -d '
> from pymol import cmd
> cmd.load("A.pdb")
> cmd.load("B.pdb")
> cmd.load("C.pdb")
> cmd.super("C*","A*")
> cmd.super("B*","A*")
> cmd.bg_color("white")
> cmd.save("output.pse")
> '
>
> If you paste the above as is in shell It should work provided you are the 
> directory containing the 3 pdb files
>
> Executing pymol with -d flag in shell means you can input pymol commands, to 
> get around indentation you can run leave an ' apostrophe at the end to paste 
> the scripts in and execute all as a string without needing to save as a file
>
> Just for reference, the -c flag is "batch processing (no GUI)" and the 
> commands above can be saved into a python file and ran using:
>
> pymol -c -r  "path_to_script"
>
> Hope this helps.
>
> Cheers,
>
> Ali
> 
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: akus8...@uni.sydney.edu.au
>
>
> On 23/6/19, 7:00 pm, "James Starlight"  wrote:
>
> hello there,
>
> As a part of my scripting routine, I would like to use pymol in no-gui
> mode (directly in the linux shell) to do the following things:
> 1) load in pymol 3 conformations of the same protein, which are
> defined as A.pdb B.pdb C.pdb
> 2) superimpose C to A using "super" or alternatively (which is better)
> "alignall" to A
> 3) change background of the session to white :-)
> 4) save the pymol session for the superimposed A B and C as the *.pse
> output file
>
> could you suggest me 1 string command for pymol, which I can directly
> use in shell terminal to do the mentioned routines in no-gui mode?
>
> thanks you!!
>
> James
>
>
> ___
> PyMOL-users mailing list
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[PyMOL] pymol in no-gui mode

2019-06-23 Thread James Starlight
hello there,

As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (which is better)
"alignall" to A
3) change background of the session to white :-)
4) save the pymol session for the superimposed A B and C as the *.pse
output file

could you suggest me 1 string command for pymol, which I can directly
use in shell terminal to do the mentioned routines in no-gui mode?

thanks you!!

James


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Re: [PyMOL] A structural superimposition and further post-processing

2017-07-18 Thread James Starlight
if just add strings in pymol's cmd the "Super version" of the script
works fine so the problem is indeed in MAC :)

2017-07-18 20:53 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> There were some errors in the executing pymol script with your commands using
> @ script.pml
> or
> run script.pml
>
> probably because of my MAC Pymol which is v 1.74 mb outdated, no?
>
> BTW on the same MAC I just have tried to install updated setup.py and
> it was the following error:
>
> Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
>   File "setup.py", line 7
> 
> ^
> SyntaxError: invalid syntax
>
> 2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>> With super instead of tmalign:
>>
>> loadall *.pdb
>> extra_fit *, reference, method=super, object=aln
>> remove not (byres aln)
>>
>> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
>> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>>
>> Cheers,
>>   Thomas
>>
>>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote:
>>>
>>> Hi Thomas,
>>>
>>> could you also send the same script but just with the Super command
>>> for the superimposition without PSICO?
>>>
>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>
>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>> READMEpsicosetup.py
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>  File "setup.py", line 10
>>>print 'Warning: could not import version'
>>>^
>>>
>>> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>>>> Hi Thomas,
>>>>
>>>> could you also send the same script but just with the Super command
>>>> for the superimposition without PSICO?
>>>>
>>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>>
>>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>>
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>>> READMEpsicosetup.py
>>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>>  File "setup.py", line 10
>>>>print 'Warning: could not import version'
>>>>^
>>>> SyntaxError: Missing parentheses in call to 'print'
>>>>
>>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>>>>> Hi Gleb,
>>>>>
>>>>> If you have PSICO installed (which provides a TMalign wrapper), then this 
>>>>> script should be sufficient:
>>>>>
>>>>> loadall *.pdb
>>>>> import psico.fitting
>>>>> extra_fit *, reference, method=tmalign, object=aln
>>>>> remove not (byres aln)
>>>>>
>>>>> https://pymolwiki.org/index.php/Psico
>>>>>
>>>>> Cheers,
>>>>>  Thomas
>>>>>
>>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> 
>>>>>> wrote:
>>>>>>
>>>>>> Dear Pymol Users!
>>>>>>
>>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>>>> transmbembrane scaffold).
>>>>>>
>>>>>> I need to write a simple script which will do the following things:
>>>>>>
>>>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>>>> "super" or "TMalign" (is better!)
>>>>>>
>>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>>>> (assuming that each pdb has several chains, some insertions like
>>>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>>>> seven-transmembrane scaffold present in reference.pdb.
>>>>>>
>>>>>> I thanks so much for the help!
>>>>>>
>>>>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>

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Re: [PyMOL] A structural superimposition and further post-processing

2017-07-18 Thread James Starlight
There were some errors in the executing pymol script with your commands using
@ script.pml
or
run script.pml

probably because of my MAC Pymol which is v 1.74 mb outdated, no?

BTW on the same MAC I just have tried to install updated setup.py and
it was the following error:

Glebs-MacBook-Pro:pymol-psico-master Own$ python setup.py
  File "setup.py", line 7

^
SyntaxError: invalid syntax

2017-07-18 19:52 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> With super instead of tmalign:
>
> loadall *.pdb
> extra_fit *, reference, method=super, object=aln
> remove not (byres aln)
>
> The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
> https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
>
> Cheers,
>   Thomas
>
>> On Jul 18, 2017, at 1:39 PM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> Hi Thomas,
>>
>> could you also send the same script but just with the Super command
>> for the superimposition without PSICO?
>>
>> it's strange I have a problems of PSICO installation on MAC with python 3
>>
>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>> READMEpsicosetup.py
>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>  File "setup.py", line 10
>>print 'Warning: could not import version'
>>^
>>
>> 2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>>> Hi Thomas,
>>>
>>> could you also send the same script but just with the Super command
>>> for the superimposition without PSICO?
>>>
>>> it's strange I have a problems of PSICO installation on MAC with python 3
>>>
>>> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
>>> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
>>> READMEpsicosetup.py
>>> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>>>  File "setup.py", line 10
>>>print 'Warning: could not import version'
>>>^
>>> SyntaxError: Missing parentheses in call to 'print'
>>>
>>> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>>>> Hi Gleb,
>>>>
>>>> If you have PSICO installed (which provides a TMalign wrapper), then this 
>>>> script should be sufficient:
>>>>
>>>> loadall *.pdb
>>>> import psico.fitting
>>>> extra_fit *, reference, method=tmalign, object=aln
>>>> remove not (byres aln)
>>>>
>>>> https://pymolwiki.org/index.php/Psico
>>>>
>>>> Cheers,
>>>>  Thomas
>>>>
>>>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> 
>>>>> wrote:
>>>>>
>>>>> Dear Pymol Users!
>>>>>
>>>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>>>> reference.pdb (it consist of only one GPCR monomer - seven
>>>>> transmbembrane scaffold).
>>>>>
>>>>> I need to write a simple script which will do the following things:
>>>>>
>>>>> 1 - allign (in loop) each structure against reference.pdb using
>>>>> "super" or "TMalign" (is better!)
>>>>>
>>>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>>>> (assuming that each pdb has several chains, some insertions like
>>>>> lyzocyme which were not aligned against reference), thus keeping only
>>>>> seven-transmembrane scaffold present in reference.pdb.
>>>>>
>>>>> I thanks so much for the help!
>>>>>
>>>>> Gleb
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>

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Re: [PyMOL] A structural superimposition and further post-processing

2017-07-18 Thread James Starlight
Hi Thomas,

could you also send the same script but just with the Super command
for the superimposition without PSICO?

it's strange I have a problems of PSICO installation on MAC with python 3

Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
[GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
READMEpsicosetup.py
Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
  File "setup.py", line 10
print 'Warning: could not import version'
        ^

2017-07-18 19:37 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Hi Thomas,
>
> could you also send the same script but just with the Super command
> for the superimposition without PSICO?
>
> it's strange I have a problems of PSICO installation on MAC with python 3
>
> Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:52:12)
> [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>>
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ ls -t
> READMEpsicosetup.py
> Glebs-MacBook-Pro:pymol-psico-master 2 Own$ python setup.py
>   File "setup.py", line 10
> print 'Warning: could not import version'
> ^
> SyntaxError: Missing parentheses in call to 'print'
>
> 2017-07-18 19:05 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
>> Hi Gleb,
>>
>> If you have PSICO installed (which provides a TMalign wrapper), then this 
>> script should be sufficient:
>>
>> loadall *.pdb
>> import psico.fitting
>> extra_fit *, reference, method=tmalign, object=aln
>> remove not (byres aln)
>>
>> https://pymolwiki.org/index.php/Psico
>>
>> Cheers,
>>   Thomas
>>
>>> On Jul 18, 2017, at 11:35 AM, James Starlight <jmsstarli...@gmail.com> 
>>> wrote:
>>>
>>> Dear Pymol Users!
>>>
>>> In my work dir I have 200 pdb files of GPCRs and one receptor
>>> reference.pdb (it consist of only one GPCR monomer - seven
>>> transmbembrane scaffold).
>>>
>>> I need to write a simple script which will do the following things:
>>>
>>> 1 - allign (in loop) each structure against reference.pdb using
>>> "super" or "TMalign" (is better!)
>>>
>>> 2 - from each of the aligned pdbs, remove not superimposed regions
>>> (assuming that each pdb has several chains, some insertions like
>>> lyzocyme which were not aligned against reference), thus keeping only
>>> seven-transmembrane scaffold present in reference.pdb.
>>>
>>> I thanks so much for the help!
>>>
>>> Gleb
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>

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[PyMOL] A structural superimposition and further post-processing

2017-07-18 Thread James Starlight
Dear Pymol Users!

In my work dir I have 200 pdb files of GPCRs and one receptor
reference.pdb (it consist of only one GPCR monomer - seven
transmbembrane scaffold).

I need to write a simple script which will do the following things:

1 - allign (in loop) each structure against reference.pdb using
"super" or "TMalign" (is better!)

2 - from each of the aligned pdbs, remove not superimposed regions
(assuming that each pdb has several chains, some insertions like
lyzocyme which were not aligned against reference), thus keeping only
seven-transmembrane scaffold present in reference.pdb.

I thanks so much for the help!

Gleb

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[PyMOL] Coordination bonds

2016-07-14 Thread James Starlight
Dear PyMol users!

Using present ->  ligand sites context menu I would like to display
possible non-covalent contacts between ions embedded within the
protein.
First I tried to rename ATOM to HETATM record corresponds to ions
however pymol still don't recognize ions as ligand.

Will be very thankful for any suggestions!

James

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[PyMOL] Scripting in Pymol (+)

2016-07-12 Thread James Starlight
Dear Pymol Users!

Here I desice to continue my topic regarding scripting in Pymol;

My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly

What I need from pymol to write some script, which will
1) align (superimpose) each MD snapshot againt reference
2) copy HEME residue from reference to each of the superimpsoed
snapshot within the same position.

Thanks so much for any suggestions regarding realization !

James

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[PyMOL] Transfer of the selection from reference to the ensemble

2016-06-28 Thread James Starlight
Dear Pymol Users!

Within the Pymol session I have 2 loaded superimposed objects:
1) one experimental pdb consisted of protein with cofactors (ligand and metals);
2) ensemble of 20 md snapshots of the same proteins superimposed on
each others without any cofactors;

For my particular task  I need
1) to copy the selection (which include metals and ligand atoms) from
the reference structure to each model of the MD ensemble (via Pymol),
2) make quick geometrical optimization of side-chains (I guess it
better to do it using Chimera) within the active side of each model
from MD ensemble
3) perform post-processing - analysis of the distances between
cofactors and optimized side-chains of each MD conformers to obtain
statistical distribution of averaged distances (I guess it better to
do it via some MD software like Gromacs).

I will be very thankful for any suggestions for practical realization
of those steps!



James

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[PyMOL] Analysis of docking poses from 2 nmr-ensembles

2016-06-13 Thread James Starlight
Dear Pymol users!

I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which  consists of 20
snapshots according to docking ranking) as well as MD simulation
(ensemble 2: which consists of 10 snapshots each of which represents
binding pose which has been established during long MD run).
Loading those two ensembles in pymol as 2 different models (in
NMR-like model format)  I need to performs some analysis  to find some
shared trends in each of them e.g RMSD of the distances between common
residues-pairs found in contact map analysis
or something else. What are most trivial suggestions might be in that
particular case?


Thanks for the suggestions!


James

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Re: [PyMOL] post-processing of pdb ensemble

2016-05-25 Thread James Starlight
More precisely I would like to know how to script in pymol the
following alteration fo the chains for the multi-chain pdb


PyMOL>alter (bound_combined and chain B), chain="A"
 Alter: modified 5157 atoms.
PyMOL>alter (bound_combined and chain C), chain="B"
 Alter: modified 2285 atoms.
PyMOL>alter (bound_combined and chain D), chain="C"
 Alter: modified 2778 atoms.
PyMOL>alter (bound_combined and chain E), chain="D"
 Alter: modified 1560 atoms.
PyMOL>alter (bound_combined and chain F), chain="E"
 Alter: modified 1114 atoms.
PyMOL>alter (bound_combined and chain G), chain="F"
 Alter: modified 950 atoms.
PyMOL>alter (bound_combined and chain H), chain="G"
 Alter: modified 895 atoms.
PyMOL>alter (bound_combined and chain I), chain="H"
 Alter: modified 843 atoms.
PyMOL>alter (bound_combined and chain J), chain="I"
 Alter: modified 806 atoms.
PyMOL>alter (bound_combined and chain K), chain="J"
 Alter: modified 574 atoms.
PyMOL>alter (bound_combined and chain L), chain="K"
 Alter: modified 501 atoms.
PyMOL>alter (bound_combined and chain M), chain="L"
 Alter: modified 511 atoms.
PyMOL>alter (bound_combined and chain N), chain="M"
 Alter: modified 433 atoms.


So each step we rename chain i to the i-1 name within given model :)

Thanks!

J.

2016-05-23 19:11 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Dear Pymol users!
>
> After some post-processing of MD simulation I have extracted from the
> traejctory several snapshots as individual pdbs which I need to
> 1-  to re-assign information regarding chain letters (which was lost
> after some operations on pdbs)  for all of those structures assuming
> that within each of these pdbs residues are ordered correctly e.g from
> (1-104 which
> should be chain A) than from 1-100 (it should be chain B), than 1-70
> (in should be chain C) etc.
>
> 2- superimpose and combine all of the pdbs within one model in nmr-like 
> format.
>
> Thanks for help!
>
> James

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[PyMOL] post-processing of pdb ensemble

2016-05-23 Thread James Starlight
Dear Pymol users!

After some post-processing of MD simulation I have extracted from the
traejctory several snapshots as individual pdbs which I need to
1-  to re-assign information regarding chain letters (which was lost
after some operations on pdbs)  for all of those structures assuming
that within each of these pdbs residues are ordered correctly e.g from
(1-104 which
should be chain A) than from 1-100 (it should be chain B), than 1-70
(in should be chain C) etc.

2- superimpose and combine all of the pdbs within one model in nmr-like format.

Thanks for help!

James

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Re: [PyMOL] Contact map visualizer

2016-05-12 Thread James Starlight
Thanks Tsjerk!

now the map is accepted fine by the Pymol- however there is an problem
due to the mismatching of atoms in ref structure and the map (although
I use ref.pdf from which contact map has been produced). Probably the
source of the error is Martini's atom representation used in my system
- I've had the same issue in case of some VMD script which do the same
task.  Do any alternativeties are exist which can identify residues
(even on one of the protein) crucial for the formation of the complex
during md run with the possibility to map it to the structure for the
visualization?

J.

2016-05-12 12:52 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hey :)
>
> That's been a choice of the author. You can contact him and ask.
>
> Cheers,
>
> Tsjerk
>
> On May 12, 2016 12:25, "James Starlight" <jmsstarli...@gmail.com> wrote:
>>
>> Ok, thanks!
>>
>> however it's normal that pymol ask me for the contact map in the png
>> and not for the original xpm produced by gromacs? It seems for the
>> that to operate directly with  Pymol outputs is more trivial :-)
>>
>> J.
>>
>> 2016-05-12 6:51 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>> > Hi James,
>> >
>> > You can convert the .xpm file to .png/.jpg using tools like convert
>> > (imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm
>> > right,
>> > but it's an easy one to try.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On May 11, 2016 2:40 PM, "James Starlight" <jmsstarli...@gmail.com>
>> > wrote:
>> >>
>> >> Dear Pymol users!
>> >>
>> >> I am in charge with the analysis of protein-protein association during
>> >> long molecular dynamic simulation. In particularly I am interesting to
>> >> find residues on one of the protein which are crustal for the binding
>> >> interface established during Md.
>> >> For that purpose I am trying to use Contact map visualizer plugin to
>> >> map contact maps produced by gromacs onto the 3D structure via Pymol.
>> >> The problem that on the stage of loading of the contact map Pymol
>> >> proposed me to load only png or jpg files (not xpm produced by
>> >> g_mdmat). How it's possible to solve the issue? Any other suggestions
>> >> regarding my topic?
>> >>
>> >> Thanks!
>> >>
>> >> James
>> >>
>> >>
>> >>
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[PyMOL] Contact map visualizer

2016-05-11 Thread James Starlight
Dear Pymol users!

I am in charge with the analysis of protein-protein association during
long molecular dynamic simulation. In particularly I am interesting to
find residues on one of the protein which are crustal for the binding
interface established during Md.
For that purpose I am trying to use Contact map visualizer plugin to
map contact maps produced by gromacs onto the 3D structure via Pymol.
The problem that on the stage of loading of the contact map Pymol
proposed me to load only png or jpg files (not xpm produced by
g_mdmat). How it's possible to solve the issue? Any other suggestions
regarding my topic?

Thanks!

James

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Re: [PyMOL] Bash scripting and pymol

2016-04-29 Thread James Starlight
Yes thanks it works!

Now assuming that I want to make alitle complicated script based on
that template.

Assuming that I have 3 pdbs used as references defined in variables
ref1, ref2,ref3

now I need loop all of my pdbs from the array and superimpose each pdb
from the array agains each of reference pdb and then based on RMSD
value produced from pymol output chose only best superimposed
structure from 3 possibilities
Based on that selection I can make conclusion  that for pdb1 the ref1
is best template because of the similar fold, for pdb2 is the ref2 is
best etc...




# Set pdb array
pdb_array=("1f88" "2rh1" "3pbs" "3eml" "4LGJ" "5A2H")
pdb_array_store=$template/pymol

# Set references
ref1="${pdb_array_store}/ref/ref_gpcr.pdb"
ref1_filename=$(basename "$ref1")
R1=${ref1_filename/.pdb/}

ref2="${pdb_array_store}/ref/ref_wsp.pdb"
ref2_filename=$(basename "$ref2")
R2=${ref2_filename/.pdb/}

ref3="${pdb_array_store}/ref/ref_xz.pdb"
ref3_filename=$(basename "$ref3")
R3=${ref3_filename/.pdb/}

Here the realization of that for only 1 reference:

# download pdbs to the folder and superimpose them agains ref1!
for i in ${pdb_array[@]}; do
pdb_tit=$(basename "$i")
pymol ${ref1} -d "cd ${pdb_array_store}/tmp; fetch ${i}, async=0;
remove ${i} and not chain A; super ${i}, ${R1}; save
${pdb_array_store}/${pdb_tit}_superimposed.pdb, ${pdb_tit} and
polymer;" -c  #> ${pdb_array_store}/tmp/${pdb_tit}_pymol.log
done



now I can just define ref2 ref3 and add two additional pymol strings
within the for loop to superimpose step-by-stem each pdbs from the
${pdb_array}  agains, ref2 and ref3 in addition.
 but how to select the best superimposed structure as the outcome of
each for loop run ? In other words I need only to save
${pdb_tit}_superimposed.pdb with the lowest RMSD value assuming that
the operation was repeated 3 times for 3 different refs.

Thanks for help!

J,

2016-04-28 15:48 GMT+02:00 David Hall <li...@cowsandmilk.net>:
> You need to add “,async=0” to your fetch calls.
>
> http://pymolwiki.org/index.php/Fetch
>
>
>
>> On Apr 28, 2016, at 4:51 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> Hi,
>>
>> My script is
>>
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> pdb_array_store=$template/pymol
>>
>>
>> # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process 
>> them!
>> mkdir ${pdb_array_store}
>> for i in ${pdb_array[@]}; do
>> pdb_tit=$(basename "$i")
>> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
>> ${pdb_tit}" -c ;
>> rm ${pdb_array_store}/*.log
>> done
>>
>>
>> while executing it sends error
>>
>> PyMOL>fetch 5A2H; save
>> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
>> 5A2H
>> please wait ...
>> Selector-Error: Invalid selection name "5A2H".
>> ( 5A2H )<--
>> Save: wrote 
>> "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
>> PyMOL: normal program termination.
>>
>> if I change save selection just to 'polymer' it saved empty pdbs-
>> where might be an error here?
>>
>> Thanks!
>>
>> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
>>> Hi,
>>>
>>> You need
>>>
>>> for i in ${pdb_array[@]}
>>> do
>>> ...
>>> done
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
>>>>
>>>> so As I tried to do it but it was not worked :-O)
>>>>
>>>> #pdbs list
>>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>>> #where to save
>>>> pdb_array_store=$template/pymol/
>>>>
>>>>
>>>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>>>> #mkdir ${pdb_array_store}
>>>> for i in `cat ${pdb_array}` ; do wget
>>>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>>>> done
>>>>
>>>> result
>>>> cat: 1UBI: No such file or directory
>>>>
>>>> 2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>>>>> Please give me an example of the list of 3 pdbs instead of just cat $1
>>>>> :)
>>>>> as well as proper 

Re: [PyMOL] Bash scripting and pymol

2016-04-28 Thread James Starlight
Hi,

My script is

pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
pdb_array_store=$template/pymol


# A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them!
mkdir ${pdb_array_store}
for i in ${pdb_array[@]}; do
pdb_tit=$(basename "$i")
pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
${pdb_tit}" -c ;
rm ${pdb_array_store}/*.log
done


while executing it sends error

PyMOL>fetch 5A2H; save
/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
5A2H
 please wait ...
Selector-Error: Invalid selection name "5A2H".
( 5A2H )<--
 Save: wrote 
"/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
 PyMOL: normal program termination.

if I change save selection just to 'polymer' it saved empty pdbs-
where might be an error here?

Thanks!

2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>:
> Hi,
>
> You need
>
> for i in ${pdb_array[@]}
> do
> ...
> done
>
> Cheers,
>
> Tsjerk
>
> On Apr 27, 2016 4:44 PM, "James Starlight" <jmsstarli...@gmail.com> wrote:
>>
>> so As I tried to do it but it was not worked :-O)
>>
>> #pdbs list
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> #where to save
>> pdb_array_store=$template/pymol/
>>
>>
>> # A simple FETCHER: download pdbs to the folder and pre-process them!
>> #mkdir ${pdb_array_store}
>> for i in `cat ${pdb_array}` ; do wget
>> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
>> done
>>
>> result
>> cat: 1UBI: No such file or directory
>>
>> 2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> > Please give me an example of the list of 3 pdbs instead of just cat $1
>> > :)
>> >  as well as proper syntax of how to save each pdb after fetching in
>> > pymol using same command line
>> > Forgot to mention important points:
>> > 1) that list should be physically in my script like in python
>> > 2) I use pymol because I will need to process each of the pdb- e,g to
>> > remove from them ligands or water etc
>> >
>> > Thanks!
>> >
>> > 2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> >> Please give me an example of the list of 3 pdbs instead of cat $1  as
>> >> well as how to save syntax of how to save each pdb
>> >>
>> >>
>> >> Thanks!
>> >>
>> >> J
>> >>
>> >> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>> >>> If you really want to use pymol, this works
>> >>>
>> >>> #!/bin/bash
>> >>> #myscript.bash
>> >>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>> >>>
>> >>>
>> >>> Then on the command line
>> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>> >>>
>> >>>
>> >>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com>
>> >>> wrote:
>> >>>
>> >>> Must you use pymol?
>> >>>
>> >>>
>> >>> Try directly from the PDB
>> >>>
>> >>> #!/bin/bash
>> >>> #myscript.bash
>> >>>
>> >>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
>> >>> done
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Then on the command line
>> >>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>> >>>
>> >>>
>> >>> J
>> >>>
>> >>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com>
>> >>> wrote:
>> >>>
>> >>> Dear Pymol users!
>> >>>
>> >>> I need to add a few strings to my simple bash script which will creat
>> >>> a list of pdb files and than will call pymol without GUI from the
>> >>> terminal to fetch all the pdbs and save it to the desired location.
>> >>> For one pdb it should be smth like
>> >>>
>> >>> pdbs="1f88"
>> >>>
>> >>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> >>> ${tmp}/pymol_${pdbs}.log
>>

Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight
so As I tried to do it but it was not worked :-O)

#pdbs list
pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
#where to save
pdb_array_store=$template/pymol/


# A simple FETCHER: download pdbs to the folder and pre-process them!
#mkdir ${pdb_array_store}
for i in `cat ${pdb_array}` ; do wget
http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
done

result
cat: 1UBI: No such file or directory

2016-04-27 12:29 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Please give me an example of the list of 3 pdbs instead of just cat $1 :)
>  as well as proper syntax of how to save each pdb after fetching in
> pymol using same command line
> Forgot to mention important points:
> 1) that list should be physically in my script like in python
> 2) I use pymol because I will need to process each of the pdb- e,g to
> remove from them ligands or water etc
>
> Thanks!
>
> 2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
>> Please give me an example of the list of 3 pdbs instead of cat $1  as
>> well as how to save syntax of how to save each pdb
>>
>>
>> Thanks!
>>
>> J
>>
>> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>>> If you really want to use pymol, this works
>>>
>>> #!/bin/bash
>>> #myscript.bash
>>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>>>
>>>
>>> Then on the command line
>>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>>
>>>
>>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com> wrote:
>>>
>>> Must you use pymol?
>>>
>>>
>>> Try directly from the PDB
>>>
>>> #!/bin/bash
>>> #myscript.bash
>>>
>>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
>>>
>>>
>>>
>>>
>>> Then on the command line
>>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>>
>>>
>>> J
>>>
>>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>>
>>> Dear Pymol users!
>>>
>>> I need to add a few strings to my simple bash script which will creat
>>> a list of pdb files and than will call pymol without GUI from the
>>> terminal to fetch all the pdbs and save it to the desired location.
>>> For one pdb it should be smth like
>>>
>>> pdbs="1f88"
>>>
>>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>>> ${tmp}/pymol_${pdbs}.log
>>>
>>> will be thankful for the correction of this string as well as example
>>> how it can be adapted for a list of pdbs in bash.
>>>
>>> Thanks!
>>>
>>> J
>>>
>>> --
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>>> your business applications. It resolves application problems quickly and
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>>>
>>>
>>>

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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight
Please give me an example of the list of 3 pdbs instead of just cat $1 :)
 as well as proper syntax of how to save each pdb after fetching in
pymol using same command line
Forgot to mention important points:
1) that list should be physically in my script like in python
2) I use pymol because I will need to process each of the pdb- e,g to
remove from them ligands or water etc

Thanks!

2016-04-27 12:18 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Please give me an example of the list of 3 pdbs instead of cat $1  as
> well as how to save syntax of how to save each pdb
>
>
> Thanks!
>
> J
>
> 2016-04-27 12:09 GMT+02:00 Jordan Willis <jwillis0...@gmail.com>:
>> If you really want to use pymol, this works
>>
>> #!/bin/bash
>> #myscript.bash
>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> On Apr 27, 2016, at 2:55 AM, Jordan Willis <jwillis0...@gmail.com> wrote:
>>
>> Must you use pymol?
>>
>>
>> Try directly from the PDB
>>
>> #!/bin/bash
>> #myscript.bash
>>
>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
>>
>>
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> J
>>
>> On Apr 27, 2016, at 2:41 AM, James Starlight <jmsstarli...@gmail.com> wrote:
>>
>> Dear Pymol users!
>>
>> I need to add a few strings to my simple bash script which will creat
>> a list of pdb files and than will call pymol without GUI from the
>> terminal to fetch all the pdbs and save it to the desired location.
>> For one pdb it should be smth like
>>
>> pdbs="1f88"
>>
>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> ${tmp}/pymol_${pdbs}.log
>>
>> will be thankful for the correction of this string as well as example
>> how it can be adapted for a list of pdbs in bash.
>>
>> Thanks!
>>
>> J
>>
>> --
>> Find and fix application performance issues faster with Applications Manager
>> Applications Manager provides deep performance insights into multiple tiers
>> of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
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>>
>>
>>

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[PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight
Dear Pymol users!

I need to add a few strings to my simple bash script which will creat
a list of pdb files and than will call pymol without GUI from the
terminal to fetch all the pdbs and save it to the desired location.
For one pdb it should be smth like

pdbs="1f88"

pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
${tmp}/pymol_${pdbs}.log

will be thankful for the correction of this string as well as example
how it can be adapted for a list of pdbs in bash.

Thanks!

J

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Re: [PyMOL] Cartoon visualization of per-residue txt data

2015-04-12 Thread James Starlight
Hi Tsjerk,


the interesting option for coloring which I found to set sensitivity
of the visualization in my case:

spectrum b, red_orange_white, minimum=-1, maximum=0.1


are there any same commands to set transparency level according to the
B-factor value? Here the issue is with the proper selection

E.g
PyMOLselect not-relevent, b  0
results only in small atoms selected

and
PyMOLselect ss, b = 0
Selector-Error: Invalid selection.
b--


Regards,

James

2015-04-10 21:12 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
 Hi James,

 The selection keyword 'b' exists for just that purpose: to make selections
 based on the b-factor value.

 color red, b  0

 Cheers,

 Tsjerk

 On Fri, Apr 10, 2015 at 5:19 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 some specification regarding B-factors visualization for my task:

 is it possible within the open pymol session

 1) to select only residues with non-zero B-factors as specified
 selection (here I would like to present it as the stics and display it
 names as the label)

 2) to define residues with zero B-factors as another specified
 selection (for those one I'd like to apply specified color filter for
 instance and transparency as for not relevant in my case)

 Thanks!

 J

 2015-04-10 15:27 GMT+02:00 James Starlight jmsstarli...@gmail.com:
  Hi Osvaldo and thank you very much- it works perfect!
 
  The only question which I have- is it possible to modify existing
  color-pattern of the B-factor colouring (from the spectrum
  visualization)? for instance I need to colour by white all residues
  with 0.0 B-factors and as the rainbow from cold to hot gradient
  residues with non-zero B-factors: where residues with most negative
  values should correspond to the hot colours, and with positive - to
  cold (because here this valus in fact correspond to the binding free
  energy so more negative- better contribution to dG).
 
 
  Thanks again,
 
  James
 
  2015-04-10 14:44 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com:
  Hi James,
 
  cmd.alter() is not working because you forget the to add the .
 
  You can use PyMol as a regular Python library, write an script and then
  run
  it, from the command line, as:
 
  python my_script.py
 
  Your script should looks like the following:
 
  import __main__
  __main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI
  import pymol
  from pymol import cmd, stored
  pymol.finish_launching()
  import other_useful_library
 
  cmd.load(OR5P3_androstenone.pdb)
 
  # open the file of new values (just 1 column of numbers, one for each
  alpha carbon)
  inFile = open(OR5P3_androstenone.dat, 'r')
 
  # create the global, stored array
  newB = []
 
  # read the new B factors from file
  for line in inFile.readlines(): newB.append( float(line) )
 
  # close the input file
  inFile.close()
 
  # clear out the old B Factors
  cmd.alter(OR5P3_androstenone, b=0.0)
 
  # update the B Factors with new properties
  cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0))
 
  # color the protein based on the new B Factors of the alpha carbons
  cmd.spectrum(b, OR5P3_androstenone and n. CA)
 
  # save new pdb
  cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone)
 
  Cheers,
  Osvaldo.
 
 
  On Fri, Apr 10, 2015 at 9:03 AM, James Starlight
  jmsstarli...@gmail.com
  wrote:
 
  so to be more precise the issue is how to adapt the following script
  (which used python interpetator  directly from pymol to change
  B-factors within loaded pdb) to use it as the external script loaded
  from command line e.g pymol -r script.py
 
  # here the code what should I to adapt:
 
  cmd.load(OR5P3_androstenone.pdb)
 
  # open the file of new values (just 1 column of numbers, one for each
  alpha carbon)
  inFile = open(OR5P3_androstenone.dat, 'r')
 
  # create the global, stored array
  newB = []
 
  # read the new B factors from file
  for line in inFile.readlines(): newB.append( float(line) )
 
  # close the input file
  inFile.close()
 
  # clear out the old B Factors
  cmd.alter(OR5P3_androstenone, b=0.0)
 
  # update the B Factors with new properties
  cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0))
 
  # color the protein based on the new B Factors of the alpha carbons
  cmd.spectrum(b, OR5P3_androstenone and n. CA)
 
  # save new pdb
  cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone)
 
 
 
  # so as you can see here I tried to move some pynol command like alter
  to the cmd.alter with its options but the script didn't worked.
 
  J.
 
  2015-04-09 16:52 GMT+02:00 James Starlight jmsstarli...@gmail.com:
   also to specify:
  
   I've already done this for one pdb and one dat file using just
   sequence command from the pymol with loaded protA.pdb
  
   inFile = open(./test.dat, 'r')
  
   # create the global, stored array
   stored.newB = []
  
   # read the new B factors from file
   for line in inFile.readlines(): stored.newB.append( float(line) )
  
   # close the input file
   inFile.close

Re: [PyMOL] Pymol molecular visualisation

2015-04-12 Thread James Starlight
Thanks !
still have not found solution for grid-mode display:
1- I need to show names of each opened object near its cartoon

2- I need to increase spacing of grid border (m.b like just empty
space)- to better discriminate between opened objects in case of its
high zooming

J

2015-04-11 14:51 GMT+02:00 João M. Damas jmda...@itqb.unl.pt:
 1- See http://www.pymolwiki.org/index.php/Ray_Trace_Gain. However, from my
 experience, I don't think the setting works too well, so what I usually do
 is to increase the resolution of the raytrace, which makes the black outline
 thinner.

 On Fri, Apr 10, 2015 at 4:48 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear Pymol users!

 Here I will ask some question regarding visualization issues in pymol.

 1- Using ray_trace_mode, 1 I need to decrease at least twisty width of
  black countour line (especially in the loop segments).

 2- Being in the split mode (visualization of the several objects on
 one screen) I need to show title of each of the objects somewhere near
 of its cartoon area (e,g in right upper corner)- just to know on the
 produced picture names of the corresponded cartoon.

 3- Also please have a look on my another topic regarding visualization
 of B-factor gradients: actually I need to revert its existing color
 pattern and select residues according to it's actual B-factor values
 (E.g with B-factor=0, with negative and/or positive) for its
 subsequent selective visualization.

 Thanks a lot for the advises!


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Re: [PyMOL] Cartoon visualization of per-residue txt data

2015-04-12 Thread James Starlight
and also a question-
how it would be possible to do something with the selection based on
the b-factors

e.g

PyMOLselect ss, b  -0.2
 Selector: selection ss defined with 119 atoms.

than I've tried to make  visualization of the residues within the ss
to display residues names from the label context menu, which resulted
in the

Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ss )--
Selector-Error: Misplaced ).
Selector-Error: Malformed selection.

also I've tried just to copy 'ss' to new object:

( ( name CA+C1*+C1' and ( byres ( ss )--
Selector-Error: Misplaced ).
Selector-Error: Malformed selection.
( ss )--


James

2015-04-12 15:12 GMT+02:00 James Starlight jmsstarli...@gmail.com:
 Hi Tsjerk,


 the interesting option for coloring which I found to set sensitivity
 of the visualization in my case:

 spectrum b, red_orange_white, minimum=-1, maximum=0.1


 are there any same commands to set transparency level according to the
 B-factor value? Here the issue is with the proper selection

 E.g
 PyMOLselect not-relevent, b  0
 results only in small atoms selected

 and
 PyMOLselect ss, b = 0
 Selector-Error: Invalid selection.
 b--


 Regards,

 James

 2015-04-10 21:12 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:
 Hi James,

 The selection keyword 'b' exists for just that purpose: to make selections
 based on the b-factor value.

 color red, b  0

 Cheers,

 Tsjerk

 On Fri, Apr 10, 2015 at 5:19 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 some specification regarding B-factors visualization for my task:

 is it possible within the open pymol session

 1) to select only residues with non-zero B-factors as specified
 selection (here I would like to present it as the stics and display it
 names as the label)

 2) to define residues with zero B-factors as another specified
 selection (for those one I'd like to apply specified color filter for
 instance and transparency as for not relevant in my case)

 Thanks!

 J

 2015-04-10 15:27 GMT+02:00 James Starlight jmsstarli...@gmail.com:
  Hi Osvaldo and thank you very much- it works perfect!
 
  The only question which I have- is it possible to modify existing
  color-pattern of the B-factor colouring (from the spectrum
  visualization)? for instance I need to colour by white all residues
  with 0.0 B-factors and as the rainbow from cold to hot gradient
  residues with non-zero B-factors: where residues with most negative
  values should correspond to the hot colours, and with positive - to
  cold (because here this valus in fact correspond to the binding free
  energy so more negative- better contribution to dG).
 
 
  Thanks again,
 
  James
 
  2015-04-10 14:44 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com:
  Hi James,
 
  cmd.alter() is not working because you forget the to add the .
 
  You can use PyMol as a regular Python library, write an script and then
  run
  it, from the command line, as:
 
  python my_script.py
 
  Your script should looks like the following:
 
  import __main__
  __main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI
  import pymol
  from pymol import cmd, stored
  pymol.finish_launching()
  import other_useful_library
 
  cmd.load(OR5P3_androstenone.pdb)
 
  # open the file of new values (just 1 column of numbers, one for each
  alpha carbon)
  inFile = open(OR5P3_androstenone.dat, 'r')
 
  # create the global, stored array
  newB = []
 
  # read the new B factors from file
  for line in inFile.readlines(): newB.append( float(line) )
 
  # close the input file
  inFile.close()
 
  # clear out the old B Factors
  cmd.alter(OR5P3_androstenone, b=0.0)
 
  # update the B Factors with new properties
  cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0))
 
  # color the protein based on the new B Factors of the alpha carbons
  cmd.spectrum(b, OR5P3_androstenone and n. CA)
 
  # save new pdb
  cmd.save(OR5P3_androstenone_newBFactors.pdb, OR5P3_androstenone)
 
  Cheers,
  Osvaldo.
 
 
  On Fri, Apr 10, 2015 at 9:03 AM, James Starlight
  jmsstarli...@gmail.com
  wrote:
 
  so to be more precise the issue is how to adapt the following script
  (which used python interpetator  directly from pymol to change
  B-factors within loaded pdb) to use it as the external script loaded
  from command line e.g pymol -r script.py
 
  # here the code what should I to adapt:
 
  cmd.load(OR5P3_androstenone.pdb)
 
  # open the file of new values (just 1 column of numbers, one for each
  alpha carbon)
  inFile = open(OR5P3_androstenone.dat, 'r')
 
  # create the global, stored array
  newB = []
 
  # read the new B factors from file
  for line in inFile.readlines(): newB.append( float(line) )
 
  # close the input file
  inFile.close()
 
  # clear out the old B Factors
  cmd.alter(OR5P3_androstenone, b=0.0)
 
  # update the B Factors with new properties
  cmd.alter(OR5P3_androstenone and n. CA, b=newB.pop(0))
 
  # color the protein based on the new B Factors of the alpha carbons
  cmd.spectrum(b, OR5P3_androstenone

Re: [PyMOL] Cartoon visualization of per-residue txt data

2015-04-09 Thread James Starlight
thanks for the information! Here I ask to provide me with some more
help because I'm not a big expert in the python .

For instance I have 2 folders- one with 10 pdb's corresponded to the
10 complexes of one receptor (289 residues) docked with 10 different
ligands; the second one is the 10 the_same_name.dat files corresponded
to the 10 logs having 1 column with the values per each residue
(totally 289 values) of the receptor. I need to associate each pdb
with each dat to exchange existing B-factors within each pdb onto the
values taken from the corresponded.dat files and associate it's
directly to the C-alpha atoms of each complex for instance. Will it be
better to rewrite here the script from the PyMol Wiki or to use
data2bfactor.py (here as I found I need to modify my dat logs
including to them number of receptor residues and chainID).

James

2015-04-08 19:00 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com:
 Hi James,

 I think what you want to do is to load your data to the b-factor column of
 the pdb file and then ask PyMol to color the protein according to the
 b-factor values. Try with this example from the PyMol wiki and let us know
 if you find some trouble.

 Regards,
 Osvaldo.

 On Wed, Apr 8, 2015 at 1:47 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear Pymol users!

 For better visualization of the MMGBSA outputs from MD performed for 10
 ligands
 agains 1 receptor-target I wonder to map per-residue decomposition
 data from each of the systems onto the receptor's 3D structure.
 Eventually I'd like to produce 10 cartoon diagrams which would differs
 in the coloring according to the difference in the contribution of
 residues from the receptor's cavity to binding for different ligands.
 I will be very thankful if someone provide me with ideas of how such
 visualization could be done using receptors structure, decomposition
 logs as the inputs and/or pymol.  Here some general idea whig came in
 mind-  import column from the mmgbsa.log directly (with number of
 rows= number of receptors residues) to the receptor.pdb B-factors
 column (for instance making meaningful value for C-alpha atom and 0
 for the rest). Will be very thankful for some examples of how it could
 be achieved e.g using combination of awk_sed if more trivial way is
 not exist.


 Thanks for help!!

 James


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Re: [PyMOL] Cartoon visualization of per-residue txt data

2015-04-09 Thread James Starlight
also to specify:

I've already done this for one pdb and one dat file using just
sequence command from the pymol with loaded protA.pdb

inFile = open(./test.dat, 'r')

# create the global, stored array
stored.newB = []

# read the new B factors from file
for line in inFile.readlines(): stored.newB.append( float(line) )

# close the input file
inFile.close()

# clear out the old B Factors
alter protA, b=0.0

# update the B Factors with new properties
alter protA and n. CA, b=stored.newB.pop(0)

# color the protein based on the new B Factors of the alpha carbons
cmd.spectrum(b, protA and n. CA)


now the idea using below bash script which superimpose each pdb with
each log to call pymol from the terminal each time for each pdb and
load to it corresponded dat file producing as the result new pdb with
new B-factors (taken from the dat log)


#!/bin/bash
workdir=/data2/Gleb/script/Simulations/activation/5p3_decomposition_visu
pdb_all=${workdir}/complexes
logs_all=${workdir}/logs

# where final pdb will be saved
output=${workdir}/outputs


#looping of pdbs
for pdb in ${pdb_all}/*.pdb; do # 
 pdb_n_full=$(basename ${pdb})
 pdb_n=${pdb_n_full%.*}
 Complexes=(${Complexes[@]} ${pdb_n});
 echo ${pdb_n} has been added to the list!
done
#sort elements within ${Complexes[@]} lists!!
#echo The pdb list consist of:  ${Complexes[@]}
#echo Total number of pdbs:  ${#Complexes[@]}

#looping of tops
for log in ${logs_all}/*.dat; do # 
 log_n_full=$(basename ${log})
 log_n=${log_n_full%.*}
 Logs=(${Logs[@]} ${log_n});
 echo ${log_n} has been added to the list!
done
#sort elements within ${Logs[@] lists!!
#echo The DAT list consist of:  ${Logs[@]}
#echo Total number of logs:  ${#Logs[@]}


# So I need only to define how I will use pymol with each pair of log and pdb
#proceed each pdb in pymol using elements from both lists
for i in $(seq 1 ${#Logs[@]}); do
 # print what pdb and what DAT will be used within this loop
 echo ${Logs[i]}
 echo ${Complexes[i]}
 # here run pymol using i pdb with corresponded i dat !!
#done


I will be thankful for any ideas in the last part of that script!


James

2015-04-09 16:15 GMT+02:00 James Starlight jmsstarli...@gmail.com:
 thanks for the information! Here I ask to provide me with some more
 help because I'm not a big expert in the python .

 For instance I have 2 folders- one with 10 pdb's corresponded to the
 10 complexes of one receptor (289 residues) docked with 10 different
 ligands; the second one is the 10 the_same_name.dat files corresponded
 to the 10 logs having 1 column with the values per each residue
 (totally 289 values) of the receptor. I need to associate each pdb
 with each dat to exchange existing B-factors within each pdb onto the
 values taken from the corresponded.dat files and associate it's
 directly to the C-alpha atoms of each complex for instance. Will it be
 better to rewrite here the script from the PyMol Wiki or to use
 data2bfactor.py (here as I found I need to modify my dat logs
 including to them number of receptor residues and chainID).

 James

 2015-04-08 19:00 GMT+02:00 Osvaldo Martin aloctavo...@gmail.com:
 Hi James,

 I think what you want to do is to load your data to the b-factor column of
 the pdb file and then ask PyMol to color the protein according to the
 b-factor values. Try with this example from the PyMol wiki and let us know
 if you find some trouble.

 Regards,
 Osvaldo.

 On Wed, Apr 8, 2015 at 1:47 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear Pymol users!

 For better visualization of the MMGBSA outputs from MD performed for 10
 ligands
 agains 1 receptor-target I wonder to map per-residue decomposition
 data from each of the systems onto the receptor's 3D structure.
 Eventually I'd like to produce 10 cartoon diagrams which would differs
 in the coloring according to the difference in the contribution of
 residues from the receptor's cavity to binding for different ligands.
 I will be very thankful if someone provide me with ideas of how such
 visualization could be done using receptors structure, decomposition
 logs as the inputs and/or pymol.  Here some general idea whig came in
 mind-  import column from the mmgbsa.log directly (with number of
 rows= number of receptors residues) to the receptor.pdb B-factors
 column (for instance making meaningful value for C-alpha atom and 0
 for the rest). Will be very thankful for some examples of how it could
 be achieved e.g using combination of awk_sed if more trivial way is
 not exist.


 Thanks for help!!

 James


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[PyMOL] Cartoon visualization of per-residue txt data

2015-04-08 Thread James Starlight
Dear Pymol users!

For better visualization of the MMGBSA outputs from MD performed for 10 ligands
agains 1 receptor-target I wonder to map per-residue decomposition
data from each of the systems onto the receptor's 3D structure.
Eventually I'd like to produce 10 cartoon diagrams which would differs
in the coloring according to the difference in the contribution of
residues from the receptor's cavity to binding for different ligands.
I will be very thankful if someone provide me with ideas of how such
visualization could be done using receptors structure, decomposition
logs as the inputs and/or pymol.  Here some general idea whig came in
mind-  import column from the mmgbsa.log directly (with number of
rows= number of receptors residues) to the receptor.pdb B-factors
column (for instance making meaningful value for C-alpha atom and 0
for the rest). Will be very thankful for some examples of how it could
be achieved e.g using combination of awk_sed if more trivial way is
not exist.


Thanks for help!!

James

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[PyMOL] Automatic detection and removing of steric problems

2014-11-07 Thread James Starlight
Dear PyMol users!

I'm writing of some automatic script aimed on the embedding of the
receptors into the membrane consisted of the pre-equilibrated lipids as
well as hole for the protein. The main issue that some of the receptors
consist of the bulky PHE or TRP side chains on their surface which are
overlap with the lipids so MD simulation of this system is crushed although
of long minimization stage prior to it.  I'll be very thankful if someone
provide me with some script for PyMol or VMD for automatic detection of
these problem (overlapped) locations and removing of the overlapped lipids
detected within some cutoff radios of the protein.

Thanks for help,

James
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[PyMOL] ligand binding site visualisation

2014-11-06 Thread James Starlight
Dear Pymol users!

Typically when I'm looking at the ligand binding sites (present-show of
the receptor-ligand.pdb complexes all receptors non-canonical residues or
the different titrable forms of the standard ones (e.g HIP-protonated HIS
or ASH- protonated ASN) are recognized as the ligands as well and pymol try
to find hydrogen bonds or vdv contacts of these residues with its
surroundings. How I could prevent it to see only on the ligand surrounding
within such pdbs? What another pymol options will be useful for the ligand
sites visualization?


Thanks for help,

James
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Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-25 Thread James Starlight
From the previous task it's OK now

small question about pymol :)

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

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

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

and smth about shell informatics:

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

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

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

James

2014-09-24 11:06 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 some additional question about shell scripting (copied from the amber
 forum because I'd like to find as more sollutions of this problem as
 possible):


 I wounder about possibilities to define disulphide bond between any pairs
 of SG atoms of CYX residues using amber's tleap scripts in some automatic
 fashion.

 In my case I use tleap as part of some big script to process many
 models.pdb for further md simulation. Each of the model consist of pair of
 CYX residues (assigned by pdb2pqr) in different positions of its sequence.
 So in script I need firstly to know the number of position for each of CYX
 residues of each model and than to fill this numbers to the tleap input
 files for each model

 in bash for one model it will be look like:

 #some command to scan the sequence of model.pdb and define pair of its CYX
 residues within it as the k ans i variables
   printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
 protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
 protein protein.parm7 protein.inpcrd\nquit  ./tleap.in


 so my task is only to find some command which will scan model and find
 positions of the CYX within its sequence which could be put to the tleap as
 two digits. It will be better to find those 2 digits using pdb as an input
 and some unix command like sed or grep to find positions

 I will be very thankful for any suggestions!

 James



 2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:


 csplit -b %03d.pdb test.pdbqt /^MODEL/ {0}  somelog.log


 man csplit:

 csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}

 But you want only the first frame anyway, so no real use for csplit...

 sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
 0\|^MODEL\|^REMARK |  sed -e 's/^ENDMDL/TER/g'  firstmodel.pdb


 sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
 0\|MODEL\|REMARK\)/d' my_docking.pdb  firstmodel.pdb

 ... shorter and one process running in stead of 3.

 Cheers,

 Tsjerk

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Re: [PyMOL] Molecular Visualisation in PyMol

2014-09-25 Thread James Starlight
Hi Gian,

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

James

2014-09-22 10:16 GMT+02:00 Gianluca Santoni gianluca.sant...@ibs.fr:

 I did something similar once.
 For mainchains, you can at first calculate B-factors (similar as in
 crystallography) from md simulation, that would be added to your starting
 (or final, i don't remember) structure.
 then use the cartoon-putty representation to visualize your structure.

 You could try using something similar, like for exemple a color spectrum
 of b-factors,for the sidechains.
 In this case don't forget to exclude the N-ter and C-ter from your
 calculations, or they will completly flatten your spectrum.

 Cheers,
 Gian




 On 9/21/14 9:19 AM, James Starlight wrote:

 Dear Pymol users!


 In this topic I've decide to put all questions regarding visualisation.

 This time I'm very intresting whether it possible to add some effect of
 the  flexebility or ensemble-like dynamics on the selected elements
 (e.g selected side-chains to convey a sense of its flexibility like in
 the molecular dynamics simulation) by introdycing of some filter on this
 part like some kind of bluring). Of cource I can do it by taking several
 aligned snapshots from MD and load it in the Pymol but here I wounder if
 its also possible do from one pdb structure.

 Thanks for help,

 James


 
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-24 Thread James Starlight
Thank you very much!

Kind regards,

James

2014-09-22 18:50 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi James -

  On Sep 22, 2014, at 4:30 AM, James Starlight jmsstarli...@gmail.com
 wrote:

   Hi Jared,


  many thanks for the suggestion!
  your method works perfect (i only slightly modified dir for input file)

 # dock each model to the ligand
 for pdb in $receptors/*.pdb; do
   filename=$(basename $pdb)
   M=${filename/.pdb/}
   echo Processing of ${M} is initiated...
   #remove water and ions; change EMD to TER
   grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g' 
 ${dirr}/temp/${M}_clean.pdb
   #superimsoposition using pymol against reference
   pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi
 2-280; save ./superimposed/${M}_aligned.pdb, $M 
 ./superimposed/pymol_${M}.log
   cp $ref ./superimposed
 done


  Glad it worked for you.

  two additional questions:

 1) will it possible to use more flexibility in case of the selection of
 region for alignment in reference structure?
 super $M, $R and resi 2-280
  For instance I'd like to select all residues which are part of the alpha
 helixes of the reference. how it should be done?


  Try `$R and resi 2-280 and ss h`.  See
 http://www.pymolwiki.org/index.php/Property_Selectors for more info.
  (That page comes up as the very first result for me on Google with “pymol
 select secondary structure” as the search term.)

  2) what advantages could give me tmalign method for the superimposition
 in comparison to super and ce programs? does the coordinates of the
 reference will not changed after alignment of each mobile on it (like
 fitting in case of super) ?


  From the description here (http://www.pymolwiki.org/index.php/TMalign)
 that TMalign, like CEalign, can be useful for structures in the “twilight
 zone,” where sequence alignment by `align` or structural alignment by
 `super` may not provide a good fit.  For any of the programs, though, only
 the mobile structures should move; the target/reference coordinates should
 always remain unchanged.

  Cheers,
 Jared



  James

 2014-09-22 10:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:

  Hi Jared,


  many thanks for the suggestion!
  your method works perfect (i only slightly modified dir for input file)


 2014-09-19 20:19 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi James -

  I don’t have any experience with Profit.  However, instead of using
 something like” PyMOL’s `super` command as you asked, you could actually
 use `super` in your shell session by launching PyMOL in command line
 mode http://www.pymolwiki.org/index.php/Command_Line_Options.  Of
 course, you would need to modify it according to your file naming scheme,
 but here’s a working example.

  ###
 #!/bin/bash

  REF=reference.pdb

  # grab some related pdb files to use and make one of them the reference
 # (obviously you won’t have to do this)
 i=0
 for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
 pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
 i=$((i+1))
 done
 mv mobile0.pdb $REF

  # align all the mobile files to a selection in the reference file
 i=1
 for MOB in mobile*.pdb; do
 # strip the extensions
 R=$(echo $REF | sed 's/\.pdb$//')
 M=$(echo $MOB | sed 's/\.pdb$//')

  # superimpose and save aligned mobile coordinates
 pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
 ${M}_aligned.pdb
 done

  pymol mobile*_aligned.pdb
 ###

  You could also use CEalign if you need something citable, just switch
 the order of the arguments to it: `cealign $R and resi 1-110, $M`.

  Hope that helps.

  Cheers,
 Jared

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






  On Sep 19, 2014, at 6:03 AM, James Starlight jmsstarli...@gmail.com
 wrote:

  Dear all,

  I still need some help regarding some algorithm for structural
 superimposition of my mobile structures regarding one specified reference
 using some fitting method (to avoid changing in the position of the
 reference.pdb which is very important for me!)=something like super
 command in pymol. Using ProFit I have faced with some errors during
 superimposition regarding the chosing reference (in case where there were
 some differences in the positions of ref and mob structures its alignment
 was not perfect (the mob had not been fully aligned on the ref) obtaining
 very big RMSD (20 A!) as the result although its actual value should be in
 range of 2-5 A. I'll be thankful for possible sollutions of this problem
 using Profit is there are users experienced with this software (mb it
 should to define fitting zones or atom subsets more accurately but I have
 no ideas here ) or any other alternatives which could be used as parts of
 the shell script.

  James






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Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-24 Thread James Starlight
some additional question about shell scripting (copied from the amber forum
because I'd like to find as more sollutions of this problem as possible):


I wounder about possibilities to define disulphide bond between any pairs
of SG atoms of CYX residues using amber's tleap scripts in some automatic
fashion.

In my case I use tleap as part of some big script to process many
models.pdb for further md simulation. Each of the model consist of pair of
CYX residues (assigned by pdb2pqr) in different positions of its sequence.
So in script I need firstly to know the number of position for each of CYX
residues of each model and than to fill this numbers to the tleap input
files for each model

in bash for one model it will be look like:

#some command to scan the sequence of model.pdb and define pair of its CYX
residues within it as the k ans i variables
  printf source leaprc.ff03.r1\nprotein = loadpdb model.pdb\nsetbox
protein centers\nbond protein.${k}.SG protein.${i}.SG\nsaveamberparm
protein protein.parm7 protein.inpcrd\nquit  ./tleap.in


so my task is only to find some command which will scan model and find
positions of the CYX within its sequence which could be put to the tleap as
two digits. It will be better to find those 2 digits using pdb as an input
and some unix command like sed or grep to find positions

I will be very thankful for any suggestions!

James



2014-09-12 16:21 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:


 csplit -b %03d.pdb test.pdbqt /^MODEL/ {0}  somelog.log


 man csplit:

 csplit -f blabla -b %03d.pdb test.pdbqt /^MODEL/ {1}

 But you want only the first frame anyway, so no real use for csplit...

 sed /^ENDMDL/q my_docking.pdb | grep -v ^ROOT\|^ENDROOT\|^TORSDOF
 0\|^MODEL\|^REMARK |  sed -e 's/^ENDMDL/TER/g'  firstmodel.pdb


 sed -e '/^ENDMDL/{s/^.*/TER/;q;}' -e '/^\(ROOT\|ENDROOT\|TORSDOF
 0\|MODEL\|REMARK\)/d' my_docking.pdb  firstmodel.pdb

 ... shorter and one process running in stead of 3.

 Cheers,

 Tsjerk

 --
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-22 Thread James Starlight
Hi Jared,


many thanks for the suggestion!
your method works perfect (i only slightly modified dir for input file)

# dock each model to the ligand
for pdb in $receptors/*.pdb; do
  filename=$(basename $pdb)
  M=${filename/.pdb/}
  echo Processing of ${M} is initiated...
  #remove water and ions; change EMD to TER
  grep -v ATOM.*\(WAT\|NA+\|Cl-\) $pdb | sed -e 's/^END/TER/g' 
${dirr}/temp/${M}_clean.pdb
  #superimsoposition using pymol against reference
  pymol $ref ${dirr}/temp/${M}_clean.pdb -c -q -d super $M, $R and resi
2-280; save ./superimposed/${M}_aligned.pdb, $M 
./superimposed/pymol_${M}.log
  cp $ref ./superimposed
done

two additional questions:

1) will it possible to use more flexibility in case of the selection of
region for alignment in reference structure?
super $M, $R and resi 2-280
For instance I'd like to select all residues which are part of the alpha
helixes of the reference. how it should be done?

2) what advantages could give me tmalign method for the superimposition in
comparison to super and ce programs? does the coordinates of the reference
will not changed after alignment of each mobile on it (like fitting in case
of super) ?

James

2014-09-22 10:21 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Hi Jared,


 many thanks for the suggestion!
 your method works perfect (i only slightly modified dir for input file)


 2014-09-19 20:19 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi James -

  I don’t have any experience with Profit.  However, instead of using
 something like” PyMOL’s `super` command as you asked, you could actually
 use `super` in your shell session by launching PyMOL in command line mode
 http://www.pymolwiki.org/index.php/Command_Line_Options.  Of course,
 you would need to modify it according to your file naming scheme, but
 here’s a working example.

  ###
 #!/bin/bash

  REF=reference.pdb

  # grab some related pdb files to use and make one of them the reference
 # (obviously you won’t have to do this)
 i=0
 for pdb in 1bbd 7fab 1dba 1plg 1nl0; do
 pymol -c -d fetch ${pdb}, mobile${i}, async=0; save mobile${i}.pdb
 i=$((i+1))
 done
 mv mobile0.pdb $REF

  # align all the mobile files to a selection in the reference file
 i=1
 for MOB in mobile*.pdb; do
 # strip the extensions
 R=$(echo $REF | sed 's/\.pdb$//')
 M=$(echo $MOB | sed 's/\.pdb$//')

  # superimpose and save aligned mobile coordinates
 pymol $REF $MOB -c -q -d super $M, $R and resi 1-110; save
 ${M}_aligned.pdb
 done

  pymol mobile*_aligned.pdb
 ###

  You could also use CEalign if you need something citable, just switch
 the order of the arguments to it: `cealign $R and resi 1-110, $M`.

  Hope that helps.

  Cheers,
 Jared

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






  On Sep 19, 2014, at 6:03 AM, James Starlight jmsstarli...@gmail.com
 wrote:

  Dear all,

  I still need some help regarding some algorithm for structural
 superimposition of my mobile structures regarding one specified reference
 using some fitting method (to avoid changing in the position of the
 reference.pdb which is very important for me!)=something like super
 command in pymol. Using ProFit I have faced with some errors during
 superimposition regarding the chosing reference (in case where there were
 some differences in the positions of ref and mob structures its alignment
 was not perfect (the mob had not been fully aligned on the ref) obtaining
 very big RMSD (20 A!) as the result although its actual value should be in
 range of 2-5 A. I'll be thankful for possible sollutions of this problem
 using Profit is there are users experienced with this software (mb it
 should to define fitting zones or atom subsets more accurately but I have
 no ideas here ) or any other alternatives which could be used as parts of
 the shell script.

  James




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Re: [PyMOL] Molecular Visualisation in PyMol

2014-09-22 Thread James Starlight
Hi Jed,

so this method is working of the ensemble of the pdb files taken from the
MD simulation or NMR structure, isnt it? Could someone explain me step by
step how to obtain such inputs for the PyMol (from the step when I've load
my trajectory to the VMD).

James

2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu:

 You could extract the flexible residues into one multistate object and use
 show all_states. So, you'd only be dealing with 2 objects - Ca and residues.

 Jed
 On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com wrote:

 Dear Pymol users!


 In this topic I've decide to put all questions regarding visualisation.

 This time I'm very intresting whether it possible to add some effect of
 the  flexebility or ensemble-like dynamics on the selected elements
 (e.g selected side-chains to convey a sense of its flexibility like in the
 molecular dynamics simulation) by introdycing of some filter on this part
 like some kind of bluring). Of cource I can do it by taking several aligned
 snapshots from MD and load it in the Pymol but here I wounder if its also
 possible do from one pdb structure.

 Thanks for help,

 James


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Re: [PyMOL] Molecular Visualisation in PyMol

2014-09-22 Thread James Starlight
I should to specify that I ask this because normally VMD didn't produce
multi-state pdb from the md trajectory so it seems I need to use some
plugin to load *.dcd or *.trr


James

2014-09-22 13:53 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Hi Jed,

 so this method is working of the ensemble of the pdb files taken from the
 MD simulation or NMR structure, isnt it? Could someone explain me step by
 step how to obtain such inputs for the PyMol (from the step when I've load
 my trajectory to the VMD).

 James

 2014-09-21 20:42 GMT+04:00 Jed Goldstone jgoldst...@whoi.edu:

 You could extract the flexible residues into one multistate object and
 use show all_states. So, you'd only be dealing with 2 objects - Ca and
 residues.

 Jed
 On Sep 21, 2014 3:23 AM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear Pymol users!


 In this topic I've decide to put all questions regarding visualisation.

 This time I'm very intresting whether it possible to add some effect of
 the  flexebility or ensemble-like dynamics on the selected elements
 (e.g selected side-chains to convey a sense of its flexibility like in the
 molecular dynamics simulation) by introdycing of some filter on this part
 like some kind of bluring). Of cource I can do it by taking several aligned
 snapshots from MD and load it in the Pymol but here I wounder if its also
 possible do from one pdb structure.

 Thanks for help,

 James


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[PyMOL] Molecular Visualisation in PyMol

2014-09-21 Thread James Starlight
Dear Pymol users!


In this topic I've decide to put all questions regarding visualisation.

This time I'm very intresting whether it possible to add some effect of the
 flexebility or ensemble-like dynamics on the selected elements (e.g
selected side-chains to convey a sense of its flexibility like in the
molecular dynamics simulation) by introdycing of some filter on this part
like some kind of bluring). Of cource I can do it by taking several aligned
snapshots from MD and load it in the Pymol but here I wounder if its also
possible do from one pdb structure.

Thanks for help,

James
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Re: [PyMOL] Academical position in field of macromolecular visualization

2014-09-20 Thread James Starlight
Hi Tsjerk ,




*Thank you very much for the information!I've already familiar with some
Adam's works from the textbooks which were really impressed me! BTW do you
know any advanced tutorials foruced on the visualization in PyMol?*

*James*

2014-09-20 0:59 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 There are some research groups around that focus on scientific
 visualization. I recall there was someone talking about it at the
 Biophysical Society meeting this spring, but I don't immediately remember a
 name to go with it. I do know that some have taken up this kind of work
 commercially, like H. Adam Steinberg, who also frequents/frequented this
 list, and Chris Spronk (http://www.spronk3d.com). You could try to see
 what they do or have done and how they did it. Of course, they could
 possibly help you further too.

 Hope it helps,

 Tsjerk

 On Fri, Sep 19, 2014 at 10:09 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear Pymol users!


 It's probably that my next question will be slightly uncommon but
 presently strongly looking for new (post-doc level) position I'd like to
 obtain some advises from the expirienced persons like the auditory of this
 community.
 This time having PhD in theoretical biophysics I wounder whether its *in
 principle* possible to find an academic post-doc job focused mainly on
 molecular visualization and animation (as the trivial example of such job
 in my mind is to make a pictures and movies of the proteins and it's
 complexes using data from different resolution's experimental techniques
 and modelling). How do you think will it be easily to obtain such job for
 the person who's PhD was based on structural biology (experimentalist) or
 alternatively focused on molecular modeling and bioinformatics ? Could
 someone recommend me some workshops and on-line communities which could
 facilitate my seeking for the job?

 Many thanks for the suggestions,

 James


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 --
 Tsjerk A. Wassenaar, Ph.D.


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Re: [PyMOL] Academical position in field of macromolecular visualization

2014-09-20 Thread James Starlight
Some important point:

I've tried to scan web to locate some group involved in the molecular
visualization  (key words molecular graphics, molecular visualization
). As the result I've found alot of groups in the US but not in the Europe.
Does it some common geographic pattern ?

James

2014-09-20 10:48 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Hi Tsjerk ,




 *Thank you very much for the information!I've already familiar with some
 Adam's works from the textbooks which were really impressed me! BTW do you
 know any advanced tutorials foruced on the visualization in PyMol?*

 *James*

 2014-09-20 0:59 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 There are some research groups around that focus on scientific
 visualization. I recall there was someone talking about it at the
 Biophysical Society meeting this spring, but I don't immediately remember a
 name to go with it. I do know that some have taken up this kind of work
 commercially, like H. Adam Steinberg, who also frequents/frequented this
 list, and Chris Spronk (http://www.spronk3d.com). You could try to see
 what they do or have done and how they did it. Of course, they could
 possibly help you further too.

 Hope it helps,

 Tsjerk

 On Fri, Sep 19, 2014 at 10:09 PM, James Starlight jmsstarli...@gmail.com
  wrote:

 Dear Pymol users!


 It's probably that my next question will be slightly uncommon but
 presently strongly looking for new (post-doc level) position I'd like to
 obtain some advises from the expirienced persons like the auditory of this
 community.
 This time having PhD in theoretical biophysics I wounder whether its *in
 principle* possible to find an academic post-doc job focused mainly on
 molecular visualization and animation (as the trivial example of such job
 in my mind is to make a pictures and movies of the proteins and it's
 complexes using data from different resolution's experimental techniques
 and modelling). How do you think will it be easily to obtain such job for
 the person who's PhD was based on structural biology (experimentalist) or
 alternatively focused on molecular modeling and bioinformatics ? Could
 someone recommend me some workshops and on-line communities which could
 facilitate my seeking for the job?

 Many thanks for the suggestions,

 James


 --
 Slashdot TV.  Video for Nerds.  Stuff that Matters.

 http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk
 ___
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 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 Tsjerk A. Wassenaar, Ph.D.



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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-19 Thread James Starlight
Dear all,

I still need some help regarding some algorithm for structural
superimposition of my mobile structures regarding one specified reference
using some fitting method (to avoid changing in the position of the
reference.pdb which is very important for me!)=something like super
command in pymol. Using ProFit I have faced with some errors during
superimposition regarding the chosing reference (in case where there were
some differences in the positions of ref and mob structures its alignment
was not perfect (the mob had not been fully aligned on the ref) obtaining
very big RMSD (20 A!) as the result although its actual value should be in
range of 2-5 A. I'll be thankful for possible sollutions of this problem
using Profit is there are users experienced with this software (mb it
should to define fitting zones or atom subsets more accurately but I have
no ideas here ) or any other alternatives which could be used as parts of
the shell script.

James

2014-09-15 18:52 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Hey,

 I've occasionally deleted my profit script which do superimposition
 automatically so I'll be very thankful if someone remind me profit input
 script syntax

 for my case
 profit -h -f script.txt ref.pdb tar.pdb

 should do actual superimposition where in script.txt;
 ATOMS CA
 ZONE 2-290:2-290
 FIT
 WRITE fitted.pdb

 unfortunately this end with the error
Starting script: 'new.profit'
Unrecognised keyword: FIT
Error== Fitting has not yet been performed.
Finished script: 'new.profit'

 althought those commands made from the profit command line works perfect
 ProFitFIT
Fitting structures...
RMS: 7.134


 Where I made error?

 James


 2014-09-12 9:13 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Hi Jared,

 yes from pymol it's OK, here I've mentioned about ProFit :) but this also
 have been solved. ;)

 James

 2014-09-11 19:43 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi James -

  What version of PyMOL are you using?  For me, using Open Source PyMOL
 1.7.2.0, a typical PDB file I tested ends up with more information in that
 column, not less, after saving from PyMOL:

  Before:
 ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61
 N

 After:
 ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61
 N1+

 Are you sure the column is there in your input file, and hasn’t been
 removed before loading into PyMOL?

  Cheers,
 Jared

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






  On Sep 11, 2014, at 5:36 AM, James Starlight jmsstarli...@gmail.com
 wrote:

  I guess I've passed superimpoition- it works great - with the one
 exception- after fitting to ref.pdb the last colum (consisted of the atom
 names like C, N, O etc) from the each fitted mobile.pdb has been removed. I
 need to keep this column on the resulted pdb because I'll use this pdb as
 the initial structure for the autodock docking (actually I do
 superimposition because I have had all input docking parameters including
 XYZ of the cavity for the ref structure). If the last column is missed I
 have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using
 babel. I'll thankful to everyone who have faced with the same problem and
 could provide me with some suggestions.


  Thank for help,

  James

 2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Thanks Markus, I'll try to examine it!

 Jed,

  the main problem with the profit is that I need to superimpose
 structures in loop which are not always has the same sequence length. Is it
 possible to superimpose each structure based on some common criterium found
 for each mobile and reference automatically?

  Kind regards,

  James

 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca:

  Shot in the dark, based on reading “ensemble of the structures” and
 “ProFit”:



 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/



 CARON – Average RMSD of NMR structure ensemble



 Hope that helps!



 Markus



 *From:* James Starlight [mailto:jmsstarli...@gmail.com]
 *Sent:* Monday, September 08, 2014 6:52 AM
 *To:* pymol-users
 *Subject:* Re: [PyMOL] Access to pymol commands from the terminal



 Ok, ProFit has been passed :D

 Now I'm looking for some software which could do the same least-square
 fitting for the ensemble of the structures taken it as the separate pdbs
 from the work dir (I'm not sure if the mustang software could be useful 
 for
 this task)= because looping using ProFit might be not good for me because
 each time I need to provide new atom selection for the superimposition  
 for
 each model in the ProFit's script file.

 James



 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com:

 Boo
 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał
 napisał(a):


 
  Thomas,thanks for help- I'll try to test your script!
 
  Jed, many thanks too!
 
  if I understood correctly

[PyMOL] preparation of protein ligand complexes for the MD simulation

2014-09-17 Thread James Starlight
Dear Pymol users,

I've decide to make a copy of this topic from the amber mail list because
this problem could be solves by ones of the methods implemented in Pymol.

Here I'm facing with the problem of the preparation of protein-ligand
complexes for amber md simulation:
Following amber's tutorial I've made parametrization of the ligand using
antechamber obtaining ligand.frcmod and ligand.lib files consisted of the
parameters for my ligand and its coordinates in mol2 associated with those
topologies. Now I'd like to dock this ligand to the active site of the
receptor using autodock vina and make further tleap processing  of
complex.pdb produced by autodock to obtain all input data for simulation.
Here some problems: because (superimposed to the receptor cavity)
ligand.pdb produced by autodock have been stripped from all hydrogen’s so
its coordinates not equal to initial ligand.mol2 . How do you think will it
possible to use some method of the ligand superimposition to superimpose
initial ligand.mol2 (with correct corrdinates) agains docking pose produced
by vina and use superimposed ligand.mol2 for the preparation of my complex?

Thanks for help,

James
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Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

2014-09-17 Thread James Starlight
Hi Fotis,

thank you very much for the suggestion!

Indeed I have not had such problem with the preparation structure for NAMD
but in case of amber its really exist (the structure of the ligand provided
in the complex with the receptor.pdb must be EXACTLY the same as it was
previously parametrized using some amber program called antechamber).
So I will be interesting in two options
1) to find some shell utility for superimposition of the 2 ligands in
one-style command (because here I'm dealing with some script and I need to
do it in loop many times)
or (which is better!)

2) use pdb2pqr software (because I'm using it in the part of this script to
process complex and to add hydrogens to ligand as well)- here I noticed
that ligand should be provided as the separate .mol2 file (not pdb)- which
is a bit not comfortable for me (because I obained all docking poses from
VINA as the pdb). I guess I should here to put ligand from complex, to
convert it to mol2 and proceed 2 files (receptor and ligand) to the
pdb2pqr. But may be the better solution is exist?

James



2014-09-17 12:32 GMT+02:00 Fotis Baltoumas fotis.baltou...@gmail.com:

 Hello James,
 You can use the Pair Fitting wizard (Menu: Wizards=Pair Fitting) or the
 pair_fit command to superimpose small molecules. It's not as
 straightforward as protein super/align, since you have to define the atom
 pairs that will be superimposed, but it's fairly easy. After that, just
 make a selection of your receptor and your new ligand and save it as a
 molecule.

 However, I don't think you really have a problem here. Since the only
 issue you mention is the lack of hydrogen atoms, couldn't you just
 reintroduce them through some function in the AmberTools? I have no
 experience with Amber parameterization tools but, if they're even remotely
 like the PSF makers for CHARMM/X-PLOR/NAMD, then they can add hydrogen
 atoms for you easily.
 Another option would be to create a PQR file, either through PDB2PQR (
 http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools GUI in
 PyMOL. Part of the PQR creation includes adding hydrogen atoms, and you can
 use AMBER parameters both for proteins and for ligands (mol2 format). Your
 result would be the structure of your complex, with hydrogens, in the AMBER
 format.

 Hope I helped,
 Fotis Baltoumas

 2014-09-17 13:01 GMT+03:00 James Starlight jmsstarli...@gmail.com:

 Dear Pymol users,

 I've decide to make a copy of this topic from the amber mail list because
 this problem could be solves by ones of the methods implemented in Pymol.

 Here I'm facing with the problem of the preparation of protein-ligand
 complexes for amber md simulation:
 Following amber's tutorial I've made parametrization of the ligand using
 antechamber obtaining ligand.frcmod and ligand.lib files consisted of the
 parameters for my ligand and its coordinates in mol2 associated with those
 topologies. Now I'd like to dock this ligand to the active site of the
 receptor using autodock vina and make further tleap processing  of
 complex.pdb produced by autodock to obtain all input data for simulation.
 Here some problems: because (superimposed to the receptor cavity)
 ligand.pdb produced by autodock have been stripped from all hydrogen’s so
 its coordinates not equal to initial ligand.mol2 . How do you think will it
 possible to use some method of the ligand superimposition to superimpose
 initial ligand.mol2 (with correct corrdinates) agains docking pose produced
 by vina and use superimposed ligand.mol2 for the preparation of my complex?

 Thanks for help,

 James


 --
 Want excitement?
 Manually upgrade your production database.
 When you want reliability, choose Perforce
 Perforce version control. Predictably reliable.

 http://pubads.g.doubleclick.net/gampad/clk?id=157508191iu=/4140/ostg.clktrk
 ___
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Re: [PyMOL] preparation of protein ligand complexes for the MD simulation

2014-09-17 Thread James Starlight
all manual and GUI operations are not accepted here!
I'm dealing with the a huge number of protein-ligand complexes (many many
different proteins but only 1 ligand- so the situation is not very bad !).
But what is bad that I need to dock each complex using vina and make its
parametrization by amber

:)

James

2014-09-17 15:32 GMT+02:00 Gianluca Santoni gianluca.sant...@ibs.fr:

 Hi James,
 what usually worked for me was simply to do it manually, in editing mode
 with pymol.
 Consider that you will perform an energy minimization after, so a few
 1/10 of angstroms of difference in your initial model are not a big
 deal, in my opinion.

 Cheers,
 Gian

 On 9/17/14 3:17 PM, James Starlight wrote:
  Hi Fotis,
 
  thank you very much for the suggestion!
 
  Indeed I have not had such problem with the preparation structure for
  NAMD but in case of amber its really exist (the structure of the ligand
  provided in the complex with the receptor.pdb must be EXACTLY the same
  as it was previously parametrized using some amber program called
  antechamber).
  So I will be interesting in two options
  1) to find some shell utility for superimposition of the 2 ligands in
  one-style command (because here I'm dealing with some script and I need
  to do it in loop many times)
  or (which is better!)
 
  2) use pdb2pqr software (because I'm using it in the part of this script
  to process complex and to add hydrogens to ligand as well)- here I
  noticed that ligand should be provided as the separate .mol2 file (not
  pdb)- which is a bit not comfortable for me (because I obained all
  docking poses from VINA as the pdb). I guess I should here to put ligand
  from complex, to convert it to mol2 and proceed 2 files (receptor and
  ligand) to the pdb2pqr. But may be the better solution is exist?
 
  James
 
 
 
  2014-09-17 12:32 GMT+02:00 Fotis Baltoumas fotis.baltou...@gmail.com
  mailto:fotis.baltou...@gmail.com:
 
  Hello James,
  You can use the Pair Fitting wizard (Menu: Wizards=Pair Fitting) or
  the pair_fit command to superimpose small molecules. It's not as
  straightforward as protein super/align, since you have to define the
  atom pairs that will be superimposed, but it's fairly easy. After
  that, just make a selection of your receptor and your new ligand and
  save it as a molecule.
 
  However, I don't think you really have a problem here. Since the
  only issue you mention is the lack of hydrogen atoms, couldn't you
  just reintroduce them through some function in the AmberTools? I
  have no experience with Amber parameterization tools but, if they're
  even remotely like the PSF makers for CHARMM/X-PLOR/NAMD, then they
  can add hydrogen atoms for you easily.
  Another option would be to create a PQR file, either through PDB2PQR
  (http://nbcr-222.ucsd.edu/pdb2pqr_1.9.0/) or through the APBSTools
  GUI in PyMOL. Part of the PQR creation includes adding hydrogen
  atoms, and you can use AMBER parameters both for proteins and for
  ligands (mol2 format). Your result would be the structure of your
  complex, with hydrogens, in the AMBER format.
 
  Hope I helped,
  Fotis Baltoumas
 
  2014-09-17 13:01 GMT+03:00 James Starlight jmsstarli...@gmail.com
  mailto:jmsstarli...@gmail.com:
 
  Dear Pymol users,
 
  I've decide to make a copy of this topic from the amber mail
  list because this problem could be solves by ones of the methods
  implemented in Pymol.
 
  Here I'm facing with the problem of the preparation of
  protein-ligand complexes for amber md simulation:
  Following amber's tutorial I've made parametrization of the
  ligand using antechamber obtaining ligand.frcmod and ligand.lib
  files consisted of the parameters for my ligand and its
  coordinates in mol2 associated with those topologies. Now I'd
  like to dock this ligand to the active site of the receptor
  using autodock vina and make further tleap processing of
  complex.pdb produced by autodock to obtain all input data for
  simulation. Here some problems: because (superimposed to the
  receptor cavity) ligand.pdb produced by autodock have been
  stripped from all hydrogen’s so its coordinates not equal to
  initial ligand.mol2 . How do you think will it possible to use
  some method of the ligand superimposition to superimpose initial
  ligand.mol2 (with correct corrdinates) agains docking pose
  produced by vina and use superimposed ligand.mol2 for the
  preparation of my complex?
 
  Thanks for help,
 
  James
 
 
  
 --
  Want excitement?
  Manually upgrade your production database.
  When you want reliability, choose Perforce
  Perforce version control

Re: [PyMOL] Access to pymol commands from the terminal

2014-09-15 Thread James Starlight
Hey,

I've occasionally deleted my profit script which do superimposition
automatically so I'll be very thankful if someone remind me profit input
script syntax

for my case
profit -h -f script.txt ref.pdb tar.pdb

should do actual superimposition where in script.txt;
ATOMS CA
ZONE 2-290:2-290
FIT
WRITE fitted.pdb

unfortunately this end with the error
   Starting script: 'new.profit'
   Unrecognised keyword: FIT
   Error== Fitting has not yet been performed.
   Finished script: 'new.profit'

althought those commands made from the profit command line works perfect
ProFitFIT
   Fitting structures...
   RMS: 7.134


Where I made error?

James


2014-09-12 9:13 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Hi Jared,

 yes from pymol it's OK, here I've mentioned about ProFit :) but this also
 have been solved. ;)

 James

 2014-09-11 19:43 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

  Hi James -

  What version of PyMOL are you using?  For me, using Open Source PyMOL
 1.7.2.0, a typical PDB file I tested ends up with more information in that
 column, not less, after saving from PyMOL:

  Before:
 ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61
 N

 After:
 ATOM   1312  NH1 ARG A 198   0.544  14.093  19.655  1.00 34.61
 N1+

 Are you sure the column is there in your input file, and hasn’t been
 removed before loading into PyMOL?

  Cheers,
 Jared

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






  On Sep 11, 2014, at 5:36 AM, James Starlight jmsstarli...@gmail.com
 wrote:

  I guess I've passed superimpoition- it works great - with the one
 exception- after fitting to ref.pdb the last colum (consisted of the atom
 names like C, N, O etc) from the each fitted mobile.pdb has been removed. I
 need to keep this column on the resulted pdb because I'll use this pdb as
 the initial structure for the autodock docking (actually I do
 superimposition because I have had all input docking parameters including
 XYZ of the cavity for the ref structure). If the last column is missed I
 have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using
 babel. I'll thankful to everyone who have faced with the same problem and
 could provide me with some suggestions.


  Thank for help,

  James

 2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Thanks Markus, I'll try to examine it!

 Jed,

  the main problem with the profit is that I need to superimpose
 structures in loop which are not always has the same sequence length. Is it
 possible to superimpose each structure based on some common criterium found
 for each mobile and reference automatically?

  Kind regards,

  James

 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca:

  Shot in the dark, based on reading “ensemble of the structures” and
 “ProFit”:



 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/



 CARON – Average RMSD of NMR structure ensemble



 Hope that helps!



 Markus



 *From:* James Starlight [mailto:jmsstarli...@gmail.com]
 *Sent:* Monday, September 08, 2014 6:52 AM
 *To:* pymol-users
 *Subject:* Re: [PyMOL] Access to pymol commands from the terminal



 Ok, ProFit has been passed :D

 Now I'm looking for some software which could do the same least-square
 fitting for the ensemble of the structures taken it as the separate pdbs
 from the work dir (I'm not sure if the mustang software could be useful for
 this task)= because looping using ProFit might be not good for me because
 each time I need to provide new atom selection for the superimposition  for
 each model in the ProFit's script file.

 James



 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com:

 Boo
 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał
 napisał(a):


 
  Thomas,thanks for help- I'll try to test your script!
 
  Jed, many thanks too!
 
  if I understood correctly align.profit should contain thefollowing
 lines:
 
  # using ProFIT to align the model to 2hi4
  open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
  print $PROFIT ATOMS CA\n;
  print $PROFIT ZONE 34-513:1-480\n;
  print $PROFIT FIT\n;
  print $PROFIT WRITE $folder/$dir/$pdbnew\n;
  close $PROFIT;
 
  shouldn't it?
 
  that that file is provided to 1 command line
  `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;
  where 2hi4.pdb is my ref
  $pdbnew variable assosiated with the target pdb
 
  one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition
  print $PROFIT ATOMS CA\n;
 
 
  James
 
 

 
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  Info

Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-12 Thread James Starlight
Hi,

some new question.

I need to some combination of shell utilities to split multi_model.pdb on
several pdbs  as well as separate command to seek multi_model.pdb and to
save only this model as the separare model1.pdb. I've tried to do it using
grep
grep '^MODEL 1' my_docking.pdb  model1.pdb

but results were empty.

James

2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Thanks you very much!

 James

 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:

 Hi

 Small correction to Gianlucas suggestion

  will direct the output to a file, overwriting the contents
  will direct the output to a file, appending the contents

 Venlig hilsen
 Folmer Fredslund
 Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr:

 Don't even need cat
 simply do

 grep PPC ref.pdb  tar_i.pdb

 redirecting std out with  appends it directly to the file (after the
 last line)

 Cheers

 On 9/5/14 6:48 PM, James Starlight wrote:
  Dear Pymol users!
 
  I've decided to open new topic focused on the implementation of the
  common shell utilities like grep awk and sed for the structural
  bioinformatics tasks like processing and editing of the large sets of
 pdbs.
 
  In my current task I need to copy all lipids from one pdb (called it
  ref) to another call it tar_i.pdb (both files have the same 3D shape
 and
  have been superimposed before that): so in that case I guess lipids
  could be recognized by residue name in pdb file (PPC) as well as by its
  #4 column number (what is actually do grep).  So the algorithm might
 be:
  select from the ref.pdb all strings where #4 column is PPC and merge it
  (by means of CAT I guess) with the tar_i.pdb. Please show me some
  example of the one-line method of this realization.
 
  Thanks,
 
  James
 
 
 
 --
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  Video for Nerds.  Stuff that matters.
  http://tv.slashdot.org/
 
 
 
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 --
 Gianluca Santoni,
 Dynamop Group
 Institut de Biologie Structurale
 6 rue Jules Horowitz
 38027 Grenoble Cedex 1
 France
 _
 Please avoid sending me Word or PowerPoint attachments.
 See http://www.gnu.org/philosophy/no-word-attachments.html


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Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-12 Thread James Starlight
Hi Tsjerk,

thank you very much for help.

this is a little bioinformatics question so probably it's better to ask it
here some expert of this topic like you :)

because in my case I need to further proceed each split model model (e,g
delete some lines or make changing) piping with some commands

e,g in my case each model after spliting consist of

MODEL 1
ROOT
ATOMS
ENDROOT
TORSDOF 0
ENDMDL

i'd like to remove lines consisted of ROOT ENDROOT TORSDOF 0 and change
ENDMDL to TER

i've tried to do it

csplit -b %04d.pdb my_docking.pdb /^MODEL/ {*} | grep -v '^ENDROOT' |
grep -v '^TORSDOF 0' |  sed -e 's/^ENDMDL/TER/g'

but the resulted files still consist of unused lines

BTW might the csplit be used to extract only ONE (e,g first) model from the
multi-pdb file?

James

2014-09-12 11:39 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 These are the sort of questions that'll be answered elsewhere. Most
 notably on stackoverflow:
 http://stackoverflow.com/questions/18364411/using-regex-to-tell-csplit-where-to-split-the-file

 csplit -b %04d.pdb file.pdb /^MODEL/ {*}

 Cheers,

 Tsjerk


 On Fri, Sep 12, 2014 at 11:25 AM, James Starlight jmsstarli...@gmail.com
 wrote:

 Hi,

 some new question.

 I need to some combination of shell utilities to split multi_model.pdb on
 several pdbs  as well as separate command to seek multi_model.pdb and to
 save only this model as the separare model1.pdb. I've tried to do it using
 grep
 grep '^MODEL 1' my_docking.pdb  model1.pdb

 but results were empty.

 James

 2014-09-08 15:48 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Thanks you very much!

 James

 2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:

 Hi

 Small correction to Gianlucas suggestion

  will direct the output to a file, overwriting the contents
  will direct the output to a file, appending the contents

 Venlig hilsen
 Folmer Fredslund
 Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr
 :

 Don't even need cat
 simply do

 grep PPC ref.pdb  tar_i.pdb

 redirecting std out with  appends it directly to the file (after the
 last line)

 Cheers

 On 9/5/14 6:48 PM, James Starlight wrote:
  Dear Pymol users!
 
  I've decided to open new topic focused on the implementation of the
  common shell utilities like grep awk and sed for the structural
  bioinformatics tasks like processing and editing of the large sets
 of pdbs.
 
  In my current task I need to copy all lipids from one pdb (called it
  ref) to another call it tar_i.pdb (both files have the same 3D shape
 and
  have been superimposed before that): so in that case I guess lipids
  could be recognized by residue name in pdb file (PPC) as well as by
 its
  #4 column number (what is actually do grep).  So the algorithm might
 be:
  select from the ref.pdb all strings where #4 column is PPC and merge
 it
  (by means of CAT I guess) with the tar_i.pdb. Please show me some
  example of the one-line method of this realization.
 
  Thanks,
 
  James
 
 
 
 --
  Slashdot TV.
  Video for Nerds.  Stuff that matters.
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Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-12 Thread James Starlight
Thank you very much!

James

2014-09-12 12:36 GMT+02:00 Marko Hyvonen mh...@cam.ac.uk:

 On 12/09/2014 11:26, James Starlight wrote:

 grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\^MODEL\^REMARK|


 I think you are missing few | in there:

 grep -v ^ROOT\|^ENDROOT\|^TORSDOF 0\|^MODEL\|^REMARK

 and depending on the shell, you might be able get away with \ by using
 single quotation marks
 grep -v '^ROOT|^ENDROOT|^TORSDOF 0|^MODEL|^REMARK'

 Marko


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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-11 Thread James Starlight
I guess I've passed superimpoition- it works great - with the one
exception- after fitting to ref.pdb the last colum (consisted of the atom
names like C, N, O etc) from the each fitted mobile.pdb has been removed. I
need to keep this column on the resulted pdb because I'll use this pdb as
the initial structure for the autodock docking (actually I do
superimposition because I have had all input docking parameters including
XYZ of the cavity for the ref structure). If the last column is missed I
have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using
babel. I'll thankful to everyone who have faced with the same problem and
could provide me with some suggestions.


Thank for help,

James

2014-09-09 12:35 GMT+04:00 James Starlight jmsstarli...@gmail.com:

 Thanks Markus, I'll try to examine it!

 Jed,

 the main problem with the profit is that I need to superimpose structures
 in loop which are not always has the same sequence length. Is it possible
 to superimpose each structure based on some common criterium found for each
 mobile and reference automatically?

 Kind regards,

 James

 2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca:

  Shot in the dark, based on reading “ensemble of the structures” and
 “ProFit”:



 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/



 CARON – Average RMSD of NMR structure ensemble



 Hope that helps!



 Markus



 *From:* James Starlight [mailto:jmsstarli...@gmail.com]
 *Sent:* Monday, September 08, 2014 6:52 AM
 *To:* pymol-users
 *Subject:* Re: [PyMOL] Access to pymol commands from the terminal



 Ok, ProFit has been passed :D

 Now I'm looking for some software which could do the same least-square
 fitting for the ensemble of the structures taken it as the separate pdbs
 from the work dir (I'm not sure if the mustang software could be useful for
 this task)= because looping using ProFit might be not good for me because
 each time I need to provide new atom selection for the superimposition  for
 each model in the ProFit's script file.

 James



 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com:

 Boo
 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał
 napisał(a):


 
  Thomas,thanks for help- I'll try to test your script!
 
  Jed, many thanks too!
 
  if I understood correctly align.profit should contain thefollowing
 lines:
 
  # using ProFIT to align the model to 2hi4
  open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
  print $PROFIT ATOMS CA\n;
  print $PROFIT ZONE 34-513:1-480\n;
  print $PROFIT FIT\n;
  print $PROFIT WRITE $folder/$dir/$pdbnew\n;
  close $PROFIT;
 
  shouldn't it?
 
  that that file is provided to 1 command line
  `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;
  where 2hi4.pdb is my ref
  $pdbnew variable assosiated with the target pdb
 
  one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition
  print $PROFIT ATOMS CA\n;
 
 
  James
 
 

 
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 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a):

 Thomas,thanks for help- I'll try to test your script!

 Jed, many thanks too!



 if I understood correctly align.profit should contain thefollowing lines:



 # using ProFIT to align the model to 2hi4
 open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
 print $PROFIT ATOMS CA\n;
 print $PROFIT ZONE 34-513:1-480\n;
 print $PROFIT FIT\n;
 print $PROFIT WRITE $folder/$dir/$pdbnew\n;
 close $PROFIT;



 shouldn't it?



 that that file is provided to 1 command line

 `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;

 where 2hi4.pdb is my ref

 $pdbnew variable assosiated with the target pdb



 one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition

 print $PROFIT ATOMS CA\n;





 James






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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-09 Thread James Starlight
Thanks Markus, I'll try to examine it!

Jed,

the main problem with the profit is that I need to superimpose structures
in loop which are not always has the same sequence length. Is it possible
to superimpose each structure based on some common criterium found for each
mobile and reference automatically?

Kind regards,

James

2014-09-08 20:32 GMT+04:00 Markus Heller mhel...@cdrd.ca:

  Shot in the dark, based on reading “ensemble of the structures” and
 “ProFit”:



 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/



 CARON – Average RMSD of NMR structure ensemble



 Hope that helps!



 Markus



 *From:* James Starlight [mailto:jmsstarli...@gmail.com]
 *Sent:* Monday, September 08, 2014 6:52 AM
 *To:* pymol-users
 *Subject:* Re: [PyMOL] Access to pymol commands from the terminal



 Ok, ProFit has been passed :D

 Now I'm looking for some software which could do the same least-square
 fitting for the ensemble of the structures taken it as the separate pdbs
 from the work dir (I'm not sure if the mustang software could be useful for
 this task)= because looping using ProFit might be not good for me because
 each time I need to provide new atom selection for the superimposition  for
 each model in the ProFit's script file.

 James



 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com:

 Boo
 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał
 napisał(a):


 
  Thomas,thanks for help- I'll try to test your script!
 
  Jed, many thanks too!
 
  if I understood correctly align.profit should contain thefollowing lines:
 
  # using ProFIT to align the model to 2hi4
  open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
  print $PROFIT ATOMS CA\n;
  print $PROFIT ZONE 34-513:1-480\n;
  print $PROFIT FIT\n;
  print $PROFIT WRITE $folder/$dir/$pdbnew\n;
  close $PROFIT;
 
  shouldn't it?
 
  that that file is provided to 1 command line
  `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;
  where 2hi4.pdb is my ref
  $pdbnew variable assosiated with the target pdb
 
  one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition
  print $PROFIT ATOMS CA\n;
 
 
  James
 
 

 
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 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a):

 Thomas,thanks for help- I'll try to test your script!

 Jed, many thanks too!



 if I understood correctly align.profit should contain thefollowing lines:



 # using ProFIT to align the model to 2hi4
 open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
 print $PROFIT ATOMS CA\n;
 print $PROFIT ZONE 34-513:1-480\n;
 print $PROFIT FIT\n;
 print $PROFIT WRITE $folder/$dir/$pdbnew\n;
 close $PROFIT;



 shouldn't it?



 that that file is provided to 1 command line

 `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;

 where 2hi4.pdb is my ref

 $pdbnew variable assosiated with the target pdb



 one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition

 print $PROFIT ATOMS CA\n;





 James






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Re: [PyMOL] Shell utilities for structural bioinformatics

2014-09-08 Thread James Starlight
Thanks you very much!

James

2014-09-05 20:18 GMT+02:00 Folmer Fredslund folm...@gmail.com:

 Hi

 Small correction to Gianlucas suggestion

  will direct the output to a file, overwriting the contents
  will direct the output to a file, appending the contents

 Venlig hilsen
 Folmer Fredslund
 Den 05/09/2014 19.16 skrev Gianluca Santoni gianluca.sant...@ibs.fr:

 Don't even need cat
 simply do

 grep PPC ref.pdb  tar_i.pdb

 redirecting std out with  appends it directly to the file (after the
 last line)

 Cheers

 On 9/5/14 6:48 PM, James Starlight wrote:
  Dear Pymol users!
 
  I've decided to open new topic focused on the implementation of the
  common shell utilities like grep awk and sed for the structural
  bioinformatics tasks like processing and editing of the large sets of
 pdbs.
 
  In my current task I need to copy all lipids from one pdb (called it
  ref) to another call it tar_i.pdb (both files have the same 3D shape and
  have been superimposed before that): so in that case I guess lipids
  could be recognized by residue name in pdb file (PPC) as well as by its
  #4 column number (what is actually do grep).  So the algorithm might be:
  select from the ref.pdb all strings where #4 column is PPC and merge it
  (by means of CAT I guess) with the tar_i.pdb. Please show me some
  example of the one-line method of this realization.
 
  Thanks,
 
  James
 
 
 
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-08 Thread James Starlight
Ok, ProFit has been passed :D

Now I'm looking for some software which could do the same least-square
fitting for the ensemble of the structures taken it as the separate pdbs
from the work dir (I'm not sure if the mustang software could be useful for
this task)= because looping using ProFit might be not good for me because
each time I need to provide new atom selection for the superimposition  for
each model in the ProFit's script file.

James

2014-09-07 11:11 GMT+02:00 Maciek Dziubiński pona...@gmail.com:

 Boo
 7 wrz 2014 09:26 Jamesno Starligois ht jmsstarli...@gmail.comnapisał
 napisał(a):

 
  Thomas,thanks for help- I'll try to test your script!
 
  Jed, many thanks too!
 
  if I understood correctly align.profit should contain thefollowing lines:
 
  # using ProFIT to align the model to 2hi4
  open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
  print $PROFIT ATOMS CA\n;
  print $PROFIT ZONE 34-513:1-480\n;
  print $PROFIT FIT\n;
  print $PROFIT WRITE $folder/$dir/$pdbnew\n;
  close $PROFIT;
 
  shouldn't it?
 
  that that file is provided to 1 command line
  `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;
  where 2hi4.pdb is my ref
  $pdbnew variable assosiated with the target pdb
 
  one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition
  print $PROFIT ATOMS CA\n;
 
 
  James
 
 
 
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 7 wrz 2014 09:26 James Starlight jmsstarli...@gmail.com napisał(a):

 Thomas,thanks for help- I'll try to test your script!

 Jed, many thanks too!

 if I understood correctly align.profit should contain thefollowing lines:

 # using ProFIT to align the model to 2hi4
 open $PROFIT,  align.profit or die Cannot open file
 align.profit\n;
 print $PROFIT ATOMS CA\n;
 print $PROFIT ZONE 34-513:1-480\n;
 print $PROFIT FIT\n;
 print $PROFIT WRITE $folder/$dir/$pdbnew\n;
 close $PROFIT;

 shouldn't it?

 that that file is provided to 1 command line
 `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
 $folder/$dir/$pdbnew`;
 where 2hi4.pdb is my ref
 $pdbnew variable assosiated with the target pdb

 one question about align.profit: will the output aligned mobile.pdb
 consist of all atoms? I've found that only CA atoms are used for the
 superimposition
 print $PROFIT ATOMS CA\n;


 James



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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-07 Thread James Starlight
Thomas,thanks for help- I'll try to test your script!

Jed, many thanks too!

if I understood correctly align.profit should contain thefollowing lines:

# using ProFIT to align the model to 2hi4
open $PROFIT,  align.profit or die Cannot open file align.profit\n;
print $PROFIT ATOMS CA\n;
print $PROFIT ZONE 34-513:1-480\n;
print $PROFIT FIT\n;
print $PROFIT WRITE $folder/$dir/$pdbnew\n;
close $PROFIT;

shouldn't it?

that that file is provided to 1 command line
`profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
$folder/$dir/$pdbnew`;
where 2hi4.pdb is my ref
$pdbnew variable assosiated with the target pdb

one question about align.profit: will the output aligned mobile.pdb consist
of all atoms? I've found that only CA atoms are used for the superimposition
print $PROFIT ATOMS CA\n;


James
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-05 Thread James Starlight
Thanks Matthew,


I'll try to use this opportunity! BTW does anybody knows some simple Linux
utility to perform structural superimposition of 2 pdbs and obtain the
superimposed (target.pdb) in separate pdb file? This time I'm writing big
docking script where I need to superimpose each receptor against some
reference.pdb and use superimposed pdb for docking. Because I'll work with
huge pdb datasets I relly don’t want to call python each time.

James


2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:



 You could make a python script that import pymol and does what you want
 from there.

 Some thing like this (untested);

 import __main__
 __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
 import pymol
 pymol.finish_launching()
 from pymol import cmd

 reffile = sys.argv[1]
 tarfile = sys.argv[2]
 outfile = sys.argv[3]

 cmd.load(reffile, 'ref')
 cmd.load(tarfile, 'tar')
 cmd.align('ref', 'tar')
 cmd.save(outfile, 'ref')


 Then on the command line call it like: python my_align.py reffile.pdb
 target.pdb output.pdb

 On 09/04/2014 11:06 AM, James Starlight wrote:

   thank you very much!

 so now only my question regarding the usage of the pymol commands in
 command line is still open

  BTW could someone suggest me the shell utility to make quick
 superimposition of the tar.pdb to  ref.pdb and save superimposed tar.pdb as
 the separate pdb  (the TMalign is not good because it produce pdb with both
 merged layers (and its backbone trace only) as the result if -o flagg is
 provided)

  Kind regards,

  Gleb


 2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  You can use sed
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
 's/^END/TER/g'   merged.pdb


 On 09/04/2014 10:54 AM, James Starlight wrote:

  thanks!

 and do I need to pipe the below command to smth
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb

  if I need to change 'END' to 'TER' in the merged.pdb ?


 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  Use the -h flag with grep to suppress the filename.
 Also, you don't need to pipe to cat, you can write directly to the file.

 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb



 On 09/04/2014 10:38 AM, James Starlight wrote:

..and one question about grep (really didn't find it in the tutorial)

 using
 grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb

  I've obtained good pdb BUT each line prior to the ATOM the name of the
 pdb of the previous files have been added eg:

 tarr_se.pdb:ATOM  1  N   ASP X   1  35.722   8.306  92.256
 0.00  0.00   N
 tarr_se.pdb:ATOM  2  CA  ASP X   1  35.252   8.836  93.529
 0.00  0.00   C
 tarr_se.pdb:ATOM  3  C   ASP X   1  35.797  10.339  93.708
 0.00  0.00   C
 tarr_se.pdb:ATOM  4  O   ASP X   1  34.979  11.297  93.674
 0.00  0.00   O
 tarr_se.pdb:ATOM  5  CB  ASP X   1  35.593   7.984  94.698
 0.00  0.00   C
 tarr_se.pdb:ATOM  6  CG  ASP X   1  34.692   8.171  95.960
 0.00  0.00   C
 tarr_se.pdb:ATOM  7  OD1 ASP X   1  33.481   8.453  95.823
 0.00  0.00   O
 tarr_se.pdb:ATOM  8  OD2 ASP X   1  35.257   8.362  97.046
 0.00  0.00   O1-
 tarr_se.pdb:ATOM  9  HA  ASP X   1  34.180   9.033  93.580
 0.00  0.00   H
 tarr_se.pdb:ATOM 10  HB2 ASP X   1  35.496   6.916  94.504
 0.00  0.00   H
 tarr_se.pdb:ATOM 11  HB3 ASP X   1  36.648   7.969  94.970
 0.00  0.00   H

  such pattern are always produced by grep
  so I'd like that tarr_se.pdb: have not been included (of course I can
 it remove easily after merging but this step is not good for me :) )

  Also i'll be very thankful for any useful grep awk sed tutorial in case
 of the bioinformatics application

  James


 2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com:

one question :)

  could someone explain me the ussage the pymol commands from the shell
 on the example
 e.g i need to load 2 pdbs in pymol make its superimposition and than
 save one of the superimposed pdb
  like
 load ref.pdb tar.pdb
 super tar, ref
 save tar  tar_superimposed.pdb

  I've tried to do part of this using
 pymol ref.pdb tarr.pdb -cd super tarr ref

  but eventually obtained error

  James


 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:

   Thanks Guys!
  I'll check the tutorials.

  All the best,

  James


 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:

  (sed '1d' protein.pdb; sed '1d' lipid.pdb)  merged.pdb

 --or--

  tail -q -n '+2' protein.pdb lipid.pdb  merged.pdb

 -David



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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-05 Thread James Starlight
should to add

than I've used both TMalign and mammoth utilities but didn't understand how
to obtain superimposed output as the full-atomic pdb's. I will be thankful
if someone could share with me its experience :)

James


2014-09-05 12:00 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Thanks Matthew,


 I'll try to use this opportunity! BTW does anybody knows some simple Linux
 utility to perform structural superimposition of 2 pdbs and obtain the
 superimposed (target.pdb) in separate pdb file? This time I'm writing big
 docking script where I need to superimpose each receptor against some
 reference.pdb and use superimposed pdb for docking. Because I'll work with
 huge pdb datasets I relly don’t want to call python each time.

 James


 2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:



 You could make a python script that import pymol and does what you want
 from there.

 Some thing like this (untested);

 import __main__
 __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
 import pymol
 pymol.finish_launching()
 from pymol import cmd

 reffile = sys.argv[1]
 tarfile = sys.argv[2]
 outfile = sys.argv[3]

 cmd.load(reffile, 'ref')
 cmd.load(tarfile, 'tar')
 cmd.align('ref', 'tar')
 cmd.save(outfile, 'ref')


 Then on the command line call it like: python my_align.py reffile.pdb
 target.pdb output.pdb

 On 09/04/2014 11:06 AM, James Starlight wrote:

   thank you very much!

 so now only my question regarding the usage of the pymol commands in
 command line is still open

  BTW could someone suggest me the shell utility to make quick
 superimposition of the tar.pdb to  ref.pdb and save superimposed tar.pdb as
 the separate pdb  (the TMalign is not good because it produce pdb with both
 merged layers (and its backbone trace only) as the result if -o flagg is
 provided)

  Kind regards,

  Gleb


 2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  You can use sed
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
 's/^END/TER/g'   merged.pdb


 On 09/04/2014 10:54 AM, James Starlight wrote:

  thanks!

 and do I need to pipe the below command to smth
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb

  if I need to change 'END' to 'TER' in the merged.pdb ?


 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  Use the -h flag with grep to suppress the filename.
 Also, you don't need to pipe to cat, you can write directly to the file.

 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb



 On 09/04/2014 10:38 AM, James Starlight wrote:

..and one question about grep (really didn't find it in the
 tutorial)

 using
 grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb

  I've obtained good pdb BUT each line prior to the ATOM the name of the
 pdb of the previous files have been added eg:

 tarr_se.pdb:ATOM  1  N   ASP X   1  35.722   8.306  92.256
 0.00  0.00   N
 tarr_se.pdb:ATOM  2  CA  ASP X   1  35.252   8.836  93.529
 0.00  0.00   C
 tarr_se.pdb:ATOM  3  C   ASP X   1  35.797  10.339  93.708
 0.00  0.00   C
 tarr_se.pdb:ATOM  4  O   ASP X   1  34.979  11.297  93.674
 0.00  0.00   O
 tarr_se.pdb:ATOM  5  CB  ASP X   1  35.593   7.984  94.698
 0.00  0.00   C
 tarr_se.pdb:ATOM  6  CG  ASP X   1  34.692   8.171  95.960
 0.00  0.00   C
 tarr_se.pdb:ATOM  7  OD1 ASP X   1  33.481   8.453  95.823
 0.00  0.00   O
 tarr_se.pdb:ATOM  8  OD2 ASP X   1  35.257   8.362  97.046
 0.00  0.00   O1-
 tarr_se.pdb:ATOM  9  HA  ASP X   1  34.180   9.033  93.580
 0.00  0.00   H
 tarr_se.pdb:ATOM 10  HB2 ASP X   1  35.496   6.916  94.504
 0.00  0.00   H
 tarr_se.pdb:ATOM 11  HB3 ASP X   1  36.648   7.969  94.970
 0.00  0.00   H

  such pattern are always produced by grep
  so I'd like that tarr_se.pdb: have not been included (of course I can
 it remove easily after merging but this step is not good for me :) )

  Also i'll be very thankful for any useful grep awk sed tutorial in
 case of the bioinformatics application

  James


 2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com:

one question :)

  could someone explain me the ussage the pymol commands from the shell
 on the example
 e.g i need to load 2 pdbs in pymol make its superimposition and than
 save one of the superimposed pdb
  like
 load ref.pdb tar.pdb
 super tar, ref
 save tar  tar_superimposed.pdb

  I've tried to do part of this using
 pymol ref.pdb tarr.pdb -cd super tarr ref

  but eventually obtained error

  James


 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:

   Thanks Guys!
  I'll check the tutorials.

  All the best,

  James


 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:

  (sed '1d' protein.pdb; sed '1d' lipid.pdb)  merged.pdb

 --or--

  tail -q -n '+2' protein.pdb lipid.pdb

Re: [PyMOL] Access to pymol commands from the terminal

2014-09-05 Thread James Starlight
Thanks Tsjerk!

Today I've tried some software of pairs alignment (like ce, tmalign and
mammoth) and found that it's not good for me because the positions of
reference and target are both altered as the result of the alignment by
means of the rotational matrix superimposition method. In my case I need to
move completely atoms of ref.pdb to the tar.pdb positions (whats pymol's
super command is actual do!)  because I need to copy some docking
parameters (like docking box xyz vectors) from ref to each of the target.
So I'd be very thankful if someone shown me most trivial case to use super
command from the Pymol from the terminal in a few-line method (I really
wiuld like to avoid some python scripts from my bash) like:
load ref.pdb tar.pdb
super tar.pdb ref.pdb
save tar.pdb


Thanks for help,

James


2014-09-05 13:36 GMT+02:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 I have a light version for fitting gromacs' gro files. No time to adapt
 that now for PDB, but it's not too hard.

 ./qfit.py source.gro target.gro  output.gro

 Hope it helps,

 Tsjerk


 On Fri, Sep 5, 2014 at 12:31 PM, James Starlight jmsstarli...@gmail.com
 wrote:

 should to add

 than I've used both TMalign and mammoth utilities but didn't understand
 how to obtain superimposed output as the full-atomic pdb's. I will be
 thankful if someone could share with me its experience :)

 James


 2014-09-05 12:00 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Thanks Matthew,


 I'll try to use this opportunity! BTW does anybody knows some simple
 Linux utility to perform structural superimposition of 2 pdbs and obtain
 the superimposed (target.pdb) in separate pdb file? This time I'm writing
 big docking script where I need to superimpose each receptor against some
 reference.pdb and use superimposed pdb for docking. Because I'll work with
 huge pdb datasets I relly don’t want to call python each time.

 James


 2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:



 You could make a python script that import pymol and does what you want
 from there.

 Some thing like this (untested);

 import __main__
 __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
 import pymol
 pymol.finish_launching()
 from pymol import cmd

 reffile = sys.argv[1]
 tarfile = sys.argv[2]
 outfile = sys.argv[3]

 cmd.load(reffile, 'ref')
 cmd.load(tarfile, 'tar')
 cmd.align('ref', 'tar')
 cmd.save(outfile, 'ref')


 Then on the command line call it like: python my_align.py reffile.pdb
 target.pdb output.pdb

 On 09/04/2014 11:06 AM, James Starlight wrote:

   thank you very much!

 so now only my question regarding the usage of the pymol commands in
 command line is still open

  BTW could someone suggest me the shell utility to make quick
 superimposition of the tar.pdb to  ref.pdb and save superimposed tar.pdb as
 the separate pdb  (the TMalign is not good because it produce pdb with both
 merged layers (and its backbone trace only) as the result if -o flagg is
 provided)

  Kind regards,

  Gleb


 2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  You can use sed
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed -e
 's/^END/TER/g'   merged.pdb


 On 09/04/2014 10:54 AM, James Starlight wrote:

  thanks!

 and do I need to pipe the below command to smth
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb

  if I need to change 'END' to 'TER' in the merged.pdb ?


 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  Use the -h flag with grep to suppress the filename.
 Also, you don't need to pipe to cat, you can write directly to the
 file.

 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb   
 merged.pdb



 On 09/04/2014 10:38 AM, James Starlight wrote:

..and one question about grep (really didn't find it in the
 tutorial)

 using
 grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |cat   
 merged.pdb

  I've obtained good pdb BUT each line prior to the ATOM the name of
 the pdb of the previous files have been added eg:

 tarr_se.pdb:ATOM  1  N   ASP X   1  35.722   8.306  92.256
 0.00  0.00   N
 tarr_se.pdb:ATOM  2  CA  ASP X   1  35.252   8.836  93.529
 0.00  0.00   C
 tarr_se.pdb:ATOM  3  C   ASP X   1  35.797  10.339  93.708
 0.00  0.00   C
 tarr_se.pdb:ATOM  4  O   ASP X   1  34.979  11.297  93.674
 0.00  0.00   O
 tarr_se.pdb:ATOM  5  CB  ASP X   1  35.593   7.984  94.698
 0.00  0.00   C
 tarr_se.pdb:ATOM  6  CG  ASP X   1  34.692   8.171  95.960
 0.00  0.00   C
 tarr_se.pdb:ATOM  7  OD1 ASP X   1  33.481   8.453  95.823
 0.00  0.00   O
 tarr_se.pdb:ATOM  8  OD2 ASP X   1  35.257   8.362  97.046
 0.00  0.00   O1-
 tarr_se.pdb:ATOM  9  HA  ASP X   1  34.180   9.033  93.580
 0.00  0.00   H
 tarr_se.pdb:ATOM 10  HB2 ASP X   1  35.496   6.916  94.504
 0.00  0.00   H
 tarr_se.pdb:ATOM 11  HB3

[PyMOL] Shell utilities for structural bioinformatics

2014-09-05 Thread James Starlight
Dear Pymol users!

I've decided to open new topic focused on the implementation of the common
shell utilities like grep awk and sed for the structural bioinformatics
tasks like processing and editing of the large sets of pdbs.

In my current task I need to copy all lipids from one pdb (called it ref)
to another call it tar_i.pdb (both files have the same 3D shape and have
been superimposed before that): so in that case I guess lipids could be
recognized by residue name in pdb file (PPC) as well as by its #4 column
number (what is actually do grep).  So the algorithm might be: select from
the ref.pdb all strings where #4 column is PPC and merge it (by means of
CAT I guess) with the tar_i.pdb. Please show me some example of the
one-line method of this realization.

Thanks,

James
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-05 Thread James Starlight
Hi Jed!

thanks for the advise!

As I understood some commands like FIT and WRITE should be provided being
INSIDE of the profit to obtain pdb output. Does it possible to do it in one
line style from bash like profit ref tar  output etc ? BTW profit send
errors when I try to fit mob to ref and when residue number is mismatched.
Is it possible to ignore all atoms but not amino-acids from the both pdbs
(e,g in my case ref consist of the lipids as well which I need to use on
further step to copy from ref to superimposed tar) ?

THF,

James


2014-09-05 18:41 GMT+02:00 Jed Goldstone jedg...@gmail.com:

 I have used ProFit for that task, from Andrew Martin's group at UCL. It
 does least-squares fitting, so it's reasonably quick.
 http://www.bioinf.org.uk/software/profit/index.html

 Jed

 On 9/5/2014 6:00 AM, James Starlight wrote:

 Thanks Matthew,


 I'll try to use this opportunity! BTW does anybody knows some simple
 Linux utility to perform structural superimposition of 2 pdbs and obtain
 the superimposed (target.pdb) in separate pdb file? This time I'm
 writing big docking script where I need to superimpose each receptor
 against some reference.pdb and use superimposed pdb for docking. Because
 I'll work with huge pdb datasets I relly don’t want to call python each
 time.

 James


 2014-09-04 17:12 GMT+02:00 Matthew Baumgartner mp...@pitt.edu
 mailto:mp...@pitt.edu:




 You could make a python script that import pymol and does what you
 want from there.

 Some thing like this (untested);

 import __main__
 __main__.pymol_argv = ['pymol','-cqk'] # Pymol: quiet and no GUI
 import pymol
 pymol.finish_launching()
 from pymol import cmd

 reffile = sys.argv[1]
 tarfile = sys.argv[2]
 outfile = sys.argv[3]

 cmd.load(reffile, 'ref')
 cmd.load(tarfile, 'tar')
 cmd.align('ref', 'tar')
 cmd.save(outfile, 'ref')


 Then on the command line call it like: python my_align.py
 reffile.pdb target.pdb output.pdb

 On 09/04/2014 11:06 AM, James Starlight wrote:

 thank you very much!

 so now only my question regarding the usage of the pymol commands
 in command line is still open

 BTW could someone suggest me the shell utility to make quick
 superimposition of the tar.pdb to  ref.pdb and save superimposed
 tar.pdb as the separate pdb  (the TMalign is not good because it
 produce pdb with both merged layers (and its backbone trace only)
 as the result if -o flagg is provided)

 Kind regards,

 Gleb


 2014-09-04 16:57 GMT+02:00 Matthew Baumgartner mp...@pitt.edu
 mailto:mp...@pitt.edu:

 You can use sed
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb | sed
 -e 's/^END/TER/g'   merged.pdb


 On 09/04/2014 10:54 AM, James Starlight wrote:

 thanks!

 and do I need to pipe the below command to smth
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb   
 merged.pdb

 if I need to change 'END' to 'TER' in the merged.pdb ?


 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner
 mp...@pitt.edu mailto:mp...@pitt.edu:


 Use the -h flag with grep to suppress the filename.
 Also, you don't need to pipe to cat, you can write
 directly to the file.

 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb
 lipids.pdbmerged.pdb



 On 09/04/2014 10:38 AM, James Starlight wrote:

 ..and one question about grep (really didn't find it in
 the tutorial)

 using
 grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb
 |catmerged.pdb

 I've obtained good pdb BUT each line prior to the ATOM
 the name of the pdb of the previous files have been
 added eg:

 tarr_se.pdb:ATOM  1  N ASP X   1  35.722 8.306
 92.256  0.00 0.00   N
 tarr_se.pdb:ATOM  2  CA ASP X   1  35.252 8.836
 93.529  0.00 0.00   C
 tarr_se.pdb:ATOM  3  C ASP X   1  35.797 10.339
 93.708  0.00 0.00   C
 tarr_se.pdb:ATOM  4  O ASP X   1  34.979 11.297
 93.674  0.00 0.00   O
 tarr_se.pdb:ATOM  5  CB ASP X   1  35.593 7.984
 94.698  0.00 0.00   C
 tarr_se.pdb:ATOM  6  CG ASP X   1  34.692 8.171
 95.960  0.00 0.00   C
 tarr_se.pdb:ATOM  7  OD1 ASP X   1  33.481
 8.453  95.823  0.00 0.00   O
 tarr_se.pdb:ATOM  8  OD2 ASP X   1  35.257
 8.362  97.046  0.00 0.00   O1-
 tarr_se.pdb:ATOM  9  HA ASP X   1  34.180 9.033
 93.580  0.00 0.00   H
 tarr_se.pdb:ATOM 10  HB2 ASP X   1  35.496
 6.916  94.504  0.00 0.00   H

Re: [PyMOL] Access to pymol commands from the terminal

2014-09-04 Thread James Starlight
Hi Tsjerk,

Thanks alot!
Also I have the task to merge protein.pdb and lipids.pdb with some 1 line
shell command ( like CAT) to obtain protein inserted in the lipids (the
seccond file is consist of the whole which can locate the protein). My
problem is that both protein.pdb and lipids.pdb consisted of the unusuall
first line which should be deleated before it merging (in my case it's the
HEADER lala.pdb). could you suggest me the combination of grep sed command
which should be used to deleate the first line from both pdbs and than
merge it in one-command method?

Many thanks,

James


2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 You can use pymol -cd pymolcommands. See
 http://www.pymolwiki.org/index.php/Command_Line_Options

 However, the first part is much easier with grep or sed. To remove all
 solvent molecules:

 grep -v ^ATOM.*SOL in.pdb  out.pdb

 To remove NA+/CL- too

 grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb  out.pdb

 The fitting is a bit more cumbersome :)

 Hope it helps,

 Tsjerk


 On Thu, Sep 4, 2014 at 10:19 AM, James Starlight jmsstarli...@gmail.com
 wrote:

 Dear PyMol users!

 I'd like to find possibilities for running of some pymol commands from
 the terminal. For instance in my case I' d like perform 2 simple steps
 (both in terminal not in the pymol GUI)
 to remove water and ions from my target input pdb (typical I do it via
 gromacs editconf)
 superimpose target.pdb against reference.pdb ( i do it by means of
 tmalign utility)

 Thanks for help,

 James


 --
 Slashdot TV.
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 Tsjerk A. Wassenaar, Ph.D.


--
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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-04 Thread James Starlight
one question :)

could someone explain me the ussage the pymol commands from the shell on
the example
e.g i need to load 2 pdbs in pymol make its superimposition and than save
one of the superimposed pdb
like
load ref.pdb tar.pdb
super tar, ref
save tar  tar_superimposed.pdb

I've tried to do part of this using
pymol ref.pdb tarr.pdb -cd super tarr ref

but eventually obtained error

James


2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Thanks Guys!
 I'll check the tutorials.

 All the best,

 James


 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:

  (sed '1d' protein.pdb; sed '1d' lipid.pdb)  merged.pdb

 --or--

 tail -q -n '+2' protein.pdb lipid.pdb  merged.pdb

 -David




 On Thu, Sep 4, 2014 at 6:19 AM, James Starlight jmsstarli...@gmail.com
 wrote:

 Hi Tsjerk,

 Thanks alot!
 Also I have the task to merge protein.pdb and lipids.pdb with some 1
 line shell command ( like CAT) to obtain protein inserted in the lipids
 (the seccond file is consist of the whole which can locate the protein). My
 problem is that both protein.pdb and lipids.pdb consisted of the
 unusuall first line which should be deleated before it merging (in my case
 it's the HEADER lala.pdb). could you suggest me the combination of grep sed
 command which should be used to deleate the first line from both pdbs and
 than merge it in one-command method?

 Many thanks,

 James


 2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com:

 Hi James,

 You can use pymol -cd pymolcommands. See
 http://www.pymolwiki.org/index.php/Command_Line_Options

 However, the first part is much easier with grep or sed. To remove all
 solvent molecules:

 grep -v ^ATOM.*SOL in.pdb  out.pdb

 To remove NA+/CL- too

 grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb  out.pdb

 The fitting is a bit more cumbersome :)

 Hope it helps,

 Tsjerk


 On Thu, Sep 4, 2014 at 10:19 AM, James Starlight 
 jmsstarli...@gmail.com wrote:

 Dear PyMol users!

 I'd like to find possibilities for running of some pymol commands from
 the terminal. For instance in my case I' d like perform 2 simple steps
 (both in terminal not in the pymol GUI)
 to remove water and ions from my target input pdb (typical I do it via
 gromacs editconf)
 superimpose target.pdb against reference.pdb ( i do it by means of
 tmalign utility)

 Thanks for help,

 James


 --
 Slashdot TV.
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives:
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net




 --
 Tsjerk A. Wassenaar, Ph.D.




 --
 Slashdot TV.
 Video for Nerds.  Stuff that matters.
 http://tv.slashdot.org/
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




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Re: [PyMOL] Access to pymol commands from the terminal

2014-09-04 Thread James Starlight
thanks!

and do I need to pipe the below command to smth
grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb

if I need to change 'END' to 'TER' in the merged.pdb ?


2014-09-04 16:54 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 thanks!

 and do I need to pipe the below command to smth
 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb

 if I need to change 'END' to 'TER' in the merged.pdb ?


 2014-09-04 16:41 GMT+02:00 Matthew Baumgartner mp...@pitt.edu:

  Use the -h flag with grep to suppress the filename.
 Also, you don't need to pipe to cat, you can write directly to the file.

 grep -h  '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdbmerged.pdb



 On 09/04/2014 10:38 AM, James Starlight wrote:

..and one question about grep (really didn't find it in the tutorial)

 using
 grep '^\(ATOM\|HETATM\|END\)' tarr_se.pdb lipids.pdb |catmerged.pdb

  I've obtained good pdb BUT each line prior to the ATOM the name of the
 pdb of the previous files have been added eg:

 tarr_se.pdb:ATOM  1  N   ASP X   1  35.722   8.306  92.256  0.00
 0.00   N
 tarr_se.pdb:ATOM  2  CA  ASP X   1  35.252   8.836  93.529  0.00
 0.00   C
 tarr_se.pdb:ATOM  3  C   ASP X   1  35.797  10.339  93.708  0.00
 0.00   C
 tarr_se.pdb:ATOM  4  O   ASP X   1  34.979  11.297  93.674  0.00
 0.00   O
 tarr_se.pdb:ATOM  5  CB  ASP X   1  35.593   7.984  94.698  0.00
 0.00   C
 tarr_se.pdb:ATOM  6  CG  ASP X   1  34.692   8.171  95.960  0.00
 0.00   C
 tarr_se.pdb:ATOM  7  OD1 ASP X   1  33.481   8.453  95.823  0.00
 0.00   O
 tarr_se.pdb:ATOM  8  OD2 ASP X   1  35.257   8.362  97.046  0.00
 0.00   O1-
 tarr_se.pdb:ATOM  9  HA  ASP X   1  34.180   9.033  93.580  0.00
 0.00   H
 tarr_se.pdb:ATOM 10  HB2 ASP X   1  35.496   6.916  94.504  0.00
 0.00   H
 tarr_se.pdb:ATOM 11  HB3 ASP X   1  36.648   7.969  94.970  0.00
 0.00   H

  such pattern are always produced by grep
  so I'd like that tarr_se.pdb: have not been included (of course I can it
 remove easily after merging but this step is not good for me :) )

  Also i'll be very thankful for any useful grep awk sed tutorial in case
 of the bioinformatics application

  James


 2014-09-04 16:03 GMT+02:00 James Starlight jmsstarli...@gmail.com:

one question :)

  could someone explain me the ussage the pymol commands from the shell
 on the example
 e.g i need to load 2 pdbs in pymol make its superimposition and than
 save one of the superimposed pdb
  like
 load ref.pdb tar.pdb
 super tar, ref
 save tar  tar_superimposed.pdb

  I've tried to do part of this using
 pymol ref.pdb tarr.pdb -cd super tarr ref

  but eventually obtained error

  James


 2014-09-04 15:47 GMT+02:00 James Starlight jmsstarli...@gmail.com:

   Thanks Guys!
  I'll check the tutorials.

  All the best,

  James


 2014-09-04 13:15 GMT+02:00 David Hall li...@cowsandmilk.net:

  (sed '1d' protein.pdb; sed '1d' lipid.pdb)  merged.pdb

 --or--

  tail -q -n '+2' protein.pdb lipid.pdb  merged.pdb

 -David




 On Thu, Sep 4, 2014 at 6:19 AM, James Starlight 
 jmsstarli...@gmail.com wrote:

 Hi Tsjerk,

  Thanks alot!
 Also I have the task to merge protein.pdb and lipids.pdb with some 1
 line shell command ( like CAT) to obtain protein inserted in the lipids
 (the seccond file is consist of the whole which can locate the protein). 
 My
 problem is that both protein.pdb and lipids.pdb consisted of the
 unusuall first line which should be deleated before it merging (in my 
 case
 it's the HEADER lala.pdb). could you suggest me the combination of grep 
 sed
 command which should be used to deleate the first line from both pdbs and
 than merge it in one-command method?

  Many thanks,

  James


 2014-09-04 12:48 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com:

  Hi James,

  You can use pymol -cd pymolcommands. See
 http://www.pymolwiki.org/index.php/Command_Line_Options

  However, the first part is much easier with grep or sed. To remove
 all solvent molecules:

  grep -v ^ATOM.*SOL in.pdb  out.pdb

  To remove NA+/CL- too

  grep -v ATOM.*\(SOL\|NA+\|CL-\) in.pdb  out.pdb

  The fitting is a bit more cumbersome :)

  Hope it helps,

  Tsjerk


  On Thu, Sep 4, 2014 at 10:19 AM, James Starlight 
 jmsstarli...@gmail.com wrote:

 Dear PyMol users!

  I'd like to find possibilities for running of some pymol commands
 from the terminal. For instance in my case I' d like perform 2 simple 
 steps
 (both in terminal not in the pymol GUI)
  to remove water and ions from my target input pdb (typical I do it
 via gromacs editconf)
  superimpose target.pdb against reference.pdb ( i do it by means of
 tmalign utility)

  Thanks for help,

  James


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[PyMOL] Making nmr-like ensemble from several pdbs

2014-08-27 Thread James Starlight
Dear Pymol users!

Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file

from pymol import cmd
import sys,glob

def get_file_list(files):
  file_list = glob.glob(files)
  return file_list

def load_models(files,obj,discrete=0):
  
  load_models files, object, discrete=0

  loads multiple files (using filename globbing)
  into a single object (e.g. from modelling or NMR).

  use discrete=1 if you want to color individual states separately

  e.g. load_models prot_*.pdb, prot
  
  if type(files) == type('string'):
file_list = get_file_list(files)
  else:
file_list = files

  if file_list:
file_list.sort()
for name in file_list:
  cmd.load(name,obj,discrete=discrete)
  else:
print No files found for pattern %s % files

cmd.extend('load_models',load_models)


Many thanks for help,

James
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Re: [PyMOL] Making nmr-like ensemble from several pdbs

2014-08-27 Thread James Starlight
also please tell me how is it possible to include ter record at the end of
each model.

James


2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Dear Pymol users!

 Using below script I can load all pdbs from the work dir into 1 nmr-like
 object. Could you suggest me how this script could be modified to make
 alignment (or it's better structural alignment) of all pdbs against first
 loaded pdb file

 from pymol import cmd
 import sys,glob

 def get_file_list(files):
   file_list = glob.glob(files)
   return file_list

 def load_models(files,obj,discrete=0):
   
   load_models files, object, discrete=0

   loads multiple files (using filename globbing)
   into a single object (e.g. from modelling or NMR).

   use discrete=1 if you want to color individual states separately

   e.g. load_models prot_*.pdb, prot
   
   if type(files) == type('string'):
 file_list = get_file_list(files)
   else:
 file_list = files

   if file_list:
 file_list.sort()
 for name in file_list:
   cmd.load(name,obj,discrete=discrete)
   else:
 print No files found for pattern %s % files

 cmd.extend('load_models',load_models)


 Many thanks for help,

 James

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Re: [PyMOL] Making nmr-like ensemble from several pdbs

2014-08-27 Thread James Starlight
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?


Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case of each model and obtained back ensemble with
the processed conformers.


At this time using such nmr ensemble I've faced with the below error

FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N

I don't why this error occurs (I have not this in case of ONE model from
the ensemble)

James


2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:

 split_states NMR-ensemble object name
 alignto 1st NMR model name, method=cealign


 On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:

 also please tell me how is it possible to include ter record at the end
 of each model.

 James


 2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Dear Pymol users!

 Using below script I can load all pdbs from the work dir into 1 nmr-like
 object. Could you suggest me how this script could be modified to make
 alignment (or it's better structural alignment) of all pdbs against first
 loaded pdb file

 from pymol import cmd
 import sys,glob

 def get_file_list(files):
   file_list = glob.glob(files)
   return file_list

 def load_models(files,obj,discrete=0):
   
   load_models files, object, discrete=0

   loads multiple files (using filename globbing)
   into a single object (e.g. from modelling or NMR).

   use discrete=1 if you want to color individual states separately

   e.g. load_models prot_*.pdb, prot
   
   if type(files) == type('string'):
 file_list = get_file_list(files)
   else:
 file_list = files

   if file_list:
 file_list.sort()
 for name in file_list:
   cmd.load(name,obj,discrete=discrete)
   else:
 print No files found for pattern %s % files

 cmd.extend('load_models',load_models)


 Many thanks for help,

 James




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 ==

 Thomas Evangelidis

 PhD student
 University of Athens
 Faculty of Pharmacy
 Department of Pharmaceutical Chemistry
 Panepistimioupoli-Zografou
 157 71 Athens
 GREECE

 email: tev...@pharm.uoa.gr

   teva...@gmail.com


 website: https://sites.google.com/site/thomasevangelidishomepage/

 ===

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 *- Ernest Rutherford*


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Re: [PyMOL] Making nmr-like ensemble from several pdbs

2014-08-27 Thread James Starlight
is it working here?
https://www.sendspace.com/file/8i0aqo

James


2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de:

 On 27/08/14 07:56, James Starlight wrote:
  Hi
 
  both of them are present in my ensemble. the problem is not here- if it
  possible i could upload the ensemble.pdb to some server if someone could
  check it.
 
  James
 

 Hi,

 Go for some paste bins or do a gist on github.

 Justin


 --
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 Institute of Complex Systems
 ICS-6 Structural Biochemistry
 Research Centre Juelich
 52425 Juelich, Germany
 phone: +49 2461 61 2117



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Re: [PyMOL] Making nmr-like ensemble from several pdbs

2014-08-27 Thread James Starlight
*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
legitimate chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier A, B, etc. to
denote different models of the same monomer (as in e.g. 2TRX). Make sure
you supply only the one you want. For NMR structures, you get a window
where you can choose which model to use.

i guess it indicate that in principle some ensembles are possible as the
input :) Alternatively do you know any other tools (software) for the
processing of the ensembles with such options for the analysis?

James


2014-08-27 15:05 GMT+02:00 Thomas Evangelidis teva...@gmail.com:




 On 27 August 2014 15:43, James Starlight jmsstarli...@gmail.com wrote:

 and than how to quick merged aligned conformers back to the NMR ensemble
 including TER record between each model in it?


 Actually I'm looking for the possibility to load this ensemble to the
 http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states
 for the titrable residues in case of each model and obtained back ensemble
 with the processed conformers.

 I think H++ server processes one structure per job. Where did you find
 that you can upload an ensemble?



 At this time using such nmr ensemble I've faced with the below error

 FAILURE: Sequence discontinuity occurred between residues 289 and 1 at
 the line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N

 I don't why this error occurs (I have not this in case of ONE model from
 the ensemble)

 James


 2014-08-27 13:10 GMT+02:00 Thomas Evangelidis teva...@gmail.com:

 split_states NMR-ensemble object name
 alignto 1st NMR model name, method=cealign


 On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:

 also please tell me how is it possible to include ter record at the end
 of each model.

 James


 2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:

 Dear Pymol users!

 Using below script I can load all pdbs from the work dir into 1
 nmr-like object. Could you suggest me how this script could be modified to
 make alignment (or it's better structural alignment) of all pdbs against
 first loaded pdb file

 from pymol import cmd
 import sys,glob

 def get_file_list(files):
   file_list = glob.glob(files)
   return file_list

 def load_models(files,obj,discrete=0):
   
   load_models files, object, discrete=0

   loads multiple files (using filename globbing)
   into a single object (e.g. from modelling or NMR).

   use discrete=1 if you want to color individual states separately

   e.g. load_models prot_*.pdb, prot
   
   if type(files) == type('string'):
 file_list = get_file_list(files)
   else:
 file_list = files

   if file_list:
 file_list.sort()
 for name in file_list:
   cmd.load(name,obj,discrete=discrete)
   else:
 print No files found for pattern %s % files

 cmd.extend('load_models',load_models)


 Many thanks for help,

 James




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 --

 ==

 Thomas Evangelidis

 PhD student
 University of Athens
 Faculty of Pharmacy
 Department of Pharmaceutical Chemistry
 Panepistimioupoli-Zografou
 157 71 Athens
 GREECE

 email: tev...@pharm.uoa.gr

   teva...@gmail.com


 website: https://sites.google.com/site/thomasevangelidishomepage/

 ===

 *Physics is the only real science. The rest are just stamp collecting.*

 *- Ernest Rutherford*





 --

 ==

 Thomas Evangelidis

 PhD student
 University of Athens
 Faculty of Pharmacy
 Department of Pharmaceutical Chemistry
 Panepistimioupoli-Zografou
 157 71 Athens
 GREECE

 email: tev...@pharm.uoa.gr

   teva...@gmail.com


 website: https://sites.google.com/site/thomasevangelidishomepage/

 ===

 *Physics is the only real science. The rest are just stamp collecting.*

 *- Ernest Rutherford*


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[PyMOL] Saving trajectory outputs

2014-07-25 Thread James Starlight
Dear Pymol Users!

I wounder whether it will be possible  to save big ensemble of the loaded
into pymol Pdb's files as the trajectory output (like dcd format) what are
actually can be performed by vmd (e.g by means of
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/).
The problem in last case is that I don't know how to perform
superimposition of my conformers agains refeence frame (alternatively what
is easily performed in pymol). I'll be thankful for any suggestions.

Best wishes,

James
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[PyMOL] python scripting in pymol

2014-04-05 Thread James Starlight
Dear PyMol users!

I'm learning of the python scripting for the solution of typical structural
bioinformatics problems. This time I'd like to integrate in pymol simple
script which will search for the selected motifs (just several amino acids
situated in adjacent positions along the sequence) and marked selection
data assuming that I'm working with  ensemble of homologue proteins having
common motifs. Could someone provide me with the example of such script
included pymol syntax in code? During further steps I'd like to improve
such script for searching  of motis situated in adjacent space position in
3D pdb structures but not in its sequences.


Thanks for help,


James
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[PyMOL] AutoDock plugin

2013-12-06 Thread James Starlight
Dear PyMol users!

I've forced with the problem of the installation of AutoDock plugin
pymoawiki.org/index.php/Autodock_plugin  in recent pymol version. I've
tried to install it manually from the downloaded py script but at the
starting of pymol below error has bbeen appeared

Unable to initialize plugin 'autodock' (pmg_tk.startup.autodock).
Unable to initialize plugin 'autodock_plugin'
(pmg_tk.startup.autodock_plugin).

Also I've tried to search for the plugin in the pymol repositories but have
not found it. How it could be solved ?


James
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Re: [PyMOL] AutoDock plugin

2013-12-06 Thread James Starlight
Thomas,

Thanks for suggestions.

1)I have installed Numpy.

2)   File /usr/lib/python2.7/dist-packages/pymol/parser.py, line 260, in
parse
exec(layer.com2+\n,self.pymol_names,self.pymol_names)
  File string, line 1, in module
  File /usr/share/pyshared/pmg_tk/startup/autodock_plugin.py, line 62, in
module
from numpy import *
  File /usr/share/pyshared/numpy/__init__.py, line 137, in module
import add_newdocs
  File /usr/share/pyshared/numpy/add_newdocs.py, line 9, in module
from numpy.lib import add_newdoc
  File /usr/share/pyshared/numpy/lib/__init__.py, line 4, in module
from type_check import *
  File /usr/share/pyshared/numpy/lib/type_check.py, line 8, in module
import numpy.core.numeric as _nx
  File /usr/share/pyshared/numpy/core/__init__.py, line 5, in module
import multiarray
ImportError: No module named multiarray


What  package is needed which consist of multiarray module ?

James


2013/12/6 Thomas Holder spel...@users.sourceforge.net

 Hi James,

 import pmg_tk.startup.autodock_plugin

 should tell you what's wrong. My next guess is that you don't have numpy
 installed.

 For the missing bonds in your example, PyMOL thinks those atoms are
 cations because of the symbol in the last column. By default, PyMOL doesn't
 make bonds to cations. But this will work:

 PyMOLunset pdb_unbond_cations,
 PyMOLload example.pdb

 Hope that helps.

 Cheers,
   Thomas

 On 06 Dec 2013, at 11:04, James Starlight jmsstarli...@gmail.com wrote:

  Thomas,
 
  I have this problem within the recent pymol 1.6.0.0 version installed on
 Linux Debian (all others plugins work correct. Also Autodock plugin is not
 seen in the repository)
 
  By the way in this Pymol version I've forced with some problems with the
 ligands representation. For example I've obtained typical docking output
 from the AutoDock consisted of 10 poses (in separate models) but some atoms
 of this ligands is visualized as a blank atoms. Below the atoms of the one
 model are provided as the example.
 
  HETATM1  CAG P0G R   1  -0.073  -2.031  12.923  1.00  0.00
  .001 A
  HETATM2  CAH P0G R   1  -0.624  -2.630  11.797  1.00  0.00
  .001 A
  HETATM3  CAI P0G R   1   0.713  -0.894  12.787  1.00  0.00
  .007 A
  HETATM4  CAJ P0G R   1  -0.383  -2.091  10.540  1.00  0.00
  .007 A
  HETATM5  CAW P0G R   1  -2.339   3.404   5.677  1.00  0.00
  .008 A
  HETATM6  CAL P0G R   1  -1.712   3.845   4.518  1.00  0.00
  .015 A
  HETATM7  CAK P0G R   1  -1.825   5.176   4.131  1.00  0.00
  .039 A
  HETATM8  CAB P0G R   1   0.291   2.102   8.752  1.00  0.00
  .046 C
  HETATM9  CAC P0G R   1  -1.618   0.656   9.433  1.00  0.00
  .046 C
  HETATM   10  CAA P0G R   1   1.806   0.879  11.409  1.00  0.00
  .049 C
  HETATM   11  CAV P0G R   1   0.396  -0.946  10.403  1.00  0.00
  .050 A
  HETATM   12  CAT P0G R   1   0.950  -0.354  11.529  1.00  0.00
  .056 A
  HETATM   13  NAP P0G R   1  -0.642   0.506   7.208  1.00  0.00
  .064 N
  HETATM   14  CAO P0G R   1   0.652  -0.375   9.023  1.00  0.00
  .077 C
  HETATM   15  CAU P0G R   1  -2.570   6.062   4.900  1.00  0.00
  .095 A
  HETATM   16  CAX P0G R   1  -3.197   5.612   6.048  1.00  0.00
  .102 A
  HETATM   17  CAY P0G R   1  -3.084   4.294   6.426  1.00  0.00
  .107 A
  HETATM   18  CBA P0G R   1  -0.335   0.720   8.612  1.00  0.00
  .122 C
  HETATM   19  HAQ P0G R   1  -3.677   7.418   6.890  1.00  0.00
  .169 H
  HETATM   20  CAZ P0G R   1  -2.233   1.990   6.093  1.00  0.00
  .179 C
  HETATM   21  HAF P0G R   1  -2.600   0.245   5.251  1.00  0.00
  .210 H
  HETATM   22  HAE P0G R   1  -2.798   7.416   3.572  1.00  0.00
  .217 H
  HETATM   23  CAS P0G R   1  -4.971   5.977   7.513  1.00  0.00
  .246 C
  HETATM   24  CAN P0G R   1  -0.768   1.610   6.272  1.00  0.00
  .269 C
  HETATM   25  OAD P0G R   1  -5.901   6.691   7.854  1.00  0.00
  .271 O
  HETATM   26  CAM P0G R   1  -4.980   4.505   7.870  1.00  0.00
  .278 C
  HETATM   27 2HAP P0G R   1  -1.522   0.012   7.182  1.00  0.00
  .278 H
  HETATM   28 3HAP P0G R   1   0.062  -0.118   6.840  1.00  0.00
  .278 H
  HETATM   29  NAQ P0G R   1  -3.925   6.442   6.827  1.00  0.00
  .321 N
  HETATM   30  OAR P0G R   1  -3.718   3.912   7.572  1.00  0.00
  .339 O
  HETATM   31  OAE P0G R   1  -2.682   7.366   4.523  1.00  0.00
  .358 O
  HETATM   32  OAF P0G R   1  -2.799   1.167   5.067  1.00  0.00
  .389 O
 
 
  2013/12/6 Thomas Holder spel...@users.sourceforge.net
  Hi James,
 
  is it recent version of PyMOL, or recent version of Windows which makes
 trouble? On Windows, the plugin tries to write to the PyMOL installation
 folder, which fails if you don't have write permissions there. This needs
 to be fixed, the plugin should write to the users folder also on Windows.
 
  Cheers,
Thomas
 
  On 06 Dec 2013, at 08:47, James Starlight jmsstarli...@gmail.com
 wrote:
 
   Dear

Re: [PyMOL] Working with the pdb ensemble

2013-12-06 Thread James Starlight
Hi Jared,


The issue is that the all ligands are copied in one sele (and than
extracted to one object). Consequently I'd like to split it to separate
objects as the lig1.pdb lig2.pdb etc

James


2013/12/7 Sampson, Jared jared.samp...@nyumc.org

  Hi James - If I understand you correctly, you just need to give a
 selection argument to the save command.

  save ligand1.pdb, sele1
 save ligand2.pdb, sele2
 etc...

  See http://pymolwiki.org/index.php/Save for more info.

  Cheers,
 Jared

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  On Dec 6, 2013, at 12:03 PM, James Starlight jmsstarli...@gmail.com
  wrote:

   Dear PyMol users!

  I'd be thankfull if you provide me with the easliest way how I could save
 selection to the separate pdbs. For example I've loaded 10 pdbs of the
 receptor and selected from in each 10 ligands. This selection is defined in
 one object (extracted or coppied from sele). How I could save it as 10
 pdbs?

  Also I have a question about addtion of the hyrogens to each ligand in
 ensemble. How I could add hydrogens in accordance to the specified
 protonation states of the ligands (manually providing total charge)?

  Thanks for help,
  James
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[PyMOL] Rendering in pymol

2013-11-29 Thread James Starlight
Der Pymol users!

I wounder to know if it possible to increase rendering rate mainly at the
expense of the GPU usage. At my desktop with core i7 and 6 cpu (12 cpus in
the hyper-threading mode) I've spend  ~ 2 hours to render image consisted
of ensemble of conformations (~ 30 aligned pdbs) using only CPUs.

set ray_trance mode, 1
ray 3000
png ./1.png


Does it possible to add some loading to the gpu as well?


James
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[PyMOL] RMSD calculation for the pdb ensemble

2013-11-21 Thread James Starlight
Dear PyMol users!

I'm looking for python script which would perform the

1- loading ensemble of the pdbs to the pymol (assuming that it could be
done by loadDir script)

2- Perform structural alighnemnt of all loaded structures against reference
0.pdb  by means of buit-in TMalighn module
this could be done by means of for loop I suppose

3-  wtite to the ./output the pdbs which are differ agains reference
(0.pdb) strongly on  the selected RMSD value (e.g I have 100 structures
extrracted from MD trajectory. I define in my script rmds=1.0 and I'd like
that the only structures have been writed to the ./output wich have 1 A, 2
A, 3 A (value differ on the 1 A as defined in script) etc rmsd agains
reference (0.pdb). As the result I'd like to select only small part of the
conformers with the uniform RSMD difference
Don't known how to script it :)

Thanks for any usefull examples,

James
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Re: [PyMOL] Caver 3.0 pugin

2013-11-17 Thread James Starlight
Hi Stephen,

you should try lattest CAVER which could be downloaded from
http://www.caver.cz

before installing it via Pymol plugin menu, you should to open
caver-3.0-1.py and find here
CAVER3_LOCATION = directory/where/caver3/is/located

and modify this on your path providing it to the jar file directly ( in
this version there is no jar path in pymol plugin itself).

Does anyone use it for the analysis of the ligand sites? I've test it with
the GPCR and found 3 possible pathways. I'n not sure how It have been
clustered but now I'n looking for the method for the steered MD along
caver-predicted pathes

James


2013/11/17 Stephen P. Molnar s.mol...@sbcglobal.net

  I would be interested in just how the problem has been solved!

 I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL
 v-1.6.0.0 compiled from the latest svn and functioning perfectly on my
 system.

 Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without
 any complaints.  Yet when I try to use the plugin I get:

 ERROR: Directory incorrectly specified -plugin.jar not found, check
 directory/where/jar/with/plugin/is/locate/Carver2_1.jar

 Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory.
 Also other plugins are working without complaint.

 This is exactly the way the plug was working the last time that I
 attempted its installation and use.


 On 11/15/2013 03:14 PM, James Starlight wrote:

  This issue have been solved. Caver works fine. Does anyone tried to
 include path information obtained by caver to the NAMD steered md
 simulation? I'm looking for the protocol for guiding namd forces along the
 direction obtaned from CAVER.


  James


 2013/11/15 James Starlight jmsstarli...@gmail.com

   Dear Pymol Users!


  In the latest 3.0 releases of the CAVER plugin lack the source path for
 the caver.jar launch file. Could you tell me how I could define this path
 manually from pymol shell? I've try to make calculations with thus plugin
 having Caver 3.0 dir in the work folder but obtained error that
 /where/caver3 not found


  Thanks for help

  James




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[PyMOL] Caver 3.0 pugin

2013-11-15 Thread James Starlight
Dear Pymol Users!


In the latest 3.0 releases of the CAVER plugin lack the source path for the
caver.jar launch file. Could you tell me how I could define this path
manually from pymol shell? I've try to make calculations with thus plugin
having Caver 3.0 dir in the work folder but obtained error that
/where/caver3 not found


Thanks for help

James
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Re: [PyMOL] Caver 3.0 pugin

2013-11-15 Thread James Starlight
This issue have been solved. Caver works fine. Does anyone tried to include
path information obtained by caver to the NAMD steered md simulation? I'm
looking for the protocol for guiding namd forces along the direction
obtaned from CAVER.


James


2013/11/15 James Starlight jmsstarli...@gmail.com

 Dear Pymol Users!


 In the latest 3.0 releases of the CAVER plugin lack the source path for
 the caver.jar launch file. Could you tell me how I could define this path
 manually from pymol shell? I've try to make calculations with thus plugin
 having Caver 3.0 dir in the work folder but obtained error that
 /where/caver3 not found


 Thanks for help

 James

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Re: [PyMOL] Automatic mutation introduction

2013-11-12 Thread James Starlight
Thanks! I'll try all pf this possibilities- especially I'm interesting in
Modeller because its 1) python-based and 2) produce suitable input for MD
(fixing side-chains or loops missed in the X-ray input data)


James


2013/11/11 Ron Jacak ron.ja...@gmail.com

 Hi James,

 SCWRL is a good suggestion.  You may also want to take a look at Rosetta (
 https://www.rosettacommons.org/).  It uses the Dunbrack 2010 rotamer
 library but also includes a dozen or so other score terms to aid in
 repacking and minimizing mutations.  There's also a server (
 http://rosettadesign.med.unc.edu/), since the installation and
 compilation can take some time.

 Best,
 -Ron

 On Nov 10, 2013, at 2:27 PM, James Starlight wrote:

  Dear PyMol users!
 
 
  I'm looking for the possible python script which using the pymol source
 would introduce selected mutations in the defined PDB file and produce PDB
 output containing such protein with the selected substitution residues. It
 would be also good if rotamers for mutation residues would be backbone
 dependent or taken from the existing rotamer libraries (although its not
 essence because I can run minimization on the mutants)
 
  Previously I've done such tasks with selectivity mutations via pymol-GUI
 but now I'd like to obtain big series of the mutant of studied protein for
 further examinations of such mutants by means of molecular dynamics
 simulation.
  Could someone provide me with such script if it could not be very
 complicated to make it?
 
 
  Thanks for help,
 
  James
 
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[PyMOL] Automatic mutation introduction

2013-11-10 Thread James Starlight
Dear PyMol users!


I'm looking for the possible python script which using the pymol source
would introduce selected mutations in the defined PDB file and produce PDB
output containing such protein with the selected substitution residues. It
would be also good if rotamers for mutation residues would be backbone
dependent or taken from the existing rotamer libraries (although its not
essence because I can run minimization on the mutants)

Previously I've done such tasks with selectivity mutations via pymol-GUI
but now I'd like to obtain big series of the mutant of studied protein for
further examinations of such mutants by means of molecular dynamics
simulation.
Could someone provide me with such script if it could not be very
complicated to make it?


Thanks for help,

James
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[PyMOL] Cartoon transparency

2013-06-06 Thread James Starlight
Dear PyMol users!


I want to set transparency on the selected carton region of my protein ( I
have closed GFP barell with the chromophore inside it so I'd like set
transparency of some beta-shits to make chromophore easily visible ).


In PyMol I've selected region corresponded to that Beta-sheets and than used

set cartoon_transparency, 0.5, sele



unfortunatelly there were no any changes after this :(

How I could solve it ?



Thanks for help,


James
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[PyMOL] sorting pdb ensembles based on rmsd

2013-04-30 Thread James Starlight
Dear PyMol users!


I have a set of conformations extracted from the MD trajectory (on the
equal time-steps). After loading of all that pdb's into pymol (each
conformer= separate pdb file) I want to sort that structures based on the
RMSD relative to the reference conformer (e.g step0.pdb ) in the selected
range (e.g select and sort only structures with RMSD = 0.5 to the 0.pdb. So
if I have 100 conformers I want that pymol select only 5 structures with
rmsd (measured by TMalign plugin for instance) to reference equal to 0.5,
1, 1.5, 2.0, 2.5 and 3.0 Angstroms, respectively).

Does it possible to make such sorting ?


James
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[PyMOL] Visualization of the protein-ligand interactions

2013-04-24 Thread James Starlight
Dear Pymol users!


I want to examine protein-ligand interactions observed in the md trajectory
using Pymol.

For such task I have 100 snapshots of the protein-ligand complex which I've
loaded into the pymol. Now I want to extract from all snapshots 100 ligands
as the separate 100 objects and save it in the mol2. Actually I can do such
task in the simplest way extracting all ligands in one object but I need as
a result 100 mol2 files. Could someone show me example of some script which
could do such tasks?

Also I'll be very thankful if someone can provide me with some tool which
can be used for investigation of the ligand dynamics along MD trajectory (
in particular I want to visualize all binding poses and define all polar
contacts along trajectory). For such task I've being used pymol as well as
pose view loading snapshots to that programs but that way is not
appropriate for analyzing of the ensembles of the binding poses obtained
from md run.


Thanks for help,


James
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Re: [PyMOL] Visualization of the protein-ligand interactions

2013-04-24 Thread James Starlight
Thomas, thanks for help!


As I understood fconv can be used for the split several mol2 (or pdb) files
which was placed in 1 model to the several pdb files, doesnt it ?

In past I forced with some problems with  g_hbond. Is there any other way
to monitor h bonds along the trajectory (e.g in vmd) ?

PoseView is used as the separate software or web server
http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze polar
interactions both in pymol as well as via pose view).


James

2013/4/24 Thomas Evangelidis teva...@gmail.com


 I want to examine protein-ligand interactions observed in the md
 trajectory using Pymol.

 For such task I have 100 snapshots of the protein-ligand complex which
 I've loaded into the pymol. Now I want to extract from all snapshots 100
 ligands as the separate 100 objects and save it in the mol2. Actually I can
 do such task in the simplest way extracting all ligands in one object but I
 need as a result 100 mol2 files. Could someone show me example of some
 script which could do such tasks?


 Save all ligands in a multi-mol mol2 file and then split if with fconv -s.

 http://pc1664.pharmazie.uni-marburg.de/download/fconv



 Also I'll be very thankful if someone can provide me with some tool which
 can be used for investigation of the ligand dynamics along MD trajectory (
 in particular I want to visualize all binding poses and define all polar
 contacts along trajectory). For such task I've being used pymol as well as
 pose view loading snapshots to that programs but that way is not
 appropriate for analyzing of the ensembles of the binding poses obtained
 from md run.


 I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges
 with the respective VMD plugin. Then I make a table with frequences of each
 polar interaction, pick up a frame that contains as many important
 interactions as possible, load it in PyMOL and draw dotted lines between
 the interacting atoms.

 PS: I didn't know about PoseView plugin, it seems to be a very useful
 addition to PyMOL :)

 Thomas

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 ==

 Thomas Evangelidis

 PhD student
 University of Athens
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 email: tev...@pharm.uoa.gr

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Re: [PyMOL] Fwd: Visualization of the protein-ligand interactions

2013-04-24 Thread James Starlight
Thomas,

actually I used very routine way. Firstly I've  extract conformers of
protein-ligand complexes from the trajectory. Than I've loaded it into
pymol and visualize possible interactions. Than I've selected most
representative conformers and loaded it separately into pose view to obtain
2D maps. I understand that its very routine but I had not any other
alternatives.

By the way during usage of the g_hbond with the below flags

g_hbond -f fitted.trr -s complex.gro -n index.ndx  -hbm ./hb/hbmap.xpm
-life ./hb/hblife.xvg

In the index file I've specified ligand and protein as two groups.  should
I define second group more accurately ( e.g only possible amino acids from
the ligand binding pocket) ?
I've forced with the problem of the interpretation of the hbmap. As I
understood that could be used for the monitoring of the h-bond occurring
and breaking between protein and ligand during MD run. How it could be
visualize to observe particular amino-acids on the first (protein) group
which contribute to H-bonds ?

James

2013/4/24 Thomas Evangelidis teva...@gmail.com






 As I understood fconv can be used for the split several mol2 (or pdb)
 files which was placed in 1 model to the several pdb files, doesnt it ?

 fconv can do miracles :) check it out !

 fconv -h



 In past I forced with some problems with  g_hbond. Is there any other way
 to monitor h bonds along the trajectory (e.g in vmd) ?


 In contrast, I encountered problems with the H-bonds VMD plugin, that's
 why I resorted to g_hbond. Beware that g_hbonds will count the frequencies
 of salt-bridges too.


 PoseView is used as the separate software or web server
 http://poseview.zbh.uni-hamburg.de/poseview ( I mean that I analyze
 polar interactions both in pymol as well as via pose view).


 If you find a way to draw the most important protein-ligand interactions
 throughout the trajectory with PoseView, then I would be very interested to
 know how.



 James

 2013/4/24 Thomas Evangelidis teva...@gmail.com


 I want to examine protein-ligand interactions observed in the md
 trajectory using Pymol.

 For such task I have 100 snapshots of the protein-ligand complex which
 I've loaded into the pymol. Now I want to extract from all snapshots 100
 ligands as the separate 100 objects and save it in the mol2. Actually I can
 do such task in the simplest way extracting all ligands in one object but I
 need as a result 100 mol2 files. Could someone show me example of some
 script which could do such tasks?


 Save all ligands in a multi-mol mol2 file and then split if with fconv
 -s.

 http://pc1664.pharmazie.uni-marburg.de/download/fconv



 Also I'll be very thankful if someone can provide me with some tool
 which can be used for investigation of the ligand dynamics along MD
 trajectory ( in particular I want to visualize all binding poses and define
 all polar contacts along trajectory). For such task I've being used pymol
 as well as pose view loading snapshots to that programs but that way is not
 appropriate for analyzing of the ensembles of the binding poses obtained
 from md run.


 I usually monitor H-bonds with g_hbond from GROMACS Tools and
 Salt-Bridges with the respective VMD plugin. Then I make a table with
 frequences of each polar interaction, pick up a frame that contains as many
 important interactions as possible, load it in PyMOL and draw dotted lines
 between the interacting atoms.

 PS: I didn't know about PoseView plugin, it seems to be a very useful
 addition to PyMOL :)

 Thomas




 --

 ==

 Thomas Evangelidis

 PhD student
 University of Athens
 Faculty of Pharmacy
 Department of Pharmaceutical Chemistry
 Panepistimioupoli-Zografou
 157 71 Athens
 GREECE

 email: tev...@pharm.uoa.gr

   teva...@gmail.com


 website: https://sites.google.com/site/thomasevangelidishomepage/




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[PyMOL] loadDir script

2013-04-02 Thread James Starlight
Dear PyMol users!


I've forced with the problem of the loading of the my structural ensemble
(pdb files of the protein listed as 1.pdb 2.pdb 3.pdb ..;. 100.pdb) into
pymol via loadDir.pml script. In particular after loading of my ensemble in
the right contex pymol's window I want to preserve structural order
according to the pdb's names ( so that structures were listed in order from
1 to the 100.pdbs but not in the random (mixed) order). What additions to
the loadDir script should I do to make such ordering ?



James
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Re: [PyMOL] loadDir script

2013-04-02 Thread James Starlight
Thank you!

Does it possible to include
order *, yes

to some pymol's setting file that the ordering  be automatically each time
when I load pdb ensemble? (I dont what to include it to the loadDir.pml
script itself).

James

2013/4/2 Thomas Holder thomas.hol...@schrodinger.com

 Hi James,

 please try, after loading the files:

 PyMOL order *, yes

 Cheers,
   Thomas

 James Starlight wrote, On 04/02/13 19:28:
  Pete,
 
  thanks for suggestion.
 
  I've tried to use loadDir with the pdb's subset where each file had name
  like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still
  wrong :(
 
 
 
  also is loadDir script I found block
 
  for c in glob( g ):
  cmd.load(c)
 
  if ( group != None ):
  cmd.group( group, basename(c).split(.)[0],
 add )
 
  what should I change here to sort files correctly?
 
 
  James

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor


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