date:20161018

Re: [PyMOL] Iterating through all objects and calculate RMS

2016-10-18 Thread Subha K

Oh yeah, thanks a lot Gabriel Marques.

I figured out the rms_cur part too.

On Tue, Oct 18, 2016 at 12:23 PM, Gabriel Marques <
gabriel.marq...@schrodinger.com> wrote:

> Looks like you’re missing a space in the string ‘and resn UNK’, it should
> be: i + ‘ and resn UNK’
>
> Regards,
> Gabriel Marques
>
> On Oct 18, 2016, at 1:57 PM, Subha K  wrote:
>
> Hi There,
>
> I am trying to calculate the rmsd of all ligands loaded in the pymol with
> reference to a reference ligand using a script. My current script looks
> like this,
>
>
> myobjects = cmd.get_object_list()
> print myobjects
> cmd.select('sele', "F60_target_14 and resn UNK")
> cmd.create('obj01', 'sele')
> for i in myobjects:
> i = i.strip()
> cmd.sele('sele', i +'and resn UNK')
> cmd.create ('obj02', 'sele')
> cmd.rms_cur ('obj02', 'obj01')
> cmd.delete ('obj02')
>
>
> obj01 will be my reference and I want to use rms_cur to all objects loaded.
> The problems here are,
> (1) My obj02 selection part is not working properly. I know I am not
> calling the myobject list in the correct way. Could somebody help me fix
> this?
> (2) I want to write the rmsd values to a file. How can I do it?
>
> Thanks for the help.
>
> Regards,
> Subha
>
>
> 
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>
>
>
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Re: [PyMOL] Iterating through all objects and calculate RMS

2016-10-18 Thread Gabriel Marques

Looks like you’re missing a space in the string ‘and resn UNK’, it should be: i 
+ ‘ and resn UNK’

Regards,
Gabriel Marques

> On Oct 18, 2016, at 1:57 PM, Subha K  wrote:
> 
> Hi There,
> 
> I am trying to calculate the rmsd of all ligands loaded in the pymol with 
> reference to a reference ligand using a script. My current script looks like 
> this,
> 
> 
> myobjects = cmd.get_object_list()
> print myobjects
> cmd.select('sele', "F60_target_14 and resn UNK")
> cmd.create('obj01', 'sele')
> for i in myobjects:
> i = i.strip()
> cmd.sele('sele', i +'and resn UNK')
> cmd.create ('obj02', 'sele')
> cmd.rms_cur ('obj02', 'obj01')
> cmd.delete ('obj02')
> 
> 
> obj01 will be my reference and I want to use rms_cur to all objects loaded.
> The problems here are, 
> (1) My obj02 selection part is not working properly. I know I am not calling 
> the myobject list in the correct way. Could somebody help me fix this?
> (2) I want to write the rmsd values to a file. How can I do it?
> 
> Thanks for the help.
> 
> Regards,
> Subha
> 
> 
> --
> Check out the vibrant tech community on one of the world's most 
> engaging tech sites, SlashDot.org! 
> http://sdm.link/slashdot___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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[PyMOL] Iterating through all objects and calculate RMS

2016-10-18 Thread Subha K

Hi There,

I am trying to calculate the rmsd of all ligands loaded in the pymol with
reference to a reference ligand using a script. My current script looks
like this,


myobjects = cmd.get_object_list()

print myobjects

cmd.select('sele', "F60_target_14 and resn UNK")

cmd.create('obj01', 'sele')

for i in myobjects:

i = i.strip()

cmd.sele('sele', i +'and resn UNK')

cmd.create ('obj02', 'sele')

cmd.rms_cur ('obj02', 'obj01')

cmd.delete ('obj02')


obj01 will be my reference and I want to use rms_cur to all objects loaded.
The problems here are,
(1) My obj02 selection part is not working properly. I know I am not
calling the myobject list in the correct way. Could somebody help me fix
this?
(2) I want to write the rmsd values to a file. How can I do it?

Thanks for the help.

Regards,
Subha
--
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Re: [PyMOL] Compile error svn 4162

2016-10-18 Thread Thomas Holder

Hi Quyen,

This should be fixed in svn rev 4163.

Cheers,
  Thomas

On 18 Oct 2016, at 01:05, QT  wrote:

> Dear all,
> 
> I'm having a compile error that I've never had before on the current svn 
> revision 4162.  Compile broke on file CifDataValueFormatter.cpp
> 
> g++ -pthread -std=c++0x -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE 
> -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_FREETYPE -DNO_MMLIBS 
> -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 
> -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/include 
> -Icontrib/uiuc/plugins/molfile_plugin/src 
> -I/home/quyen/lib64/python2.7/site-packages/numpy/core/include -I/usr/include 
> -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python2.7 -c 
> layer3/CifDataValueFormatter.cpp -o 
> build/temp.linux-x86_64-2.7/layer3/CifDataValueFormatter.o -Wno-write-strings 
> -Wno-unused-function -Wno-char-subscripts -ffast-math -funroll-loops -fcommon 
> -O3
> In file included from layer3/CifDataValueFormatter.cpp:8:0:
> layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids initialization 
> of member 'm_i'
> layer3/CifDataValueFormatter.h:20:13: error: making 'm_i' static
> layer3/CifDataValueFormatter.h:20:13: error: ISO C++ forbids in-class 
> initialization of non-const static member 'm_i'
> 
> g++ version 4.5.1
> 
> Do you have any advise on how to get past this blocker?
> 
> Best,
> Quyen

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Iterating through all objects and calculate RMS

Re: [PyMOL] Iterating through all objects and calculate RMS

[PyMOL] Iterating through all objects and calculate RMS

Re: [PyMOL] Compile error svn 4162

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