[PyMOL] show dashes lines in cartoon to connect loops not resolved in structure

[hari jayaram]

Hi ,
One of the features I like in Chimera is that breaks in the protein chain
due to unresolved residues are indicated by dashes.
Is there a plugin or built in feature that enables this in pymol.

Thanks
Hari
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[PyMOL] select polymer within ribosome cif file ?

[hari jayaram]

Hi all,
I am trying to select a particular chain ( the 5S RNA) within the E.coli
ribosome cif file ( pdb ID 4V69)

The sequence info page at rcsb indicates  that this chain has the
information given below. I dont know the chain id or segid for this chain
and in general have not worked with cif files inside pymol.

How do I select polymer 58 inside this cif structure.
Thanks in advance
Hari


Chain InfoPolymer: 58
Length: 117 residues
Chain Type: polyribonucleotide
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Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Thanks All
Engin Ozkan wrote in saying that he could get schrodinger compiled Pymol
1.8.4 to work well with same setup as mine

I then tested a self compiled 1.8.4 and with an older version 1.7.6.0 ( and
1.7.4.5) on the same setup.

I could get smooth scrolling with  1.7 series versions on the same
 hardware .
My self compiled 1.8.2.1 and 1.8.4 are not behaving well and show the Jerky
scrolling.

I compiled using a simple pymol setup.py install

I will try and troubleshoot what in the compilation is giving the poor
response with newer pymol versions ( 1.8 series)  since I  can only use the
open-source pymol

Thanks
Hari


On Wed, Jan 11, 2017 at 5:55 PM hari jayaram  wrote:

> Sorry to post back in.
>
> As I posted yesterday ,  I have been trying to get pymol working on a
> Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the
> X11 apps freezing problem is real and recurs frequently.
>
> While rotating a molecule the X session stops responding , the window
> close - window open-window minimize , red yellow green buttons gray out and
> then the whole session freezes
>
> I see this behavior on two machines I have tried using since my original
> machine where everything was working but with an earlier brew installed
> pymol ( 1.7.2 I think ) bit the dust.
>
> IS anyone else seeing this with 1.8.2.1 and OSX?
>
> Thanks
> hari
>
>
>
>
>
> I have used homebrew to install pymol version 1.8.2.1
>
> On Tue, Jan 10, 2017 at 7:02 AM hari jayaram  wrote:
>
> Hello All
> Sorry for that post. The problem got fixed by a restart.
> I failed to follow the unwritten rule of "non-Linux computers" :-) When in
> doubt---restart
>
> After a restart I tried pymol with a new user profile and it worked very
> smoothly
> I tried back with my migrated original account ...and the buttery smooth
> rotation returnedPhew :-)
>
> Sorry for the confusion
> Thanks
> Hari
>
>
>
>
> On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:
>
> Hi ,
> I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
> OSX Sierra) and then had a hardware failure.
>
> I switched computers to MacBook Air running the same version of OSX
> (Sierra 10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other
> X11 using applications) refuses to function with smooth molecule rotation
> on even a 30kDa protein.
>
> I know the Macbook Airs are not that underpowered and am wondering how to
> troubleshoot the lack of smooth rotation.
>
> I have tried:
> Reinstalling pymol (now running 1.8)
> Reinstalling Xquartz ( still running 2.7.11)
> Using an external mouse
>
>
> ANd still have rotation that gets stuck. It starts rotating smoothly and
> then locks up. I can see the Mac red/yello/green circles go gray like X11
> is sleeping when this happens . It resumes after a second and rotation
> cotinues .
>
> Looking for others having the same issue does not pull up anything. I can
> get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
> to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.
>
> Any ideas or help would be greatly appreciated since its two weeks till my
> faithful computer returns from a hardware fix.
>
> Thanks
> Hari
>
>
>
>
>
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Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Sorry to post back in.

As I posted yesterday ,  I have been trying to get pymol working on a
Macbook Air ( and MacBook Pro since yesterday ) and am now convinced the
X11 apps freezing problem is real and recurs frequently.

While rotating a molecule the X session stops responding , the window close
- window open-window minimize , red yellow green buttons gray out and then
the whole session freezes

I see this behavior on two machines I have tried using since my original
machine where everything was working but with an earlier brew installed
pymol ( 1.7.2 I think ) bit the dust.

IS anyone else seeing this with 1.8.2.1 and OSX?

Thanks
hari





I have used homebrew to install pymol version 1.8.2.1

On Tue, Jan 10, 2017 at 7:02 AM hari jayaram  wrote:

Hello All
Sorry for that post. The problem got fixed by a restart.
I failed to follow the unwritten rule of "non-Linux computers" :-) When in
doubt---restart

After a restart I tried pymol with a new user profile and it worked very
smoothly
I tried back with my migrated original account ...and the buttery smooth
rotation returnedPhew :-)

Sorry for the confusion
Thanks
Hari




On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:

Hi ,
I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
OSX Sierra) and then had a hardware failure.

I switched computers to MacBook Air running the same version of OSX (Sierra
10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using
applications) refuses to function with smooth molecule rotation on even a
30kDa protein.

I know the Macbook Airs are not that underpowered and am wondering how to
troubleshoot the lack of smooth rotation.

I have tried:
Reinstalling pymol (now running 1.8)
Reinstalling Xquartz ( still running 2.7.11)
Using an external mouse


ANd still have rotation that gets stuck. It starts rotating smoothly and
then locks up. I can see the Mac red/yello/green circles go gray like X11
is sleeping when this happens . It resumes after a second and rotation
cotinues .

Looking for others having the same issue does not pull up anything. I can
get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.

Any ideas or help would be greatly appreciated since its two weeks till my
faithful computer returns from a hardware fix.

Thanks
Hari
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Re: [PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Hello All
Sorry for that post. The problem got fixed by a restart.
I failed to follow the unwritten rule of "non-Linux computers" :-) When in
doubt---restart

After a restart I tried pymol with a new user profile and it worked very
smoothly
I tried back with my migrated original account ...and the buttery smooth
rotation returnedPhew :-)

Sorry for the confusion
Thanks
Hari




On Tue, Jan 10, 2017 at 6:49 AM hari jayaram  wrote:

> Hi ,
> I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
> OSX Sierra) and then had a hardware failure.
>
> I switched computers to MacBook Air running the same version of OSX
> (Sierra 10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other
> X11 using applications) refuses to function with smooth molecule rotation
> on even a 30kDa protein.
>
> I know the Macbook Airs are not that underpowered and am wondering how to
> troubleshoot the lack of smooth rotation.
>
> I have tried:
> Reinstalling pymol (now running 1.8)
> Reinstalling Xquartz ( still running 2.7.11)
> Using an external mouse
>
>
> ANd still have rotation that gets stuck. It starts rotating smoothly and
> then locks up. I can see the Mac red/yello/green circles go gray like X11
> is sleeping when this happens . It resumes after a second and rotation
> cotinues .
>
> Looking for others having the same issue does not pull up anything. I can
> get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
> to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.
>
> Any ideas or help would be greatly appreciated since its two weeks till my
> faithful computer returns from a hardware fix.
>
> Thanks
> Hari
>
>
>
>
>
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[PyMOL] Xquartz/pymol issues OSX Sierra: rotation stops after a few milliseconds

[hari jayaram]

Hi ,
I was happily using brew installed pymol 1.7.6  on my Macbook Pro (running
OSX Sierra) and then had a hardware failure.

I switched computers to MacBook Air running the same version of OSX (Sierra
10.12.2 ) and Xquartz (2.7.11) and now pymol ( and coot and other X11 using
applications) refuses to function with smooth molecule rotation on even a
30kDa protein.

I know the Macbook Airs are not that underpowered and am wondering how to
troubleshoot the lack of smooth rotation.

I have tried:
Reinstalling pymol (now running 1.8)
Reinstalling Xquartz ( still running 2.7.11)
Using an external mouse


ANd still have rotation that gets stuck. It starts rotating smoothly and
then locks up. I can see the Mac red/yello/green circles go gray like X11
is sleeping when this happens . It resumes after a second and rotation
cotinues .

Looking for others having the same issue does not pull up anything. I can
get smooth rotation in Chimera and Cuemol2 on this new laptop so it seems
to be a Pymol(Coot) X11/Xquartz issue that I dont know how to fix.

Any ideas or help would be greatly appreciated since its two weeks till my
faithful computer returns from a hardware fix.

Thanks
Hari
--
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Re: [PyMOL] homebrew pymol builds fine but get Symbol not found: _png_check_sig on launch

[hari jayaram]

I was able to get rid of this error by installing  a new version of a
Framework build for libpng from

http://ethan.tira-thompson.com/Mac_OS_X_Ports.html

I also switched to using the non homebrew version which I installed from
source using "python setup.py install".


Now I can get the pymol window to show up and also import pymol inside
python scripts without any error.
But as expected I cannot get the external GUI to work.

I tried installing Pmw and it complains about "tkinter" . Once I force it
to use the Tkinter as tkinter

import sys,Tkinter
sys.modules["tkinter"] = Tkinter

Then the Pmw window does not show up and crashes.

These are all old issues I am sure and I am hoping there is an easy fix.

Sorry for using a 32 bit OSX machine running 10.6.8..but I recently
resurrected it with a SSD and it actually runs faster than my Ubuntu Linux
machine running 13.04.

Hari







On Fri, Aug 2, 2013 at 10:48 AM, hari jayaram  wrote:

> Hi ,
>
> I was able to use the latest homebrew pymol formula and install pymol
> after making sure that tcl-tk was installed with --enable-threads and
> --with-x11 and python was configured --with-brewed-tk
>
>
> The pymol build proceeded to completion.
>
> However when I launch pymol I get the following error ( see below)
> Does anyone know what I am doing wrong.
>
> I am (sadly still) using a 32 bit Mac OSX Snow Leopard 10.6.8 laptop .
>
> Thanks
> Hari
>
>
> hari-jayarams-macbook-pro-17:~ hari$ pymol
> Traceback (most recent call last):
>   File "/usr/local/Cellar/pymol/
> 1.6.0.0/lib/python2.7/site-packages/pymol/__init__.py", line 185, in
> 
> import pymol
>   File "/usr/local/Cellar/pymol/
> 1.6.0.0/lib/python2.7/site-packages/pymol/__init__.py", line 499, in
> 
> from pymol import _cmd
> ImportError: dlopen(/usr/local/Cellar/pymol/
> 1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so, 2): Symbol not found:
> _png_check_sig
>   Referenced from: /usr/local/Cellar/pymol/
> 1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so
>   Expected in: flat namespace
>  in /usr/local/Cellar/pymol/
> 1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so
>
>
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[PyMOL] homebrew pymol builds fine but get Symbol not found: _png_check_sig on launch

[hari jayaram]

Hi ,

I was able to use the latest homebrew pymol formula and install pymol after
making sure that tcl-tk was installed with --enable-threads and --with-x11
and python was configured --with-brewed-tk


The pymol build proceeded to completion.

However when I launch pymol I get the following error ( see below)
Does anyone know what I am doing wrong.

I am (sadly still) using a 32 bit Mac OSX Snow Leopard 10.6.8 laptop .

Thanks
Hari


hari-jayarams-macbook-pro-17:~ hari$ pymol
Traceback (most recent call last):
  File "/usr/local/Cellar/pymol/
1.6.0.0/lib/python2.7/site-packages/pymol/__init__.py", line 185, in

import pymol
  File "/usr/local/Cellar/pymol/
1.6.0.0/lib/python2.7/site-packages/pymol/__init__.py", line 499, in

from pymol import _cmd
ImportError: dlopen(/usr/local/Cellar/pymol/
1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so, 2): Symbol not found:
_png_check_sig
  Referenced from: /usr/local/Cellar/pymol/
1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so
  Expected in: flat namespace
 in /usr/local/Cellar/pymol/
1.6.0.0/lib/python2.7/site-packages/pymol/_cmd.so
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[PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU- Solved

[hari jayaram]

Hello All,
I managed to solve the problem where many objects were not getting
included into a script created session "all" meta object  with help
from Jason .

Once I got rid of duplicate object names either using python or the
setting "auto_rename_duplicates"..I could load around 250 objects
without any issues into the session file. All resulting objects were
bound by "all" and could be toggled on and off.

I am reproducing the exchange with Jason below.

Thanks again
Hari


Jason Vertrees jason.vertr...@schrodinger.com
to: hari jayaram 
date: Thu, Mar 22, 2012 at 10:31 AM
Hari,

Thanks for the feedback.

If you have duplicate object names, look into the setting,
"autor_ename_duplicates". Also, look into using the get_unused_name
command. It's helpful for scripts like this.

Cheers,

-- Jason
-- Forwarded message --
From: hari jayaram 
Date: Thu, Mar 22, 2012 at 10:22 AM
Subject: Re: [PyMOL] Maximum number of objects/menu items in internal
GUI ? machine has lots of RAM and big GPU
To: Jason Vertrees 


Hi Jason,
I finally think I know why I was having objects that were not included
in the "all" object selection from inside Pymol when I ran my script.

When I had duplicate objects 1LZ1-remodel-1.pdb and 1LZ1-remodel-2.pdb
and both were loaded and renamed during my script to 1LZ1-remodel
..some of the objects escaped being bound by all once I added code
that does not allow duplicate object names  all of my objects are
toggled off by clicking "all".

So it definitely does not seem to be a graphics card memory issue.

I will probe further and write in once I understand exactly whats going on.

Thanks for your help

Hari

Here is the current version of my script

import cmd
import os
import pymol
import re

cpi = re.compile("(\d{6})")
pymol.finish_launching()

mymax = 60
count = 1
file_roots = []
for root,dirs,files in os.walk("Y:/Projects/Xtal structure/"):
    for afile in files:
        print "FILE",afile
        if ("pdb" in afile and "CPI-" in afile ) and not ("badcoords"
in afile) and count <= mymax :
            if afile[:10] in file_roots:
                altname = "V%d"% count + str(afile)
            else:
                altname = afile
            try:
                cmd.load(os.path.join(root,afile),altname)
                file_roots.append(afile[:10])
                count = count + 1
            except:
                print "Problem Loading:", afile
groups = []
done = []
for i in cmd.get_names():
    try:
        # To weed out duplicates
        if i[:10] not in done:
            group_pool = []
            cmd.extract ("waste%s" %i,"%s and not (resi 66 or resi
68-1114 or resi 119 or resi 123-161 or (organic within 3.5 of (resi 66
or resi 68-1114 or resi 119 or resi 123-161)) \
              or (resn HOH within 3.5 of(resi 66 or resi 68-1114 or
resi 119 or resi 123-161) ))" % i)
            cmd.delete("waste%s"%i)
            surfdonor = "surfdonor-%s" % i[:10]
            surfname = "surf-%s" % i[:10]
            cartoon_object = "cartoon-%s" % i[:10]
            ligands = "ligands-%s" % i[:10]
            solvent = "solvent-%s" %i[:10]

            # Create Object for surface and cartoon

            cmd.copy(surfdonor,i)
            cmd.copy(cartoon_object,i)

            # Create selection containing ligands and make them into
their own object
            cmd.select(ligands+"sel","organic and " + surfdonor)
            cmd.create(ligands,"(%s)"%ligands)
            cmd.delete(ligands+"sel")
            group_pool.append(ligands)

            # Create selection containing solvent
            cmd.select(solvent+"sel","resn HOH and " + surfdonor)
            cmd.create(solvent,"(%s)" % solvent)
            cmd.delete(solvent+"sel")
            group_pool.append(solvent)

            # Extract ligand object and solvent from surface clone object
            cmd.extract(surfname,"%s and not (resn HOH or organic)" % surfdonor)
            cmd.delete(surfdonor)
            group_pool.append(surfname)
            pymol.preset.ligand_cartoon(cartoon_object)
            group_pool.append(cartoon_object)
            group_pool.append(cartoon_object + "_pol_conts")
            group_pool.append(i)
            try:
                group_name = "%s%s" % (str(i[0:3]),cpi.search(i).groups()[0])
            except AttributeError:
                group_name = "group"+ i
            print group_name
            cmd.group(group_name," ".join(group_pool))
            done.append(i[:10])
        else:
            print "SKIPPING"*3, i
    except :
            print "Problem with" , i

On Thu, Mar 15, 2012 at 2:44 PM, Jason 

Re: [PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU

[hari jayaram]

Hi Jason ,
Thanks for your email.
I tried this with script with around 50 pdbs - that would be around 200
objects in the final session present in 50 groups.
The proteins are all in the 14-18 kDa range and monomeric.

My async_builds is off
My auto_defer_builds is set at 500

I used two versions :

1.5.0.3 on Windows XP 64 bit
with  Quadro FX 880M

And
1.4.1 on a 64 bit Ubuntu Machine
With Quadro FX 3700

On both versions and machines I had the same behavior.

The Interesting thing is that, in  the final session rotation is very
smooth ..and all the object seem to be loaded and responding fine. Its only
that most of the objects dont seem to be encompassed by "all"..So hiding
everything is not possible in this  session rendering the session very
cluttered and the groups un-useable.  Any idea what else may be affecting
my session.



Thanks
Hari



On Thu, Mar 15, 2012 at 11:13 AM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Hari,
>
> I've tried your script on hundreds of objects and it seems to work
> fine for me. What version of PyMOL are you using?
>
> Do you have the async_builds setting on? If so, set to what value?
> What about the auto_defer_builds settings?
>
> I wonder if your video card is out of memory.
>
> Cheers,
>
> -- Jason
>
> On Fri, Mar 9, 2012 at 5:59 PM, hari jayaram  wrote:
> > Hi I am scripting a visualization that involves roughly thirty to fifty
> PDB
> > files with four objects each i.e 120 to 150 objects.  I have a 64 bit
> > machine with 16 GB RAM and a Quadro FX 3700 card running Ubuntu Lucid.
> >
> > At the end of the script I get a menu with what seems like all of the
> > objects suitably processed and grouped.
> > After this  when I click "all"  and say hide..everything , a whole lot of
> > objects still stay displayed . Getting the ids for some of them by right
> > clicking , it seems like they are not being included on the internal GUI
> > menu even when I scroll to the bottom.
> > These objects are clearly created by my script but it seems like they are
> > not part of "all"
> > Is it that "all" is not representing all of my objects because of some
> limit
> > to number of objects that I am handling. The interesting thing is that
> even
> > when all the objects are loaded Pymol remains very performant.
> >
> > Here is my script...nothing fancy but just a loader and a grouper of PDBs
> > from a directory.
> >
> > Any help will be greatly appreciated
> > Thanks
> > Hari
> >
> >
> > import cmd
> > import os
> > import pymol
> > import re
> >
> > cpi = re.compile("(\d{6})")
> > pymol.finish_launching()
> >
> > for root,dirs,files in os.walk("/home/hari/mydownloadedPDbs/"):
> > for afile in files:
> > print "FILE",afile
> > if "pdb" in afile:
> > try:
> > cmd.load(os.path.join(root,afile))
> > except:
> > print "Problem Loading:", afile
> >
> > groups = []
> > for i in cmd.get_names():
> > try:
> > group_pool = []
> >
> > surfdonor = "surfdonor-%s" % i[:10]
> > surfname = "surf-%s" % i[:10]
> > cartoon_object = "cartoon-%s" % i[:10]
> > ligands = "ligands-%s" % i[:10]
> > solvent = "solvent-%s" %i[:10]
> >
> > # Create Object for surface and cartoon
> >
> > cmd.copy(surfdonor,i)
> > cmd.copy(cartoon_object,i)
> >
> > # Create selection containing ligands and make them into their
> own
> > object
> > cmd.select(ligands+"sel","organic and " + surfdonor)
> > cmd.create(ligands,"(%s)"%ligands)
> > cmd.delete(ligands+"sel")
> > group_pool.append(ligands)
> >
> > # Create selection containing solvent
> > cmd.select(solvent+"sel","resn HOH and " + surfdonor)
> > cmd.create(solvent,"(%s)" % solvent)
> > cmd.delete(solvent+"sel")
> > group_pool.append(solvent)
> >
> > # Extract ligand object and solvent from surface clone object
> > cmd.extract(surfname,"%s and not (resn HOH or organic)" %
> surfdonor)
> > cmd.delete(surfdonor)
> > group_pool.append(surfname)
> > pymol.preset.ligand_cartoon(cartoon_object)
> > group_pool.append(cartoo

[PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU

[hari jayaram]

Hi I am scripting a visualization that involves roughly thirty to fifty PDB
files with four objects each i.e 120 to 150 objects.  I have a 64 bit
machine with 16 GB RAM and a Quadro FX 3700 card running Ubuntu Lucid.

At the end of the script I get a menu with what seems like all of the
objects suitably processed and grouped.
After this  when I click "all"  and say hide..everything , a whole lot of
objects still stay displayed . Getting the ids for some of them by right
clicking , it seems like they are not being included on the internal GUI
menu even when I scroll to the bottom.
These objects are clearly created by my script but it seems like they are
not part of "all"
Is it that "all" is not representing all of my objects because of some
limit to number of objects that I am handling. The interesting thing is
that even when all the objects are loaded Pymol remains very performant.

Here is my script...nothing fancy but just a loader and a grouper of PDBs
from a directory.

Any help will be greatly appreciated
Thanks
Hari


import cmd
import os
import pymol
import re

cpi = re.compile("(\d{6})")
pymol.finish_launching()

for root,dirs,files in os.walk("/home/hari/mydownloadedPDbs/"):
for afile in files:
print "FILE",afile
if "pdb" in afile:
try:
cmd.load(os.path.join(root,afile))
except:
print "Problem Loading:", afile

groups = []
for i in cmd.get_names():
try:
group_pool = []

surfdonor = "surfdonor-%s" % i[:10]
surfname = "surf-%s" % i[:10]
cartoon_object = "cartoon-%s" % i[:10]
ligands = "ligands-%s" % i[:10]
solvent = "solvent-%s" %i[:10]

# Create Object for surface and cartoon

cmd.copy(surfdonor,i)
cmd.copy(cartoon_object,i)

# Create selection containing ligands and make them into their own
object
cmd.select(ligands+"sel","organic and " + surfdonor)
cmd.create(ligands,"(%s)"%ligands)
cmd.delete(ligands+"sel")
group_pool.append(ligands)

# Create selection containing solvent
cmd.select(solvent+"sel","resn HOH and " + surfdonor)
cmd.create(solvent,"(%s)" % solvent)
cmd.delete(solvent+"sel")
group_pool.append(solvent)

# Extract ligand object and solvent from surface clone object
cmd.extract(surfname,"%s and not (resn HOH or organic)" % surfdonor)
cmd.delete(surfdonor)
group_pool.append(surfname)
pymol.preset.ligand_cartoon(cartoon_object)
group_pool.append(cartoon_object)
group_pool.append(cartoon_object + "_pol_conts")
group_pool.append(i)
try:
group_name = "%s%s" % (str(i[0:3]),cpi.search(i).groups()[0])
except AttributeError:
group_name = "group"+ i
print group_name
cmd.group(group_name," ".join(group_pool))
except :
print "Problem with" , i
--
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Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

[hari jayaram]

Thanks a tonne Marc .
Turning OFF "Force Full GPU scaling" in the DFP-0 and DFP-1 settings of the
n-vidia-settings panel made all the difference.
Once I  unchecked that box it made the stereo stop flickering and switching
from coming at you to going away from you ( i.e flipping).
Stereo with the nvidia 3dvision and the planar SA2311 is now almost as good
as a CRT.


Thanks Rafael, Malcom Davis, Jason Vertrees and Marc Piuzzi for your help.

Hari



On Thu, Jul 21, 2011 at 10:43 AM, Marc Piuzzi  wrote:

> Hello Hari,
>
> I had some flickering problems when I first tried the stereo mode on an
> Alienware LCD display. There is one option in the Nvidia driver that seems
> to keep the display at 60Hz, it is called "Force Full GPU Scaling". Make
> sure that the option is turned off, otherwise you won't be able to reach
> 120Hz. Anyway, I don't think that a modeline is mandatory.
>
> However, nothing is perfect ... On my display only 2/3 of the screen
> displays a "proper" 3D effect, but it seems to be caused by the technology
> itself. You can still compensate a little by tweaking some stereo options
> (go to the edit all... menu in setting and filter for "stereo"). Adjusting
> the stereo_angle and/or the the stereo_shift might help you.
>
> Hope this helps !
>
> Marc
>
> Le 21 juil. 2011 à 14:05, hari jayaram a écrit :
>
> Thanks Rafael and Jason,
> I upgraded to the latest driver version for Linux i.e 275.19  and now have
>  stereo working with some caveats.
>
> I am running the PLANAR SA2311 at 120 Hz and 1920x1080 resolution and the
> stereo is rather finicky with the nvidia 3dvision setup.
>
> I see a lot of random stereo image flips , i.e suddenly during a rotation
> the parts of the molecule that are going into the plane of the screen, now
> start coming right at you. Also during stereo viewing , the distant parts of
> the molecule seem to not show up as stereo sometimes , i.e I see two helical
> chains , instead of one stereo chain while at the same time the  parts of
> the molecule closest to you are nicely displayed.
> Whenever that happens re-sizing the screen , makes the stereo jerk back
> into sync ..till a few minutes later it goes out of whack again.
>
> Here are what I tried to get the stereo visual to stay stable and behave:
> 1) I tried fiddling with the scroll wheel at the back of the cutoff-pyramid
> emitter box . But didnt see any difference.
> 2) A dark or bright room still had no impact
> 3) I tried turning off the other LCD sitting next to it ..and this didnt
> have any effect
> 4) The emitter position also didnt seem to effect the stability of the
> stero visual
>
> I noticed from the xorg.conf that I am using a metamode 1920x1080_120. Does
> anyone have a modeline for the SA2311W that gives them stable stereo.
> Could it be that the 275.19 driver is worse than other earlier versions
>
> longing for the stable CRT stereo from the past
>
> Hari
> Pymol Version : svn 1.4.1
> Pymol startup:
>
> Detected OpenGL version 2.0 or greater.  Shaders available.
>  Detected GLSL version 3.30.
>  OpenGL graphics engine:
>   GL_VENDOR: NVIDIA Corporation
>   GL_RENDERER: Quadro FX 3700/PCI/SSE2
>   GL_VERSION: 3.3.0 NVIDIA 275.19
>  Adapting to Quadro hardware.
>  Detected 8 CPU cores.  Enabled multithreaded rendering.
>  OpenGL quad-buffer stereo 3D detected and enabled.
>
>
>
>
>
>
>
>
>
> On Wed, Jul 20, 2011 at 2:46 PM, Jason Vertrees <
> jason.vertr...@schrodinger.com> wrote:
>
>> Hi Hari,
>>
>> Please update your driver and ensure that your monitor's refresh rate is
>> 120 Hz.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Wed, Jul 20, 2011 at 12:41 PM, hari jayaram  wrote:
>> > Hi,
>> > I am using the nvidia driver : 195.36.24
>> > OS: Ubuntu Lucid lynx 10.04 , 64 bit
>> > I have a "working" xinerama config with two LCD screens one a regular
>> dell
>> > LCD at 2560x1600 and the other a stereo capable PLANAr LCD at 1920x1080.
>> > Both screens were configured to near working stereo based on the
>> xorg.conf
>> > modified from the one Savvas N. Savvides sent to the newsgroup a while
>> back.
>> > I have the nvidia 3dvision glasses and emmitter. I have the USB and
>> > 3-pin-din to 1/8" stereo connectors going from the Linux computer to the
>> > nvidia cut-off pyramid box. The light on the box with the nvidia logo
>> stays
>> > green ,and the pymol structure on the screen  seems to flicker like
>> working
>> > stereo.
>> > My problem is that the glasses which I turn on by pressing the switch on
>>

Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

[hari jayaram]

Thanks Rafael and Jason,
I upgraded to the latest driver version for Linux i.e 275.19  and now have
 stereo working with some caveats.

I am running the PLANAR SA2311 at 120 Hz and 1920x1080 resolution and the
stereo is rather finicky with the nvidia 3dvision setup.

I see a lot of random stereo image flips , i.e suddenly during a rotation
the parts of the molecule that are going into the plane of the screen, now
start coming right at you. Also during stereo viewing , the distant parts of
the molecule seem to not show up as stereo sometimes , i.e I see two helical
chains , instead of one stereo chain while at the same time the  parts of
the molecule closest to you are nicely displayed.
Whenever that happens re-sizing the screen , makes the stereo jerk back into
sync ..till a few minutes later it goes out of whack again.

Here are what I tried to get the stereo visual to stay stable and behave:
1) I tried fiddling with the scroll wheel at the back of the cutoff-pyramid
emitter box . But didnt see any difference.
2) A dark or bright room still had no impact
3) I tried turning off the other LCD sitting next to it ..and this didnt
have any effect
4) The emitter position also didnt seem to effect the stability of the stero
visual

I noticed from the xorg.conf that I am using a metamode 1920x1080_120. Does
anyone have a modeline for the SA2311W that gives them stable stereo.
Could it be that the 275.19 driver is worse than other earlier versions

longing for the stable CRT stereo from the past

Hari
Pymol Version : svn 1.4.1
Pymol startup:

Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 3.30.
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro FX 3700/PCI/SSE2
  GL_VERSION: 3.3.0 NVIDIA 275.19
 Adapting to Quadro hardware.
 Detected 8 CPU cores.  Enabled multithreaded rendering.
 OpenGL quad-buffer stereo 3D detected and enabled.









On Wed, Jul 20, 2011 at 2:46 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hi Hari,
>
> Please update your driver and ensure that your monitor's refresh rate is
> 120 Hz.
>
> Cheers,
>
> -- Jason
>
> On Wed, Jul 20, 2011 at 12:41 PM, hari jayaram  wrote:
> > Hi,
> > I am using the nvidia driver : 195.36.24
> > OS: Ubuntu Lucid lynx 10.04 , 64 bit
> > I have a "working" xinerama config with two LCD screens one a regular
> dell
> > LCD at 2560x1600 and the other a stereo capable PLANAr LCD at 1920x1080.
> > Both screens were configured to near working stereo based on the
> xorg.conf
> > modified from the one Savvas N. Savvides sent to the newsgroup a while
> back.
> > I have the nvidia 3dvision glasses and emmitter. I have the USB and
> > 3-pin-din to 1/8" stereo connectors going from the Linux computer to the
> > nvidia cut-off pyramid box. The light on the box with the nvidia logo
> stays
> > green ,and the pymol structure on the screen  seems to flicker like
> working
> > stereo.
> > My problem is that the glasses which I turn on by pressing the switch on
> the
> > ear-piece also have a green light, but the shutters dont seem to flicker
> and
> > I consequently dont see stereo. Pymol does echo that a stereo capable
> > monitor is present and enables stereo on startup.
> > What am I doing wrong. I tried both "Option" "3" and "Option" "10" in
> > devices section. But in the end I still dont have my glasses "wake up".
> > Sorry to plague the bb with this stereo post. I am hoping I am 90% there
> to
> > getting working stereo.
> > My Xinerama xorg.conf file is pasted here
> > Thanks for your help.
> > Hari
> >
> > # nvidia-settings: X configuration file generated by nvidia-settings
> > # nvidia-settings:  version 1.0  (buildd@yellow)  Fri Apr  9 11:51:21
> UTC
> > 2010
> > # nvidia-xconfig: X configuration file generated by nvidia-xconfig
> > # nvidia-xconfig:  version 1.0  (buildmeister@builder58)  Fri Mar 12
> > 02:12:40 PST 2010
> > # Device Config 1
> > # Same device but diff device id
> > # DUPLIACTES BECAUSE FILE APPENDED BY NVIDIA_SETTINGS IN UBUNTU
> > Section "ServerLayout"
> > # Removed Option "Xinerama" "1"
> > # Removed Option "Xinerama" "0"
> > Identifier "Dual Layout"
> > Screen  0  "Screen0" 0 0
> > Screen  1  "Screen1" RightOf "Screen0"
> > InputDevice"Keyboard0" "CoreKeyboard"
> > InputDevice"Mouse0" "CorePointer"
> > InputDevice"Mouse0" "SendCoreEvents"
> > Option "Clone" "off&qu

[PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

[hari jayaram]

Hi,
I am using the nvidia driver : 195.36.24
OS: Ubuntu Lucid lynx 10.04 , 64 bit

I have a "working" xinerama config with two LCD screens one a regular dell
LCD at 2560x1600 and the other a stereo capable PLANAr LCD at 1920x1080.
Both screens were configured to near working stereo based on the xorg.conf
modified from the one Savvas N. Savvides sent to the newsgroup a while back.

I have the nvidia 3dvision glasses and emmitter. I have the USB and
3-pin-din to 1/8" stereo connectors going from the Linux computer to the
nvidia cut-off pyramid box. The light on the box with the nvidia logo stays
green ,and the pymol structure on the screen  seems to flicker like working
stereo.

My problem is that the glasses which I turn on by pressing the switch on the
ear-piece also have a green light, but the shutters dont seem to flicker and
I consequently dont see stereo. Pymol does echo that a stereo capable
monitor is present and enables stereo on startup.

What am I doing wrong. I tried both "Option" "3" and "Option" "10" in
devices section. But in the end I still dont have my glasses "wake up".
Sorry to plague the bb with this stereo post. I am hoping I am 90% there to
getting working stereo.

My Xinerama xorg.conf file is pasted here
Thanks for your help.
Hari


# nvidia-settings: X configuration file generated by nvidia-settings
# nvidia-settings:  version 1.0  (buildd@yellow)  Fri Apr  9 11:51:21 UTC
2010

# nvidia-xconfig: X configuration file generated by nvidia-xconfig
# nvidia-xconfig:  version 1.0  (buildmeister@builder58)  Fri Mar 12
02:12:40 PST 2010
# Device Config 1
# Same device but diff device id
# DUPLIACTES BECAUSE FILE APPENDED BY NVIDIA_SETTINGS IN UBUNTU

Section "ServerLayout"

# Removed Option "Xinerama" "1"
# Removed Option "Xinerama" "0"
Identifier "Dual Layout"
Screen  0  "Screen0" 0 0
Screen  1  "Screen1" RightOf "Screen0"
InputDevice"Keyboard0" "CoreKeyboard"
InputDevice"Mouse0" "CorePointer"
InputDevice"Mouse0" "SendCoreEvents"
Option "Clone" "off"
Option "Xinerama" "1"
EndSection

Section "Files"
EndSection

Section "InputDevice"

# generated from default
Identifier "Mouse0"
Driver "mouse"
Option "Protocol" "auto"
Option "Device" "/dev/psaux"
Option "Emulate3Buttons" "no"
Option "ZAxisMapping" "4 5"
EndSection

Section "InputDevice"

# generated from default
Identifier "Keyboard0"
Driver "kbd"
EndSection

Section "Modes"
Identifier "Modes[0]"
ModeLine "2560x1600" 268.00 2560 2608 2640 2720 1600 1603 1609 1646
+hsync +vsync
EndSection

Section "Modes"
Identifier "Modes[1]"
ModeLine "1920x1080@60" 148.50 1920 2008 2052 2200 1080 1084 1089
1125 +hsync +vsync
EndSection

Section "Monitor"
Identifier "Monitor[0]"
VendorName "Unknown"
ModelName  "Dell"
UseModes   "Modes[0]"
HorizSync   29.0 - 113.0
VertRefresh 49.0 - 86.0
Option "DPMS"
EndSection

Section "Monitor"
Identifier "Monitor[1]"
VendorName "Unknown"
ModelName  "Dell"
UseModes   "Modes[1]"
HorizSync   30.0 - 140.0
VertRefresh 56.0 - 120.0
Option "DPMS"
EndSection

Section "Monitor"
Identifier "Monitor0"
VendorName "Unknown"
ModelName  "Dell"
HorizSync   29.0 - 113.0
VertRefresh 49.0 - 86.0
EndSection

Section "Monitor"
Identifier "Monitor1"
VendorName "Unknown"
ModelName  "PLN SA2311W"
HorizSync   30.0 - 140.0
VertRefresh 56.0 - 120.0
EndSection

Section "Device"
Identifier "Device0"
Driver "nvidia"
VendorName "NVIDIA Corporation"
BoardName  "Quadro FX 3700"
Option "Stereo" "10"
#Monitor"Monitor0"
Option "XineramaStereoFlipping" "1"
Option "NoPowerConnectorCheck"
Option "AllowDFPStereo" "1"
Option "UBB" "1"
BusID  "PCI:3:0:0"
Screen  0
EndSection

Section "Device"
Identifier "Device1"
Driver "nvidia"
VendorName "NVIDIA Corporation"
BoardName  "Quadro FX 3700"
Option "Stereo" "10"
#Monitor"Monitor1"
Option "XineramaStereoFlipping" "1"
Option "NoPowerConnectorCheck"
Option "AllowDFPStereo" "1"
Option "UBB" "1"
BusID  "PCI:3:0:0"
Screen  1
EndSection

Section "Screen"

#BusID  "PCI:3:0:0"
Identifier "Screen[0]"
Device "Device0"
Monitor"Monitor[0]"
DefaultDepth24
Option "Stereo" "10"
SubSection "Display"
Viewport0 0
Depth   24
Modes  "2560x1600"
EndSubSection
EndSection

Section "Screen"
Identifier "Screen[1]"
Device "Device0"
Monitor"Mon

Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

[hari jayaram]

Hi Jason
Thanks for your detailed reply and for pointers on the iterate command
for mapping the bfactors.

I think I understand whats going on and there was a fault in my
understanding i.e I was wrong.

Even though my script puts the conservation record as b-factor to all
atoms of any given residue .
If I say color surface by spectrum b-factors *.ca , pymol colors only
the calpha atoms by the range of b-factors ( 0 to 11). The remainder
non-calpha atom surfaces still have their default cpk based color.

I conveniently assumed the command  color surface by spectrum
b-factors *.ca would have colored all the residues in the surface
representation by the value of the b-factor for their corresponding
c-alpha atom.

In my case when I then used  color by bfactors ( all atoms in object
by implication). The hetatoms were getting dragged into the definition
for all atoms and skewing the range.

I was wrong in that the range was misreported.
Thanks for the clarification.
hari






On Tue, Jul 5, 2011 at 2:42 PM, Jason Vertrees
 wrote:
> Hi Hari,
>
>> I am using svn pymol rev 3953 on a 64 bit Ubuntu box.
>> I have a custom script that maps extent of conservation into the
>> b-factor record of a pdb for visualization.
>>
>> I noticed a small feature in pymol
>>
>> My protein atoms in chain A have b-factors from 0 to 11 to indicate
>> conservation extent , . The Heteroatoms , in this pdb also in  chain A
>> have their ususal b-factors in the 60s.
>> Now if I ask for the surface to be colored by bfactors spectrum for *.ca.
>>
>> Pymol echoes
>>
>>
>>  Spectrum: range ( 0.0 to 11.0).
>
> We can quickly test the ranges to ensure PyMOL is acting appropriately:
>
> withHET, withoutHET = [], []
> iterate *, withHET.append(b)
> iterate n. CA, withoutHET.append(b)
>
> # print range w/HET
>
> print min(withHET), max(withHET)
>
> # print range wout/HET
>
> print min(withoutHET), max(withoutHET)
>
> and we can color by:
>
> # color by spectrum
>
> spectrum b, rainbow, n. CA
>
>
> The problem I think you're having is that the colors don't expand to
> the surface as you want.  I created a script awhile back to do just
> this; see http://www.pymolwiki.org/index.php/Expand_To_Surface.
>
> Please let us know if this helps.
>
> Cheers,
>
> -- Jason
>
>>
>> But the colors on the surface clearly also include the heteroatoms
>> .which are all above 55 and in chain A.
>> So the whole protein surface ends up blue since majority of values are below 
>> 11.
>>
>> I did get around this by removing the heteroatoms to a different chain
>> . But it seems there is a discrepancy between what is echoed to the
>> stdout and the color-range pymol displays on the screen in this
>> instance.
>>
>> Hope this is not some setting that I am messing up on my side
>>
>> Thanks
>> hari
>>
>> --
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> ___
>> 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
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>

--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security 
threats, fraudulent activity, and more. Splunk takes this data and makes 
sense of it. IT sense. And common sense.
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[PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

[hari jayaram]

Hi,
I am using svn pymol rev 3953 on a 64 bit Ubuntu box.
I have a custom script that maps extent of conservation into the
b-factor record of a pdb for visualization.

I noticed a small feature in pymol

My protein atoms in chain A have b-factors from 0 to 11 to indicate
conservation extent , . The Heteroatoms , in this pdb also in  chain A
have their ususal b-factors in the 60s.
Now if I ask for the surface to be colored by bfactors spectrum for *.ca.

Pymol echoes


 Spectrum: range ( 0.0 to 11.0).


But the colors on the surface clearly also include the heteroatoms
.which are all above 55 and in chain A.
So the whole protein surface ends up blue since majority of values are below 11.

I did get around this by removing the heteroatoms to a different chain
. But it seems there is a discrepancy between what is echoed to the
stdout and the color-range pymol displays on the screen in this
instance.

Hope this is not some setting that I am messing up on my side

Thanks
hari

--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security 
threats, fraudulent activity, and more. Splunk takes this data and makes 
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

[hari jayaram]

Hi Jason,
Thanks for your reply. This was indeed a driver problem . Ubuntu had pushed
a natty kernel 
headers
to
lucid users by mistake and that update broke my nvidia 195.36.24 x86_64
driver. To fix it , In desperation,  I updated to the 270.xx series nvidia
driver from the nvidia website which I then used to compile and run pymol .
That configuration gives the errors that I mentioned in my  email.

Coot and the other opengl programs worked well when I was running the 270.xx
series driver , but pymol was compiling but giving the "bad Request" errors.
This is probably related to the the 270.xx problems that other users wrote
in about.

Regardless, I reverted to the 195.36.24 series driver , re-ran the distutils
build and now have pymol 1.4.1 running on my machine


Thanks for your help.

Hari




I have since

On Wed, Jun 8, 2011 at 5:05 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:

> Hari,
>
> >  Hit ESC anytime to toggle between text and graphics.
> >  Detected OpenGL version 2.0 or greater.  Shaders available.
> > X Error of failed request:  BadRequest (invalid request code or no such
> > operation)
> >   Major opcode of failed request:  128 (GLX)
> >   Minor opcode of failed request:  169 ()
> >   Serial number of failed request:  46
> >   Current serial number in output stream:  46
>
> This sounds like a driver problem.  Can you run the 'glxgears'
> program?  Does it give the same error?  Do you have the latest driver
> installed?
>
> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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[PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

[hari jayaram]

Hi I just build the svn build of pymol 3951 on 64 bit Ubuntu Lucid  .
I first had to  installing libglew and libglew-dev after which the build
progressed fine , but when I run the built pymol I get the following errors
( below)  and pymol does not launch.

I tried with a clean repo checked out from svn and get the same error. I
also tried the makefile route but get a cetypes.h include error.
I know the distutils way is the recommended approach..

Any help to resurrect my pymol will be greatly appreciated.

Thanks
Hari

 hari@hari:~/pymol-read-only/trunk/pymol$ ./pymol
 PyMOL(TM) Molecular Graphics System, Version 1.4.1.
 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.

 Detected OpenGL version 2.0 or greater.  Shaders available.
X Error of failed request:  BadRequest (invalid request code or no such
operation)
  Major opcode of failed request:  128 (GLX)
  Minor opcode of failed request:  169 ()
  Serial number of failed request:  46
  Current serial number in output stream:  46
 PyMOL: abrupt program termination.

Thanks
hari
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Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

[hari jayaram]

Hi Jason ,
Thanks to your example I figured it out and it seems like there is
small problem with the status message text even when it fails.

So if I had a created object obj01

This works:
set cartoon_cylindrical_helices , 1, obj01

This does not work:
set cartoon_cylindrical_helices , 1 , (obj01)

In both cases pymol echoes a
"cartoon_cylindrical_helices set for 222 atoms in object "obj01" "
in the status text. The only difference is the parentheses around the
object.
I guess the correct syntax is to not have the parentheses around the
object name.

Thanks for all your help
Hari



On Thu, Jun 17, 2010 at 8:14 PM, hari jayaram  wrote:
> Hi Jason , and Nat ,
> I just tried it on my mac laptop and the set
> cartoon_cylindrical_helices  works just as it should.
>
> Followng that I tried it on two separate ubuntu 64 bit boxes , running
> pymol version 1.2 and 1.3 and  python version 2.5 and 2.6 , both of
> them dont do the right thing i.e allow the property to be set only for
> the object and instead propagate the property to all objects.
>
> I must admit that both of ubuntu builds were compiled by me , but
> everything is working just fine , other than this property setting as
> far as I know.
>
> Are your or anyone else seeing this  on their machine.
> Thanks
>
> Hari
>
>
>
> On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees
>  wrote:
>> Hi Hari,
>>
>> The following,
>>
>> fetch 1cll 1ggz, async=0
>> set cartoon_cylindrical_helices, 1, 1cll
>> as cartoon
>>
>> works just fine for me.
>>
>> Can you send me your PSE or pdb files?  Are you setting anything else?
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram  wrote:
>>> I am trying to show a molecule in ribbon representation , where all
>>> the helices except one helix are in ribbon form and a solitary helix
>>> is shown as a  cylinder.
>>>
>>> Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01)
>>> Followed by show cartoon , (obj01).
>>> Does not show only (obj01) as a cylinder
>>>
>>> In my tests obj01 is the object created from a selection and then the
>>> property set for that object. But it seems that this does not just
>>> create a cylindrical helix for just that object.
>>>
>>> For some reason the cartoon_cylindrical_helices property is not
>>> handled the way other set properties are and that the object alone is
>>> not allowed to have a different value than the rest of the molecules.
>>>
>>> Thanks for your help in advance
>>>
>>> Hari
>>>
>>> --
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> ___
>>> 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
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>

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Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

[hari jayaram]

Hi Jason , and Nat ,
I just tried it on my mac laptop and the set
cartoon_cylindrical_helices  works just as it should.

Followng that I tried it on two separate ubuntu 64 bit boxes , running
pymol version 1.2 and 1.3 and  python version 2.5 and 2.6 , both of
them dont do the right thing i.e allow the property to be set only for
the object and instead propagate the property to all objects.

I must admit that both of ubuntu builds were compiled by me , but
everything is working just fine , other than this property setting as
far as I know.

Are your or anyone else seeing this  on their machine.
Thanks

Hari



On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees
 wrote:
> Hi Hari,
>
> The following,
>
> fetch 1cll 1ggz, async=0
> set cartoon_cylindrical_helices, 1, 1cll
> as cartoon
>
> works just fine for me.
>
> Can you send me your PSE or pdb files?  Are you setting anything else?
>
> Cheers,
>
> -- Jason
>
> On Thu, Jun 17, 2010 at 6:41 PM, hari jayaram  wrote:
>> I am trying to show a molecule in ribbon representation , where all
>> the helices except one helix are in ribbon form and a solitary helix
>> is shown as a  cylinder.
>>
>> Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01)
>> Followed by show cartoon , (obj01).
>> Does not show only (obj01) as a cylinder
>>
>> In my tests obj01 is the object created from a selection and then the
>> property set for that object. But it seems that this does not just
>> create a cylindrical helix for just that object.
>>
>> For some reason the cartoon_cylindrical_helices property is not
>> handled the way other set properties are and that the object alone is
>> not allowed to have a different value than the rest of the molecules.
>>
>> Thanks for your help in advance
>>
>> Hari
>>
>> --
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> ___
>> 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
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>

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[PyMOL] Possible bug in set cartoon_cylindrical_helices

[hari jayaram]

I am trying to show a molecule in ribbon representation , where all
the helices except one helix are in ribbon form and a solitary helix
is shown as a  cylinder.

Can someone confirm that set cartoon_cylindrical_helices , 1 , (obj01)
Followed by show cartoon , (obj01).
Does not show only (obj01) as a cylinder

In my tests obj01 is the object created from a selection and then the
property set for that object. But it seems that this does not just
create a cylindrical helix for just that object.

For some reason the cartoon_cylindrical_helices property is not
handled the way other set properties are and that the object alone is
not allowed to have a different value than the rest of the molecules.

Thanks for your help in advance

Hari

--
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[PyMOL] Lucid Lynx Ubuntu 10.04 segmentation fault on Help-About Pymol : plugins dont work either

[hari jayaram]

Hi I am using a subversion build of pymol built using setuptools i,e
"python setup.py install" on 64 bit ubuntu Lucid Lynx 10.04.

I can use the main program without any problems , but when I try to
install and run the apbs plugin , pymol segmentation faults
immediately.

Incidentally , doing a Help- About Pymol also crashes Pymol instantly

This seems related to the Tkinter bug mentioned a few times before on
this group.

I am pasting a catchsegv for the pymol session here

Any ideas on how to resolve this
Thanks
Hari



h...@hari:~/apbs$ catchsegv pymol
 PyMOL(TM) Molecular Graphics System, Version 1.2r3pre.
 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.

 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro FX 3700/PCI/SSE2
  GL_VERSION: 3.2.0 NVIDIA 195.36.15
 Adapting to Quadro hardware.
 Detected 8 CPU cores.  Enabled multithreaded rendering.
Segmentation fault
*** Segmentation fault
Register dump:

 RAX:    RBX: 7f0a7c05e8b8   RCX: 7f0a7c05e010
 RDX: 072001ea   RSI: 07200192   RDI: 7f0a7c05e8b8
 RBP: 07200192   R8 : 7f0a7c04c388   R9 : 33ce
 R10: 0001   R11: 7f0a88105be0   R12: 7f0a7c02d800
 R13: 0002   R14: 7f0a82218e40   R15: 
 RSP: 7f0a80a68708

 RIP: 7f0a81f89ab8   EFLAGS: 00010202

 CS: 0033   FS:    GS: 

 Trap: 000e   Error: 0004   OldMask:    CR2: 07200192

 FPUCW: 037f   FPUSW: 0020   TAG: 
 RIP: 004e7f0a   RDP: 80a69d98

 ST(0)  000d   ST(1)  0033
 ST(2)  0018   ST(3)  0003
 ST(4)     ST(5)  acd2
 ST(6)  acd2   ST(7)  
 mxcsr: 1fa3
 XMM0:  ff00 XMM1:  ff00
 XMM2:  ff00 XMM3:  ff00
 XMM4:  ff00 XMM5:  ff00
 XMM6:  ff00 XMM7:  ff00
 XMM8:  ff00 XMM9:  ff00
 XMM10: ff00 XMM11: ff00
 XMM12: ff00 XMM13: ff00
 XMM14: ff00 XMM15: ff00

Backtrace:
/usr/lib/libtcl8.5.so.0(+0x80ab8)[0x7f0a81f89ab8]
/usr/lib/libtcl8.5.so.0(Tcl_CreateHashEntry+0x59)[0x7f0a81f89259]
/usr/lib/libBLT.2.so(Blt_MakeTransparentWindowExist+0xc2)[0x7f0a7b334f12]
/usr/lib/libBLT.2.so(+0x9003f)[0x7f0a7b2d703f]
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f0a81f3562f]
/usr/lib/libtcl8.5.so.0(+0x2e111)[0x7f0a81f37111]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f0a81f37223]
/usr/lib/python2.6/lib-dynload/_tkinter.so(+0x97b1)[0x7f0a828a67b1]
/usr/bin/python(PyEval_EvalFrameEx+0x516e)[0x4a7c5e]
/usr/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/usr/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809]
/usr/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550]
/usr/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/usr/bin/python(PyEval_EvalFrameEx+0x4d19)[0x4a7809]
/usr/bin/python(PyEval_EvalFrameEx+0x5a60)[0x4a8550]
/usr/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/usr/bin/python2
/usr/bin/python(PyObject_Call+0x47)[0x41f0c7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x4a1b03]
/usr/bin/python[0x4a154f]
/usr/bin/python(PyEval_EvalFrameEx+0x516e)[0x4a7c5e]
/usr/bin/python(PyEval_EvalCodeEx+0x911)[0x4a9671]
/usr/bin/python2
/usr/bin/python(PyObject_Call+0x47)[0x41f0c7]
/usr/bin/python2
/usr/bin/python(PyObject_Call+0x47)[0x41f0c7]
/usr/bin/python(PyEval_CallObjectWithKeywords+0x43)[0x4a1b03]
/usr/lib/python2.6/lib-dynload/_tkinter.so(+0x70d5)[0x7f0a828a40d5]
/usr/lib/libtcl8.5.so.0(TclInvokeStringCommand+0x7f)[0x7f0a81f3562f]
/usr/lib/libtcl8.5.so.0(+0x2e111)[0x7f0a81f37111]
/usr/lib/libtcl8.5.so.0(+0x72d26)[0x7f0a81f7bd26]
/usr/lib/libtcl8.5.so.0(+0x71169)[0x7f0a81f7a169]
/usr/lib/libtcl8.5.so.0(TclEvalObjEx+0x85)[0x7f0a81f38685]
/usr/lib/libtk8.5.so.0(+0x6d859)[0x7f0a8228b859]
/usr/lib/libtk8.5.so.0(+0x6cac1)[0x7f0a8228aac1]
/usr/lib/libtcl8.5.so.0(+0x2e111)[0x7f0a81f37111]
/usr/lib/libtcl8.5.so.0(Tcl_EvalObjv+0x43)[0x7f0a81f37223]
/usr/lib/libtcl8

[PyMOL] psw full screen , on screen menu and see typed commands in full screen mode

[hari jayaram]

Hi
I can get the animations launched from inside powerpoint to show up
and go between my stored scenes. Is there some way to toggle on the
internal_gui display from this full screen mode.

I know  the command
set internal_gui,1

But when I  type it on the full screen molecule, nothing happens.
Other commands typed without seeing what I am typing - do the right thing

Also is there some way to see typed commands in the full screen mode .

Thanks

Hari

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Re: [PyMOL] compiled Pymol on MacOSX , The Pmw menu window does not open properly and Python Icon bouncing on dock

[hari jayaram]

Hi David,
I agree fink makes it easy. But, I am trying to avoid fink , only because I
want to stay with the bleeding edge subversion build. Not to mention the
fact that my disk is always near to full and I can use every gig I can save.

Hari


On Wed, Mar 24, 2010 at 12:12 PM, David Hall  wrote:

> Do you know about the fink builds of pymol?
> http://pdb.finkproject.org/pdb/package.php/pymol-py26  .  You might
> have more success modifying that package to pull the source from
> subversion.
>
> -David
>
> On Wed, Mar 24, 2010 at 11:48 AM, hari jayaram  wrote:
> > Hi ,
> > Because I wanted to use some of the Python API commands in scripts I
> wanted
> > to install a distutils build of Pymol on my Snow Leopard System running
> > 10.6.2 .
> > I am using the svn version  3897.
> > After I installed Pmw and added the fontconfig.h containing directory to
> my
> > INCLUDE path and added other dylibs from /usr/X11R6/lib  to my include
> path
> > , I finally got the build process to complete fine and I was able to get
> the
> > pymol dark background cmd window to popup just fine . However the Pmw
> window
> > did not appear and the system either crashed or the Python icon kept
> > bouncing up and down and a crummily ghost-like Pmw window appeared
> briefly.
> > When it did crash it gave me the error:
> > Tk_MacOSXSetupTkNotifier: first [load] of TkAqua has to occur in the main
> > thread!
> > I know this is all because the cmd window is already up and there cannot
> be
> > two GUI threads going and have seen some posts from Bill Scott about this
> > issue , but can anyone help me troubleshoot this build.
> > I want to start using the subversion builds instead of the MacPymol.App
> and
> > am sure I can get over this building problem.
> > Your help will be greatly appreciated.
> > Thanks
> > Hari
> >
> >
> --
> > Download Intel® Parallel Studio Eval
> > Try the new software tools for yourself. Speed compiling, find bugs
> > proactively, and fine-tune applications for parallel performance.
> > See why Intel Parallel Studio got high marks during beta.
> > http://p.sf.net/sfu/intel-sw-dev
> > ___
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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> >
>
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[PyMOL] compiled Pymol on MacOSX , The Pmw menu window does not open properly and Python Icon bouncing on dock

[hari jayaram]

Hi ,
Because I wanted to use some of the Python API commands in scripts I wanted
to install a distutils build of Pymol on my Snow Leopard System running
10.6.2 .
I am using the svn version  3897.

After I installed Pmw and added the fontconfig.h containing directory to my
INCLUDE path and added other dylibs from /usr/X11R6/lib  to my include path
, I finally got the build process to complete fine and I was able to get the
pymol dark background cmd window to popup just fine . However the Pmw window
did not appear and the system either crashed or the Python icon kept
bouncing up and down and a crummily ghost-like Pmw window appeared briefly.

When it did crash it gave me the error:

Tk_MacOSXSetupTkNotifier: first [load] of TkAqua has to occur in the main
thread!

I know this is all because the cmd window is already up and there cannot be
two GUI threads going and have seen some posts from Bill Scott about this
issue , but can anyone help me troubleshoot this build.

I want to start using the subversion builds instead of the MacPymol.App and
am sure I can get over this building problem.
Your help will be greatly appreciated.

Thanks
Hari
--
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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Re: [PyMOL] getting Residue environment distances and residue-residue distances programatically

[hari jayaram]

Thanks a tonne David and Nathaniel,
The script in that post
<http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07745.html>is
exactly what I was looking for.

I may also give cctbx.python a try , If I remember right phenix, cns and
xplor use a similar kind of selection syntax which as Nat said is not too
different from pymol given its roots.

Thanks again
Hari


On Tue, Mar 23, 2010 at 4:03 PM, David Hall  wrote:
>
> PyMol doesn't provide programmatic access to actual bond objects.
> Instead, you have to do what was suggested 5 days ago:
>
>
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07745.html
>
> -David
>
> On Tue, Mar 23, 2010 at 3:48 PM, hari jayaram  wrote:
> > Hi
> > I want to write a python/pymol  script that will give me residue
-residue
> > distances within a pdb file programmatically
> > I know that within pymol I can get a distance object using
> > select r55 , chain A and resi 55
> > select r 22 , chain A and resi 22
> > distance (r55) ,(r22)
> > This creates the dist01 object . If I wanted to do this using a python
> > script and get a pretty print of all the distances in the distance
object ,
> > how do I do that?
> > Also pointers to other python toolkits that can allow me to make such
> > measurements outside pymol will be greatly appreciated.
> > Thanks for your help
> > Hari
> >
> >
> >
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[PyMOL] getting Residue environment distances and residue-residue distances programatically

[hari jayaram]

Hi
I want to write a python/pymol  script that will give me residue -residue
distances within a pdb file programmatically

I know that within pymol I can get a distance object using

select r55 , chain A and resi 55
select r 22 , chain A and resi 22

distance (r55) ,(r22)

This creates the dist01 object . If I wanted to do this using a python
script and get a pretty print of all the distances in the distance object ,
how do I do that?
Also pointers to other python toolkits that can allow me to make such
measurements outside pymol will be greatly appreciated.

Thanks for your help
Hari
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Re: [PyMOL] subversion 3897 compile error in Cmd.c

[hari jayaram]

Sorry for crying wolf. Everything is working fine with svn 3897  . After
Justins email I checked that my system python was suddenly set to a
different python and things were probably not getting linked up correctly
during building. Now I do get :

1) distutils builds fine
2) make , make install also builds fine

Thanks again
Hari

On Fri, Feb 26, 2010 at 12:03 PM, Justin Lecher wrote:

> Hi Hari,
>
> the distutils based build is fine.
>
> justin
>
>
>
> --
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[PyMOL] subversion 3897 compile error in Cmd.c

[hari jayaram]

Hi ,
I generally track trunk on pymol , i.e I keep my Ubuntu 64 bit linux box
updated with the latest subversion build.
While compiling revision 3897.
I had an error during the build while compiling Cmd.h saying it could not
find "ce_types.h"

That file does exist in
trunk/pymol/modules/cealign/src/ce_types.h
And copying  it to trunk/pymol/layer4/ does make it compile fully , but then
the built executable fails to launch with another  error ( see below)
So I am just wondering if anyone else is seeing this . Thanks for your help.

Hari


# Initial error without include of ce_types.h

Cmd.c:87:21: error: ce_types.h: No such file or directory
Cmd.c: In function ‘CmdCEAlign’:
Cmd.c:8506: error: ‘pcePoint’ undeclared (first use in this function)
Cmd.c:8506: error: (Each undeclared identifier is reported only once
Cmd.c:8506: error: for each function it appears in.)
Cmd.c:8506: error: expected ‘;’ before ‘coordsA’
Cmd.c:8507: error: ‘pathCache’ undeclared (first use in this function)
Cmd.c:8507: error: expected ‘;’ before ‘paths’
Cmd.c:8540: error: ‘coordsA’ undeclared (first use in this function)
Cmd.c:8540: error: expected ‘;’ before ‘getCoords’
Cmd.c:8541: error: ‘coordsB’ undeclared (first use in this function)
Cmd.c:8541: error: expected ‘;’ before ‘getCoords’
Cmd.c:8544: warning: cast to pointer from integer of different size
Cmd.c:8545: warning: cast to pointer from integer of different size
Cmd.c:8548: warning: cast to pointer from integer of different size
Cmd.c:8554: error: ‘paths’ undeclared (first use in this function)
Cmd.c:8554: error: expected ‘;’ before ‘findPath’
Cmd.c:8557: warning: cast to pointer from integer of different size
make[2]: *** [Cmd.lo] Error 1
make[2]: Leaving directory `/home/hari/pymol/trunk/pymol/layer4'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/hari/pymol/trunk/pymol'
make: *** [all] Error 2


# Error on forced compiling after copying ce_types.h into include path
Traceback (most recent call last):
  File "/home/hari/pymol/trunk/pymol/modules/launch_pymol.py", line 32, in

import pymol
  File "/home/hari/pymol/trunk/pymol/modules/pymol/__init__.py", line 472,
in 
import _cmd
ImportError: /home/hari/pymol/trunk/pymol/modules/pymol/_cmd.so: undefined
symbol: findBest
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Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...

[hari jayaram]

Hi
I am wondering if there is a linux nvidia driver update or any other
hack that allows Crystal Eyes 3 stereo products to  work with the LCD
120Hz flat panel monitors.

I should have read Warrens warning post  (Dated Jan 23 , 2009 [ccp4bb]
Caution - 120 Hz LCDs: Not CRT killers yet) , before purchasing the
Viewsonic VX2265wm 120Hz LCD. But my CRT died last week and since I
was addicted to pymol/coot-in stereo ( with Crystal Eyes 3 ) ,  I
rushed out and bought this 120 Hz LCD monitor.

Of course things dont work . And I am wondering if there is any update
from nvidia or any other workaround  that allows me to get stereo on
this setup.

Monitor : Viewsonic FuHzion VX2265wm 120Hz
Graphics card: Quadro FX 4600
OS: Ubuntu Linux X86_64 - Hardy Heron 8.04
Stereo glasses: Crystal Eyes 3 with 3pin mini din connector


Thanks for your help in advance
Hari Jayaram
Brandeis University



On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano  wrote:
>
> Donnie,
>
> This tripped me up for a while too, but I think the stereo DIN is an
> output (for projector, & Z-screens, etc.) not an input.  Suffice it to
> say that the nVidia USB dongle does not work (in my hands, with or
> without USB power) as a VESA-based emitter the way we apparently both
> hoped it would!
>
> Cheers,
> Warren
>
> > -Original Message-
> > From: Donnie Berkholz [mailto:dberkh...@gentoo.org]
> > Sent: Tuesday, February 10, 2009 9:49 AM
> > To: Warren DeLano
> > Cc: PyMOL-users@lists.sourceforge.net
> > Subject: Re: [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...
> >
> > On 23:26 Thu 22 Jan     , Warren DeLano wrote:
> > > I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle
> > > today ($599 for a 120 Hz LCD display with one pair of glasses).
> >
> > > I was very much hoping that this new display would nevertheless also
> > > work with existing nVidia Quadro-based Mac or Linux systems with
> > > existing emitters and glasses running existing OpenGL software.
> Sadly,
> > > this does not seem to be the case due at least in part to the fact
> that
> > > the phase of the sync signal coming out of the Quadro card does not
> > > match the update phase of the LCD display.  In addition, light from
> the
> > > display itself seems to corrupt the sync signal for StereoGraphics
> > > glasses.
> >
> > Hi Warren,
> >
> > Did you happen to try the new glasses + emitter with a CRT? I am
> > particularly curious whether this works on Linux, or whether it needs
> > some sort of USB driver stubs so that Linux knows what to do with
> these
> > devices.
> >
> > It comes with a stereo-DIN cable so it seems like it could work,
> > provided the emitter can get power via USB and the glasses can charge
> > via USB.
> >
> > If the new glasses can work with a CRT, then at least we could buy
> > stereo bundles now and use all of the parts of them in some sort of
> > Frankenstein setup pending support for LCD stereo.
> >
> > --
> > Thanks,
> > Donnie
> >
> > Donnie Berkholz
> > Developer, Gentoo Linux
> > Blog: http://dberkholz.wordpress.com
>
>
>
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[PyMOL] update mesh level to custom value after deleting map object

[hari jayaram]

H
I have an old pymol session file .
I have a mesh object displayed whose level I can manipulate in predetermined
ways using the Action-Level-menu. I however want to pick a level different
from the menu options provided .

A further complication is that I have deleted the original map object and
want to avoid going looking for it.

Is there a way to pick a level for a mesh object that is not pre-programmed
into the Action menu .

Thanks
Hari
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Re: [PyMOL] launch pymol from inside an IDLE ( python-ide)

[hari jayaram]

Hey Thanks a tonne Alan
After your tip , I got fink IDLE to load pymol without any problem . I also
got my home gentoo linux python 2.5 and idle to load pymol the same way.
Now I have full code completion to write up my pymol scripts if I idle
correctly.

On an academic note, Just wondering why the Mac idle2.5 goofs up. I read
something about idle running on a tkinter thread and pymol wanting to do the
same thing. Anyways I guess the solution to the problem is to install fink
on all macs in cases where I want to use IDLE for pymol script writing.

Thanks again
Hari Jayaram


On Tue, Jun 10, 2008 at 2:47 AM, Alan  wrote:

> Hi,
> Instead of using Mac IDLE, use Fink IDLE:
>  which idle2.5
> /sw/bin/idle2.5
>
> It works!
>
> Cheers,
> Alan
>
> On Tue, Jun 10, 2008 at 1:25 AM, <
> pymol-users-requ...@lists.sourceforge.net> wrote:
>
>
>> Date: Wed, 4 Jun 2008 11:24:16 -0400
>> From: "hari jayaram" 
>> Subject: [PyMOL] launch pymol from inside an IDLE ( python-ide)
>>interactive shell ?
>> To: pymol-users@lists.sourceforge.net
>> Message-ID:
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi I am trying to use python from inside of the idle (IDLE) IDE that is
>> part
>> of the MacPython 2.5.2 additional packages as IDLE.app.
>> The reason I want to do this is because I really want to get an IDE (
>> integrated development environment ) with good code completion on all
>> modules including maybe pymol.
>>
>> In any case when I do the following (see attached
>> png<http://code-itch.s3.amazonaws.com/images/idle_pymol_how.jpg>
>> )
>>
>> 1) Start IDLE and then in the IDLE shell I do
>> 2)  Import my fink python after adding it to my path
>>
>>import sys
>>sys.path.append("/sw/lib/pymol-py25/modules")
>>import pymol
>>
>> After that command I see that the idle Python shell waits for a little bit
>> and then I see  =restart .and no pymol window appears
>> Also when I try running pymol.finish_launching()
>>
>> It says pymol is not defined.
>>
>> I have tried reading some of the posts about how the import pymol method
>> is
>> the least supported method for launching pymol. I should add that on my
>> setup i.e Leopard 10.5.2 with fink pymol-py25 the above approach works
>> from
>> a standalone script as well as from a python interactive shell from
>> terminal.app or Item.app . Sadly both of these dont have popup code
>> completion..
>>
>> But I was wondering if there is some way to have my cake and eat it too
>> and
>> interact with pymol from within an IDLE shell window.
>>
>> Hari Jayaram
>>
> --
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> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
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>
>

[PyMOL] launch pymol from inside an IDLE ( python-ide) interactive shell ?

[hari jayaram]

Hi I am trying to use python from inside of the idle (IDLE) IDE that is part
of the MacPython 2.5.2 additional packages as IDLE.app.
The reason I want to do this is because I really want to get an IDE (
integrated development environment ) with good code completion on all
modules including maybe pymol.

In any case when I do the following (see attached
png<http://code-itch.s3.amazonaws.com/images/idle_pymol_how.jpg>
)

1) Start IDLE and then in the IDLE shell I do
2)  Import my fink python after adding it to my path

import sys
sys.path.append("/sw/lib/pymol-py25/modules")
import pymol

After that command I see that the idle Python shell waits for a little bit
and then I see  =restart .and no pymol window appears
Also when I try running pymol.finish_launching()

It says pymol is not defined.

I have tried reading some of the posts about how the import pymol method is
the least supported method for launching pymol. I should add that on my
setup i.e Leopard 10.5.2 with fink pymol-py25 the above approach works from
a standalone script as well as from a python interactive shell from
terminal.app or Item.app . Sadly both of these dont have popup code
completion..

But I was wondering if there is some way to have my cake and eat it too and
interact with pymol from within an IDLE shell window.

Hari Jayaram

Re: [PyMOL] load cgo into existing pymol session

[hari jayaram]

Thanks a lot Tsjerk for your help.
I am using MacPymol  0.99rc6 . Both versions of the solution you presented
worked. The only thing I had to do was to run on the command line prompt
inside pymol.

from pymol.cgo import *

Then I could run either version you suggested to get the axes to show up
( with the obj still in the file)

execfile("/Users/hari/Desktop/test.cgo")
cmd.load_cgo(obj,"test")

OR ( with the obj = removed)

cmd.load_cgo( eval( open("/Users/hari/Desktop/test.cgo").read() ), "test" )


Thanks
Hari


On Fri, Feb 22, 2008 at 4:07 AM, Tsjerk Wassenaar  wrote:

> Hi Hari,
>
> You can do it using:
>
> execfile("/Users/hari/Desktop/test.cgo")
> cmd.load_cgo(obj,"test")
>
> However, you might find it more convenient to drop the "obj =" from
> the .cgo file and load the thing with:
>
> cmd.load_cgo( eval( open("/Users/hari/Desktop/test.cgo").read() ), "test"
> )
>
> Although that seems a bit more complicated, it's in fact quite easy to
> define as a function itself. Hmm, I think I'm gonna store my CGO
> objects just like that myself :)
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, Feb 21, 2008 at 10:16 PM, hari jayaram  wrote:
> > Hi I have a running pymol session with nothing loaded.
> > I now want to load a cgo object into this session.
> > When I read in the cgo file using either command line (load
> > /Users/hari/Desktop/test.cgo  , test ) or the GUI menu , I get an object
> > entry on the side panel but nothing shows up in the viewing window.
> >
> > I can successfully load any cgo file using  a python script .  I want to
> > learn how to "inject" a cgo object like the one given below into a
> running
> > python session .
> > Can someone tell me how to do this.
> >
> > Your help is greatly appreciated
> > Thank You
> > Hari Jayaram
> > Brandeis University
> >
> > #Contents of test.cgo file
> >
> > obj = [
> >
> >BEGIN, LINES,
> >
> >COLOR, 1.0, 1.0, 1.0,
> >
> >
> >
> >
> >VERTEX, 0.0, 0.0, 0.0,
> >
> >VERTEX, 1.0, 0.0, 0.0,
> >
> >
> >
> >
> >VERTEX, 0.0, 0.0, 0.0,
> >
> >VERTEX, 0.0, 2.0, 0.0,
> >
> >
> >
> >
> >VERTEX, 0.0, 0.0, 0.0,
> >
> >VERTEX, 00, 0.0, 3.0,
> >
> >
> >
> >
> >END]
> >
> -
> >  This SF.net email is sponsored by: Microsoft
> >  Defy all challenges. Microsoft(R) Visual Studio 2008.
> >  http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
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> >  https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>

[PyMOL] load cgo into existing pymol session

[hari jayaram]

Hi I have a running pymol session with nothing loaded. I now want to load a
cgo object into this session. When I read in the cgo file using either
command line (load /Users/hari/Desktop/test.cgo  , test ) or the GUI menu ,
I get an object entry on the side panel but nothing shows up in the viewing
window.

I can successfully load any cgo file using  a python script .  I want to
learn how to "inject" a cgo object like the one given below into a running
python session .
Can someone tell me how to do this.

Your help is greatly appreciated
Thank You
Hari Jayaram
Brandeis University

#Contents of test.cgo file

obj = [

   BEGIN, LINES,

   COLOR, 1.0, 1.0, 1.0,


   VERTEX, 0.0, 0.0, 0.0,

   VERTEX, 1.0, 0.0, 0.0,


   VERTEX, 0.0, 0.0, 0.0,

   VERTEX, 0.0, 2.0, 0.0,


   VERTEX, 0.0, 0.0, 0.0,

   VERTEX, 00, 0.0, 3.0,


   END]

Re: [PyMOL] how to get pymol sec structure assignments printed out to a file

[hari jayaram]

Thanks a tonne!!!
It worked
so I did

ffout=open('secstruc.txt','w')
iterate name ca, ffout.write(repr((chain, resi, ss)))
ffout.close()


And the file was written to the pymol install directory..
This has convinced me of the power of pymols design and python in 
general..lots of learning to do.
Thanks again
Hari Jayaram
Brandeis University


On 6/17/05, T.A.Wassenaar  wrote:
> 
> 
> 
> I think you can try:
> 
> ffout=open('secstruc.txt','w')
> iterate name ca, ffout.write(repr((chain, resi, ss)))
> 
> Hope it works, but otherwise Warren will correct me :)
> 
> Tsjerk
> 
> On Fri, 17 Jun 2005 11:12:53 -0400
> hari jayaram  wrote:
> > I am sorry for being so needy ..Is there a way to
> >quickly write this out to
> > a file..I am a total python non savant and I have spent
> >the last hour
> > struggling with file open and write commands and gotten
> >nowhere.
> > So how do I write out the result of
> >
> > iterate name ca, print chain,resi,ss
> >
> > to a file .
> >
> > Thanks again
> > Hari Jayaram
> > Brandeis University
> >
> >
> > On 6/17/05, Warren DeLano  wrote:
> >>
> >> iterate name ca, print chain,resi,ss
> >>
> >>
> >> --
> >> Warren L. DeLano, Ph.D.
> >> Principal Scientist
> >>
> >> . DeLano Scientific LLC
> >> . 400 Oyster Point Blvd., Suite 213
> >> . South San Francisco, CA 94080 USA
> >> . Biz:(650)-872-0942 Tech:(650)-872-0834
> >> . Fax:(650)-872-0273 Cell:(650)-346-1154
> >> . mailto:war...@delsci.com
> >>
> >>
> >> > -Original Message-
> >> > From: pymol-users-ad...@lists.sourceforge.net
> >> > [mailto:pymol-users-ad...@lists.sourceforge.net] On
> >>Behalf Of
> >> > hari jayaram
> >> > Sent: Friday, June 17, 2005 5:33 AM
> >> > To: pymol-users@lists.sourceforge.net
> >> > Subject: [PyMOL] how to get pymol sec structure
> >>assignments
> >> > printed out
> >> >
> >> > Hi
> >> > I was just wondering how to get the pymol secondary
> >>structure
> >> > assignments printed out .
> >> > I was looking to manually do this for all the helix
> >>and
> >> > strand starts and stops..but I was wondering if there
> >>is some
> >> > way to have it print to the screen or a file the
> >>assignments
> >> > it uses for the cartoons...
> >> > like
> >> > helix from A1 to A50 ..
> >> >
> >> > Thanks for your help in advance
> >> > Hari Jayaram
> >> > Brandeis University
> >> >
> >> >
> >>
> 
>

[PyMOL] how to get pymol sec structure assignments printed out to a file

[hari jayaram]

I am sorry for being so needy ..Is there a way to quickly write this out to 
a file..I am a total python non savant and I have spent the last hour 
struggling with file open and write commands and gotten nowhere.
So how do I write out the result of

iterate name ca, print chain,resi,ss

to a file .

Thanks again
Hari Jayaram
Brandeis University


On 6/17/05, Warren DeLano  wrote:
> 
> iterate name ca, print chain,resi,ss
> 
> 
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
> 
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
> 
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > hari jayaram
> > Sent: Friday, June 17, 2005 5:33 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] how to get pymol sec structure assignments
> > printed out
> >
> > Hi
> > I was just wondering how to get the pymol secondary structure
> > assignments printed out .
> > I was looking to manually do this for all the helix and
> > strand starts and stops..but I was wondering if there is some
> > way to have it print to the screen or a file the assignments
> > it uses for the cartoons...
> > like
> > helix from A1 to A50 ..
> >
> > Thanks for your help in advance
> > Hari Jayaram
> > Brandeis University
> >
> >
>

[PyMOL] how to get pymol sec structure assignments printed out

[hari jayaram]

Hi 
I was just wondering how to get the pymol secondary structure assignments 
printed out .
I was looking to manually do this for all the helix and strand starts and 
stops..but I was wondering if there is some way to have it print to the 
screen or a file the assignments it uses for the cartoons...
like 
helix from A1 to A50 ..

Thanks for your help in advance 
Hari Jayaram
Brandeis University

Re: [PyMOL] pymol 0.98 and r3d input and getting sec structure assignments info

[hari jayaram]

Hello Warren and pymol users,
Thanks for your help on what to fix to get r3d working in 0.98 with linux . 
.. but I still have one problem
How do I get a cgo.pyc to replace the cgo.pyc which has the bug in it. Sorry 
I dont understand anything about the inner workings of pyhton to replace the 
faulty cgo.pyc with a new fixed cgo.pyc and I use the static build provided 
by the website.

Also how do I get the list of ss elements assigned by util.ss
Thanks a lot for your help
Hari


On 6/13/05, Warren DeLano  wrote:
> 
> Hari,
> 
> This is an outright bug that I introduced when adding URL support for 
> files.
> You can change that one line of code in cgo.py from
> 
> if (mode[0:1]=='r') and (string.find(fname,':')>1):
> 
> to
> 
> if (string.find(fname,':')>1):
> 
> in order to solve the problem.
> 
> Cheers,
> Warren
> 
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
> 
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
> 
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > hari jayaram
> > Sent: Sunday, June 12, 2005 9:29 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] pymol 0.98 and r3d input and getting sec
> > structure assignments info
> >
> > Hello , I tried to open an r3d (raster3d) file in pymol
> > version 0.98 and I get the following error
> >
> > Traceback (most recent call last):
> > File "/xtal2/pymol/modules/pymol/__init__.py", line 218, in
> > exec_deferred
> > cmd.load(a,quiet=0)
> > File "/xtal2/pymol/modules/pymol/importing.py", line 549, in load
> > discrete,quiet,multiplex,zoom)
> > File "/xtal2/pymol/modules/pymol/cmd.py", line 755, in _load
> > obj = cgo.from_r3d(finfo)
> > File "/xtal2/pymol/modules/pymol/cgo.py", line 167, in from_r3d
> > if (mode[0:1]=='r') and (string.find(fname,':')>1):
> > NameError: global name 'mode' is not defined
> >
> >
> > The same exact r3d file opens up just fine on pymol 0.97. Is
> > there something I am doing wrong or do I have to do something
> > different to generate the file to work with 0.98.
> >
> > Any help will be greatly appreciated.
> >
> > Also I was curious how to get pymol to spit out the
> > secondary structure assignments it useswhen one says assign
> > sec structure in the gui. I know this was covered before but
> > my googling skills are very dull today. So any help in
> > getting info on the sec str assignments used by pymol for a
> > particular model will also be greatly appreciated.
> > Thanks
> > hari
> >
> >
> 
> 
>

[PyMOL] pymol 0.98 and r3d input and getting sec structure assignments info

[hari jayaram]

Hello , I tried to open an r3d (raster3d) file in pymol version 0.98 and I 
get the following error

Traceback (most recent call last):
File "/xtal2/pymol/modules/pymol/__init__.py", line 218, in exec_deferred
cmd.load(a,quiet=0)
File "/xtal2/pymol/modules/pymol/importing.py", line 549, in load
discrete,quiet,multiplex,zoom)
File "/xtal2/pymol/modules/pymol/cmd.py", line 755, in _load
obj = cgo.from_r3d(finfo)
File "/xtal2/pymol/modules/pymol/cgo.py", line 167, in from_r3d
if (mode[0:1]=='r') and (string.find(fname,':')>1):
NameError: global name 'mode' is not defined


The same exact r3d file opens up just fine on pymol 0.97. Is there something 
I am doing wrong or do I have to do something different to generate the file 
to work with 0.98.

Any help will be greatly appreciated.

Also I was curious how to get pymol to spit out the secondary structure 
assignments it useswhen one says assign sec structure in the gui. I know 
this was covered before but my googling skills are very dull today. So any 
help in getting info on the sec str assignments used by pymol for a 
particular model will also be greatly appreciated.
Thanks
hari

Re: [PyMOL] v0.98 slow (includes: ray abort info...)

[hari jayaram]

Hi , I really like the slow transitions between scenes in Pymol 0.98. It is 
a great benefit to structure presentation.

I had just one question is there a way to slow down the transitions by a 
custom amount. 

Any help/suggestions will be greatly appreciated
Hari Jayaram
Brandeis University

On 5/27/05, Warren DeLano  wrote:
> 
> Mark,
> 
> 0.98 should rarely be more4X slower to ray-trace than 0.97 unless you are
> running out of RAM.
> 
> To get the faster but orthoscopic 0.97 raytracing behavior, "set
> orthoscopic" before raytracing.
> 
> > Oh yeah, please make a clean way of aborting from a
> > ray-trace...please.
> 
> Actually, it exists...but it is not 100% general:
> 
> To be able abort from ray tracing, it is necessary to run it asychronously
> (ray async=1). This is the default if you press the "ray" button in the
> Tcl/Tk GUI.
> 
> Provide that a ray trace is running asychronously, then you can in abort 
> it
> in 0.98 by clicking on the OpenGL window to get focus and then hitting the
> backspace or delete keys.
> 
> Cheers,
> Warren
> 
> 
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
> 
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
> 
> 
> > -Original Message-
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Mark Wilke
> > Sent: Friday, May 27, 2005 11:08 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] v0.98 slow
> >
> > I last used pymol about a year ago (not sure which version),
> > but typical ray-tracing jobs of simple cartoon-ribbons etc
> > took mere seconds to a few minutes at most. I just upgraded
> > to the new v0.98 and made some similar figures, but the
> > ray-tracing is taking 30 min to 1 hr or more. This is pretty
> > much unusable if you need to ray-trace several times to get
> > the figure to look how you want. Am I the only one
> > experiencing slow ray-tracing with pymol? I'm using the
> > windows build provided on the pymol website. I tried 2 PC computers:
> >
> > (1) 1.4 GHz athlon
> > 512 MB ram
> > Geforce2 GTS (64MB) Graphics Card
> > WinXP
> >
> > (2) Dell Inspiron XPS Gen 2 Desktop Replacement
> > 2 GHz cpu (pentium m 760)
> > Geforce go 6800 ultra
> > 1 GB ram
> > WinXP media centre edition
> >
> > The Dell is more than powerful enough to render rapidly...but
> > both computers behaved similarly. Anyone have any ideas?
> >
> > - Mark
> >
> > Oh yeah, please make a clean way of aborting from a
> > ray-trace...please.
> >
> >
> >
> >
> >
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> 
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