[PyMOL] citing pymol script in thesis--copyright issues?

[Lapolla, Suzanne M (HSC)]

Not sure who on the forum would know the answer to this question but I am sure 
someone will. I used many of the python scripts in pymol for my MS thesis, 
including the get_distance script that I also made  modifications to. I 
mentioned all these scritps in my thesis and of course cited the PyMol papers 
and sourceforge. One of my committee members wants me to have an appendix in my 
thesis of the get_distance script I modified. My question is, are there any 
copyright issues with this? Should I just  cite PyMol again and in the appendix 
on the modified script make sure to note what modifications I did versus what 
was there originally?  Thanks.

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[PyMOL] ? about polarpairs.py script

[Lapolla, Suzanne M (HSC)]

I am running this script with my structure, and the result I get is states how 
many polar pairs I have but not the location, which I thought the script was 
supposed to do. Here is the printout I get when running the script in pymol:

Settings: cutoff=4.0angstrom angle=63.0degree
Found 2 polar contacts

Maybe something wrong with the code? Any advice/suggestions would be useful. 
Thanks in advance.
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[PyMOL] modify command in object menu panel

[Lapolla, Suzanne M (HSC)]

Under the Action (A) popup menu there is the option modify and you can do 
residues or atoms within a certain Angstrom range. So when you do this, at 
least in my hands, the answer/output  becomes highlighted, but a selection of 
this result is not created. Is this what is supposed to happen. Guess I am a 
bit confused as to how this command works;   I did not find anything about it 
on the pymol wiki or my notes.  Thanks in advance.
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Re: [PyMOL] PyMOLWiki Update

[Lapolla, Suzanne M (HSC)]

Great! Thank you Microlytic! I assume that the PyMol wiki site will still have 
the same web address?

From: Jason Vertrees [jason.vertr...@gmail.com]
Sent: Friday, June 20, 2014 8:00 AM
To: pymol-users
Cc: Melanie Adams-Cioaba
Subject: [PyMOL] PyMOLWiki Update

Greetings,

It is my pleasure to let you know that 
Microlytic,
 a company that makes tools for crystallographers, has graciously offered to 
host the PyMOLWiki. The wiki has been successfully transferred and is serving. 
(The search and the port : problems have been fixed. Please let me know if 
you find any other problems.)

Please join me in thanking 
Microlytic
 for helping serve the PyMOL community.

Cheers,

-- Jason

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Re: [PyMOL] command question RE printing out distances to text file

[Lapolla, Suzanne M (HSC)]

Thanks for your input Jared. I have not had a chance yet to try ANdrea's 
suggestions but will and will also try yours, and see what works best for me 
and get back to you and the forum--which has been so helpful!

From: Sampson, Jared [jared.samp...@nyumc.org]
Sent: Tuesday, June 17, 2014 5:54 PM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne - The reason you have been getting only one distance in your output 
file is that your script is opening the file in “write” mode:

f=open('distnew.txt','w')

This will overwrite the contents of distnew.txt each time the script is run.  
If you want to keep all the distances without changing the rest of your script, 
you could open the file in “append” mode.

f=open('distnew.txt',’a’)

This way, each line will just get added to the bottom of the script.  Keep in 
mind that if you want to start over with a new list of distances, you’ll need 
either to change the filename that gets opened (as you’ve done with 
“distnew.txt”) or delete the existing file.  For this reason, I would go with 
one of the other approaches mentioned by Andreas, or look into using a list to 
define the atoms to which you’d like to measure the distance from the first 
atom, and loop through that list.  Perhaps something like this (untested) bit 
of script would be useful, especially if you have many different atoms to check:


first_atom = 'B///297/cb'
second_atoms_list = ['A///17/cb', 'A///18/cb', 'A///19/cb']

with open("dist.txt", 'w') as f:
for second_atom in second_atoms_list:
f.write("%8.3f\n" % cmd.distance("tmp", first_atom, second_atom))


Good luck!

Cheers,
Jared

On Jun 17, 2014, at 2:21 PM, Lapolla, Suzanne M (HSC) 
mailto:suzanne-lapo...@ouhsc.edu>> wrote:

Another follow up question to this. I decided to use the measure distance 
python script on the pymol wiki to do this, and I was able to do it 
successfully with a range of residues, but my question is about the output txt 
file. When I run the script I get the correct distances (all 3 of them) to show 
on the GUI but the text file that is generated (distnew.txt) only lists one 
distance--so perhaps the script needs to be modified for this as well for the 
residues measured?

The original script is at the link 
http://www.pymolwiki.org/index.php/Measure_Distance<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=HgvRHXkBNYGOysfvJcLojtIMeUFGMwyeOeg9H0RbBr0%3D%0A&s=439e1d97d8ba13b7f5cbabee32757f69dbeb6ec35476f43fd8eecc19d2e1539e>
and my modified version is below. Suggestions appreciated! Thank you.

# This script writes the distance from
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.

# import PyMOL's command namespace
from pymol import cmd

# open dist.txt for writing
f=open('distnew.txt','w')

# calculate the distance and store it in dst
dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')

# write the formatted value of the distance (dst)
# to the output file
f.write("%8.3f\n"%dst)

# close the output file.
f.close()

From: Robert Campbell 
[robert.campb...@queensu.ca<mailto:robert.campb...@queensu.ca>]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

 d = cmd.distance(sele1,sele2)
 print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder 
mailto:thomas.hol...@schrodinger.com>> wrote:

Hi Suzanne,

you can use the get_distance command. It doesn't generate a distance
object but prints the distance to the external window.

https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b

Cheers,
 Thomas

On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
mailto:suzanne-lapo...@ouhsc.edu>> wrote:

Fellow Pymol Users:
I may have asked 

Re: [PyMOL] command question RE printing out distances to text file

[Lapolla, Suzanne M (HSC)]

Ah I see--I will try and let you know how it works. Thanks again!

From: Andreas Warnecke [4ndreas.warne...@gmail.com]
Sent: Tuesday, June 17, 2014 2:18 PM
To: Lapolla, Suzanne M (HSC)
Cc: Robert Campbell; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

One more addition to the reply:

I failed to notice that you are trying to input a range of residues '17-19'

Make sure to input single atom selections to get correct distances and not an 
average:
A straightforward way to get that name is to click on the atom while in the 
'editing mode' of pymol: pymol will print: "you clicked" followed by a name 
that can be copy-pasted.
e.g.  "You clicked /lys///LYS`2/CA -> (pk1)" can be used to copy-paste 
/lys///LYS`2/CA

Another alternative is to use selections to identify one atom:
e.g.
cmd.distance('chain B and resi 297 and name CB','chain A and resi 17 and name 
CB')

Then your example becomes:

from pymol import cmd

# open dist.txt for writing
f=open('distnew.txt','w')

# calculate the distance and store it in dst
dst1=cmd.distance('chain B and resi 297 and name CB','chain A and resi 17 and 
name CB')
dst2=cmd.distance('chain B and resi 297 and name CB','chain A and resi 18 and 
name CB')
dst3=cmd.distance('chain B and resi 297 and name CB','chain A and resi 19 and 
name CB')

# and then for writing the output file
f.write("%8.3f\n"%dst1)
f.write("%8.3f\n"%dst2)
f.write("%8.3f\n"%dst3)

f.close()

Cheers,

Andreas


On Tue, Jun 17, 2014 at 8:45 PM, Andreas Warnecke 
<4ndreas.warne...@gmail.com<mailto:4ndreas.warne...@gmail.com>> wrote:
Hej Suzanne,

you will need to append the other two distances to the script to get them 
printed.
Following your example that would be something like:

# calculate the distance and store it in dst
dst1=cmd.distance('tmp','B///297/cb','A///17-19/cb')
dst2=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the selections in 
this line!
dst3=cmd.distance('tmp','B///297/cb','A///17-19/cb') # change the selections in 
this line!

# and then for writing the output file
f.write("%8.3f\n"%dst1)
f.write("%8.3f\n"%dst2)
f.write("%8.3f\n"%dst3)

inserting these blocks in your script hopefully will do the trick.

Cheers,

Andreas


On Tue, Jun 17, 2014 at 8:21 PM, Lapolla, Suzanne M (HSC) 
mailto:suzanne-lapo...@ouhsc.edu>> wrote:
Another follow up question to this. I decided to use the measure distance 
python script on the pymol wiki to do this, and I was able to do it 
successfully with a range of residues, but my question is about the output txt 
file.  When I run the script I get the correct distances (all 3 of them) to 
show on the GUI but the text file that is generated (distnew.txt) only lists 
one distance--so perhaps the script needs to be modified for this as well for 
the residues measured?

The original script is at the link 
http://www.pymolwiki.org/index.php/Measure_Distance<https://urldefense.proofpoint.com/v1/url?u=http://www.pymolwiki.org/index.php/Measure_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=EqubiL9cuYdYV13TK4bGte5vmf3Plq1xmWomVmdYlKU%3D%0A&s=992466ee53608d828281d0abbd95dc2742e6c75173eb93ae511f357e3225548b>
and my modified version is below. Suggestions appreciated! Thank you.

# This script writes the distance from
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.

# import PyMOL's command namespace
from pymol import cmd

# open dist.txt for writing
f=open('distnew.txt','w')

# calculate the distance and store it in dst
dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')

# write the formatted value of the distance (dst)
# to the output file
f.write("%8.3f\n"%dst)

# close the output file.
f.close()

From: Robert Campbell 
[robert.campb...@queensu.ca<mailto:robert.campb...@queensu.ca>]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d

Re: [PyMOL] command question RE printing out distances to text file

[Lapolla, Suzanne M (HSC)]

Another follow up question to this. I decided to use the measure distance 
python script on the pymol wiki to do this, and I was able to do it 
successfully with a range of residues, but my question is about the output txt 
file.  When I run the script I get the correct distances (all 3 of them) to 
show on the GUI but the text file that is generated (distnew.txt) only lists 
one distance--so perhaps the script needs to be modified for this as well for 
the residues measured?

The original script is at the link 
http://www.pymolwiki.org/index.php/Measure_Distance
and my modified version is below. Suggestions appreciated! Thank you.

# This script writes the distance from 
# atom mol1///25/ha to atom mol1///26/ha
# out to the file "dist.txt"
# Simply change your selections to see different distances.
 
# import PyMOL's command namespace
from pymol import cmd
 
# open dist.txt for writing
f=open('distnew.txt','w')
 
# calculate the distance and store it in dst
dst=cmd.distance('tmp','B///297/cb','A///17-19/cb')
 
# write the formatted value of the distance (dst)
# to the output file
f.write("%8.3f\n"%dst)
 
# close the output file.
f.close()

From: Robert Campbell [robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder  wrote:

> Hi Suzanne,
>
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
>
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
>
> Cheers,
>   Thomas
>
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
>  wrote:
>
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.
>




--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821

https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlc&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225

--
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Find What Matters Most in Your Big Data with HPCC Systems
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Re: [PyMOL] command question RE printing out distances to text file

[Lapolla, Suzanne M (HSC)]

Thank you Robert and Thomas--I will try both and see what works best for my 
needs. 

From: Robert Campbell [robert.campb...@queensu.ca]
Sent: Monday, June 09, 2014 10:04 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] command question RE printing out distances to text file

Hi Suzanne,

You can also get the distance printed in the external GUI or terminal window
by using the "cmd.distance" version of the command.  So either you can
assign the distance to a variable and print it or you can print the result
directly.

Assuming you have two selections, sele1 and sele2 specifying the atoms of
interest you can do:

  d = cmd.distance(sele1,sele2)
  print sele1,sele2,d


Cheers,
Rob

On Mon, 2014-06-09
13:13 EDT, Thomas Holder  wrote:

> Hi Suzanne,
>
> you can use the get_distance command. It doesn't generate a distance
> object but prints the distance to the external window.
>
> https://urldefense.proofpoint.com/v1/url?u=http://pymolwiki.org/index.php/Get_Distance&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=921f4dfed39cd38f4ae7a70dfb937844d4e3faf1bc967c2f4d1f2944fa2ea31b
>
> Cheers,
>   Thomas
>
> On 06 Jun 2014, at 23:03, Lapolla, Suzanne M (HSC)
>  wrote:
>
> > Fellow Pymol Users:
> > I may have asked this question before...but if so have forgotten. I am
> > measuring distances between 2 atoms in 2 different objects using the
> > distance command, and it is working perfectly, but I wonder if there is
> > a command I can use/add so that those distances can be printed in the
> > external gui as well as being shown in the viewer. I will be doing lots
> > of these at the same time and the screen will get crowded. Thank you in
> > advance.
>




--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821

https://urldefense.proofpoint.com/v1/url?u=http://pldserver1.biochem.queensu.ca/~rlc&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=aaad7877cf1640401ae708b7b5f5a2fbe03abec4d2f0ef509e7360c0017ee225

--
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
https://urldefense.proofpoint.com/v1/url?u=http://www.hpccsystems.com/&k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0A&r=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0A&m=fr2bAoLQoVgp9h2t2fgBvfGVVX7oQ1g14g1AODFz%2FRg%3D%0A&s=dabd029c6435c0bbe92d916555213bd7ccbd3d4ac6dcf2de28cf19c428ff0eed
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[PyMOL] command question RE printing out distances to text file

[Lapolla, Suzanne M (HSC)]

Fellow Pymol Users:
I may have asked this question before...but if so have forgotten. I am 
measuring distances between 2 atoms in 2 different objects using the distance 
command, and it is working perfectly, but I wonder if there is a command I can 
use/add so that those distances can be printed in the external gui as well as 
being shown in the viewer. I will be doing lots of these at the same time and 
the screen will get crowded. Thank you in advance.
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[PyMOL] show_bumps.py ?

[Lapolla, Suzanne M (HSC)]

I have been able to use this script successfully in the past but now for some 
reason I cannot. I load my structure and in the command line type
run show_bumps.py
show_bumps (selection of what I want to show bumps for), showbumps

and while I get a vanderwaal strain printed out on the command line, I do not 
get any  disks to show up to illustrate the bad/good contacts (like i do with 
the mutagenesis wizard).  Maybe I am typing my selection in wrong? So for 
example, if I want to see any steric clashes residue 6 has with surrounding 
residues in my structure, I would type in
show_bumps resi 6, showbumps

Thanks in advance.
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[PyMOL] rotating helix "into screen axis"

[Lapolla, Suzanne M (HSC)]

Fellow Pymol users:
Have a question about moving a selection of my protein. I would like to rotate 
a particular helix of my protein so that it rotates "into" the screen (x axis?) 
, changing the side of the helix that is shown. I know how to select the helix, 
deprotect it, protect the other regions of my protein, and move the helix via 
the screen's x axis (like rocking) and up and down (y axis)  but do not know 
how to rotate it into the screen. Hope that makes sense. Thanks in advance.
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Re: [PyMOL] manual superposition with pymol--and another question

[Lapolla, Suzanne M (HSC)]

This worked--thanks. I have another ? that may have been addressed previously 
but do not know the answer.  Is there a way to do an alignment (or maybe 
docking is a better word) on two structures/selections and input a constraint 
for that alignment? For example, i am working on generating a model RE a dimer 
of two molecules, and I have some data suggesting a range of distances between 
certain residues of the selection. Is there a way to input that data into Pymol 
before it completes the alignment, or do I need to use other docking programs 
to do that? Hope that makes sense.  Thanks.

From: Lapolla, Suzanne M (HSC)
Sent: Friday, April 04, 2014 5:11 PM
To: Thomas Holder
Subject: RE: [PyMOL] manual superposition with pymol

Thank you! I will try this and get back to you.

From: Thomas Holder [thomas.hol...@schrodinger.com]
Sent: Friday, April 04, 2014 3:16 PM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] manual superposition with pymol

Hi Suzanne,

looks like you only deprotected the CA atoms. If you have this as a named 
selection, try "A > modify > complete > molecules" and deprotect again. Or type:

PyMOL> deprotect bymol (sele)

Instead of working with one object and protecting/deprotecting of subsets of 
atoms, I suggest to extract the selection that you want to move to its own 
object. That's usually easier to handle.

Cheers,
  Thomas

On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC)  
wrote:

> I am using pymol 1.3 and having trouble with doing manual superposition with 
> my structures. I am able to download my structures, select the portion I want 
> to move manually and, after deprotecting it using the action menu move it 
> using the shift-mouse editing command. When I do this with my selection shown 
> in cartoon mode, things look great, but then when i switch to show my 
> selected residues as  sticks,  the sticks become huge --they  get bigger  
> and/or  smaller as I move the structure.  Ideas on what I may be doing wrong? 
> Hope this makes sense. Thanks, Suzanne

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[PyMOL] manual superposition with pymol

[Lapolla, Suzanne M (HSC)]

I am using pymol 1.3 and having trouble with doing manual superposition with my 
structures. I am able to download my structures, select the portion I want to 
move manually and, after deprotecting it using the action menu move it using 
the shift-mouse editing command. When I do this with my selection shown in 
cartoon mode, things look great, but then when i switch to show my selected 
residues as  sticks,  the sticks become huge --they  get bigger  and/or  
smaller as I move the structure.  Ideas on what I may be doing wrong? Hope this 
makes sense. Thanks, Suzanne
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[PyMOL] Pymol 1.7 and measurement wizard problem

[Lapolla, Suzanne M (HSC)]

I have several .pse files I made on pymol 1.3 version--that may or may not be 
of significant to what is going on--but when I open the file and try to use the 
measurement wizard on them, I am prompted to "click on the first atom", and 
when I do so, nothing happens (nothing gets selected and no error msg on the 
command line). Ideas of what the problem may be? I have pymol 1.7 on my windows 
7, 32 bit. Thank you in advance. 
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Re: [PyMOL] Still need help with fetch and pymol 1.7

[Lapolla, Suzanne M (HSC)]

Just wanted to say that your fix did solve my problem. Thanks again! 

From: David Hall [li...@cowsandmilk.net]
Sent: Monday, January 20, 2014 8:34 AM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Still need help with fetch and pymol 1.7

I think there's a bug in python's code, not pymol's
In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you 
should change line 250 from:
except UnicodeEncodeError:

to

except (UnicodeEncodeError,UnicodeDecodeError):

keeping the indentation in the file and so on. Then the code will skip the 
entries in the windows registry that are causing issues.

-David



On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) 
mailto:suzanne-lapo...@ouhsc.edu>> wrote:
I am posting this again as I have still not figured out why I am unable to 
fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the 
error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 
as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 
1st, and when that did not work I unindtalled adn then re-installed using the 
windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well).  
This forum has been a great source of help for my before so hope yoiu guys can 
help again! Thank you.

PyMOL>fetch 4bd2
 please wait ...
Exception in thread Thread-4:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 810, in __bootstrap_inner
self.run()
  File "C:\Python27\lib\threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\pymol\commanding.py", line 561, in wrapper
func(*args, **kwargs)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1348, in 
_multifetch
discrete, multiplex, zoom, type, path, file, quiet, _self)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1292, in _fetch
contents = internal.file_read(url)
  File "C:\Python27\lib\site-packages\pymol\internal.py", line 308, in file_read
handle = urllib.urlopen(finfo)
  File "C:\Python27\lib\urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
  File "C:\Python27\lib\urllib2.py", line 404, in open
response = self._open(req, data)
  File "C:\Python27\lib\urllib2.py", line 422, in _open
'_open', req)
  File "C:\Python27\lib\urllib2.py", line 382, in _call_chain
result = func(*args)
  File "C:\Python27\lib\urllib2.py", line 1403, in ftp_open
mtype = mimetypes.guess_type(req.get_full_url())[0]
  File "C:\Python27\lib\mimetypes.py", line 297, in guess_type
init()
  File "C:\Python27\lib\mimetypes.py", line 358, in init
db.read_windows_registry()
  File "C:\Python27\lib\mimetypes.py", line 258, in read_windows_registry
for subkeyname in enum_types(hkcr):
  File "C:\Python27\lib\mimetypes.py", line 249, in enum_types
ctype = ctype.encode(default_encoding) # omit in 3.x!
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal 
not in range(128)

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Re: [PyMOL] Still need help with fetch and pymol 1.7

[Lapolla, Suzanne M (HSC)]

Thank you thank you! I will try that later today--I do appreciate the help. Did 
I say thank you yet? Suzanne


From: David Hall [li...@cowsandmilk.net]
Sent: Monday, January 20, 2014 8:34 AM
To: Lapolla, Suzanne M (HSC)
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Still need help with fetch and pymol 1.7

I think there's a bug in python's code, not pymol's
In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) , you 
should change line 250 from:
except UnicodeEncodeError:

to

except (UnicodeEncodeError,UnicodeDecodeError):

keeping the indentation in the file and so on. Then the code will skip the 
entries in the windows registry that are causing issues.

-David



On Mon, Jan 20, 2014 at 8:40 AM, Lapolla, Suzanne M (HSC) 
mailto:suzanne-lapo...@ouhsc.edu>> wrote:
I am posting this again as I have still not figured out why I am unable to 
fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the 
error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 
as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 
1st, and when that did not work I unindtalled adn then re-installed using the 
windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well).  
This forum has been a great source of help for my before so hope yoiu guys can 
help again! Thank you.

PyMOL>fetch 4bd2
 please wait ...
Exception in thread Thread-4:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 810, in __bootstrap_inner
self.run()
  File "C:\Python27\lib\threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\pymol\commanding.py", line 561, in wrapper
func(*args, **kwargs)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1348, in 
_multifetch
discrete, multiplex, zoom, type, path, file, quiet, _self)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1292, in _fetch
contents = internal.file_read(url)
  File "C:\Python27\lib\site-packages\pymol\internal.py", line 308, in file_read
handle = urllib.urlopen(finfo)
  File "C:\Python27\lib\urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
  File "C:\Python27\lib\urllib2.py", line 404, in open
response = self._open(req, data)
  File "C:\Python27\lib\urllib2.py", line 422, in _open
'_open', req)
  File "C:\Python27\lib\urllib2.py", line 382, in _call_chain
result = func(*args)
  File "C:\Python27\lib\urllib2.py", line 1403, in ftp_open
mtype = mimetypes.guess_type(req.get_full_url())[0]
  File "C:\Python27\lib\mimetypes.py", line 297, in guess_type
init()
  File "C:\Python27\lib\mimetypes.py", line 358, in init
db.read_windows_registry()
  File "C:\Python27\lib\mimetypes.py", line 258, in read_windows_registry
for subkeyname in enum_types(hkcr):
  File "C:\Python27\lib\mimetypes.py", line 249, in enum_types
ctype = ctype.encode(default_encoding) # omit in 3.x!
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal 
not in range(128)

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[PyMOL] Pymol 1.4 compatable with python 3?

[Lapolla, Suzanne M (HSC)]

So, an update to my prev post/question--my computer husband was able to look at 
the error msg I get when trying to "fetch" with pymol 1.7. He says the error is 
with the python2.7 code, specifically  in a library that handles unicode 
characters--but according to the comment made in the code, this should have 
been fixed in python 3. So in short, should uninstalling python 2.7 and 
installing python 3 fix the problem? Thank you. 
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[PyMOL] Still need help with fetch and pymol 1.7

[Lapolla, Suzanne M (HSC)]

I am posting this again as I have still not figured out why I am unable to 
fetch or use the pdb plugin loader with pymol 1.7 I have cut/copied/pasted the 
error msg I get below. I have tried uninstalling and reinstalling python 2.7.6 
as well as python 1.7 (I have windows 64 bit --so I tried the 64 bit version 
1st, and when that did not work I unindtalled adn then re-installed using the 
windows 32 bit version. (I prev had pymol 1.3 but uninstalled that as well).  
This forum has been a great source of help for my before so hope yoiu guys can 
help again! Thank you. 

PyMOL>fetch 4bd2
 please wait ...
Exception in thread Thread-4:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 810, in __bootstrap_inner
self.run()
  File "C:\Python27\lib\threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\pymol\commanding.py", line 561, in wrapper
func(*args, **kwargs)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1348, in 
_multifetch
discrete, multiplex, zoom, type, path, file, quiet, _self)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1292, in _fetch
contents = internal.file_read(url)
  File "C:\Python27\lib\site-packages\pymol\internal.py", line 308, in file_read
handle = urllib.urlopen(finfo)
  File "C:\Python27\lib\urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
  File "C:\Python27\lib\urllib2.py", line 404, in open
response = self._open(req, data)
  File "C:\Python27\lib\urllib2.py", line 422, in _open
'_open', req)
  File "C:\Python27\lib\urllib2.py", line 382, in _call_chain
result = func(*args)
  File "C:\Python27\lib\urllib2.py", line 1403, in ftp_open
mtype = mimetypes.guess_type(req.get_full_url())[0]
  File "C:\Python27\lib\mimetypes.py", line 297, in guess_type
init()
  File "C:\Python27\lib\mimetypes.py", line 358, in init
db.read_windows_registry()
  File "C:\Python27\lib\mimetypes.py", line 258, in read_windows_registry
for subkeyname in enum_types(hkcr):
  File "C:\Python27\lib\mimetypes.py", line 249, in enum_types
ctype = ctype.encode(default_encoding) # omit in 3.x!
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal 
not in range(128)
 
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[PyMOL] unable to fetch PDB files with pymol 1.7

[Lapolla, Suzanne M (HSC)]

I have just downloaded pymol 1.7 along with python 2.7.6.  (I previously had 
pymol 1.3). I am able to open existing .pdb and .pse files I have saved, but if 
I try to fetch them from the PBD I get a huge error message (see below). I feel 
like this question has been asked before but cannot find it on the forum. Thank 
you in advance!  Suzanne

PyMOL>fetch 4bd2
 please wait ...
Exception in thread Thread-4:
Traceback (most recent call last):
  File "C:\Python27\lib\threading.py", line 810, in __bootstrap_inner
self.run()
  File "C:\Python27\lib\threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
  File "C:\Python27\lib\site-packages\pymol\commanding.py", line 561, in wrapper
func(*args, **kwargs)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1348, in 
_multifetch
discrete, multiplex, zoom, type, path, file, quiet, _self)
  File "C:\Python27\lib\site-packages\pymol\importing.py", line 1292, in _fetch
contents = internal.file_read(url)
  File "C:\Python27\lib\site-packages\pymol\internal.py", line 308, in file_read
handle = urllib.urlopen(finfo)
  File "C:\Python27\lib\urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
  File "C:\Python27\lib\urllib2.py", line 404, in open
response = self._open(req, data)
  File "C:\Python27\lib\urllib2.py", line 422, in _open
'_open', req)
  File "C:\Python27\lib\urllib2.py", line 382, in _call_chain
result = func(*args)
  File "C:\Python27\lib\urllib2.py", line 1403, in ftp_open
mtype = mimetypes.guess_type(req.get_full_url())[0]
  File "C:\Python27\lib\mimetypes.py", line 297, in guess_type
init()
  File "C:\Python27\lib\mimetypes.py", line 358, in init
db.read_windows_registry()
  File "C:\Python27\lib\mimetypes.py", line 258, in read_windows_registry
for subkeyname in enum_types(hkcr):
  File "C:\Python27\lib\mimetypes.py", line 249, in enum_types
ctype = ctype.encode(default_encoding) # omit in 3.x!
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd7 in position 2: ordinal 
not in range(128)
 


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Re: [PyMOL] Pymol 1.3 and 1.6 compatability?

[Lapolla, Suzanne M (HSC)]

I thought that 1.7 was not free--that you had to pay for it.  Not true? If 1.7 
is free, could you give me a link? Thank you.

From: Engin Özkan [eoz...@stanford.edu]
Sent: Tuesday, January 14, 2014 3:10 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Pymol 1.3 and 1.6 compatability?

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

Engin

On 1/14/14, 3:07 PM, Marcelo Marcet wrote:
> Hi Lapolla,
>
> Yes, you can keep your pymol v1.3 and v1.6. Just make sure that they have 
> different names. You will also be able to open your old pse files.
>
> Cheers,
> Marcelo
>
> On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC) 
>  wrote:
>
>> I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right 
>> now I have Pymol 1.3 opensource. I have a many session files (.pse) that I 
>> have made on PyMol 1.3, and want to make sure that upgrading will not be a 
>> problem.  Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? 
>> or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank 
>> you.
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[PyMOL] Pymol 1.3 and 1.6 compatability?

[Lapolla, Suzanne M (HSC)]

I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I 
have Pymol 1.3 opensource. I have a many session files (.pse) that I have made 
on PyMol 1.3, and want to make sure that upgrading will not be a problem.  Can 
I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have 
pymol 1.3 and 1.6 both on my machine at the same time? Thank you.  
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[PyMOL] resubmitting vanderwaal bumps ?

[Lapolla, Suzanne M (HSC)]

I noticed my question was truncated when I submitted it so will try again.
When I run showbumps.py on Pymol I get a vanderwaal value of about 163.
I need a good ref point as to what that number represents.
Thanks, Suzanne
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[PyMOL] VanderWaal strain number and showbumps

[Lapolla, Suzanne M (HSC)]

New to the forum but have been uisng Pymol for about a year. I have a ? Re 
using the showbumps.py script and the vanderwaal strain number  given after the 
run. The vanderwaal strain number that pymol gives after you run showbumps, is 
that in J/mol? kJ/mol? I am trying to get a handle on how destabilizing this 
mutant is, if at all. The value I get is: VDW Strain: 169.191604614. I would 
expect the smaller the #, the more favorable the interaction.
Thanks for your time
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