date:20160427

Re: [PyMOL] Dynamic reloading of plugin

2016-04-27 Thread Sampson, Jared M.

Hi Martin - 

I've also experienced this kind of tedium.  Depending on the type of extension 
it is, you could also consider writing tests for your function that can be run 
by either:

a) importing PyMOL commands into a python (.py) script and running e.g. 
`nosetests` or other unit testing software

```extension_tests.pml
import pymol
from pymol import cmd
pymol.finish_launching()
...do stuff here...
```

or,

b) run PyMOL (.pml) scripts in command line only mode.

For example, I've used approach (b) before with a setup something like this:

```test1.pml
from pymol import cmd
frag ala
python
if 'ala' in cmd.get_names(): 
   print 'OK'
else: 
   print 'Not OK'
python end
```

Then run each test from the shell:

```
pymol -cq test1.pml
```

For running many tests automatically, I've also used a "run_tests.sh" that 
looks something like this:

```run_tests.sh
#!/bin/bash
function run_test() {
 PML="test${1}.pml"
 if [ -f "$PML" ]; then
   echo ""
   echo 
""
   echo "Running Test ${1}: $PML"
   echo ""
   pymol -ckq $PML
   echo ""
 fi
}

# call `./run_tests.sh` with no args to run all the tests (up to 100)
if [ $# -lt 1 ]; then
 for i in {1..100}  # increase if you have more than 100 tests
 do
   run_test $i
 done

# call with args, e.g. `./run_tests.sh 1 2 4 7` to run specific test(s)
else
 for i in $@
 do
   run_test $i
 done
fi 
```

Hope this is helpful.  Good luck!

Cheers,
Jared




> On Apr 25, 2016, at 11:06 AM, Thomas Holder  
> wrote:
> 
> Hi Martin,
> 
> how about:
> 
> set_key F1, run script.py; function_from_script()
> 
> Reduces step 3) and 4) to hitting "F1" on the keyboard.
> 
> Cheers,
> Thomas
> 
> On 24 Apr 2016, at 06:36, Martin Hediger  wrote:
> 
>> Hi all
>> 
>> When working on a PyMOL extension script, my workflow is currently something 
>> like this:
>> 
>> 1) Start PyMOL
>> 2) Work on script
>> 3) PyMOL> run script.py
>> 4) PyMOL> function_from_script()
>> 5) See if function works, go back to 2)
>> 
>> Is it possible to have PyMOL automatically re-run the script everytime i 
>> save it?
>> 
>> Thanks and best regards
>> Martin
>> 
>> -- 
>> Martin R. Hediger, PhD
>> Mittlere Strasse 65
>> 4056 Basel
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
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Re: [PyMOL] query

2016-04-27 Thread Thomas Holder

Hi Ankita,

set depth_cue, 0

http://pymolwiki.org/index.php/Depth_cue

Cheers,
  Thomas

On 27 Apr 2016, at 11:06, H. Adam Steinberg  wrote:

> Scrolling the mouse will not move the molecule, it will reduce the fog that 
> pymol puts in the image, making it less gray.
> 
> Sent from my iPhone
> 
> On Apr 27, 2016, at 6:45 AM, ankita mehta  wrote:
> 
>> No, I can not do this becos i have to show the complex that is protein in a 
>> fix orientation.
>> Suggest some alternative..
>> Thanks!
>> 
>> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:
>> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and 
>> down! 
>> Usually (if you have not changed any settings), SCROLLING UP should solve 
>> your problem.
>> 
>> Cheers.
>> 
>> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta  wrote:
>> Hii,
>> I want to save the image in pymol
>> I am using white background but it gives me dull colouring of the protein 
>> which is at the background than the protein part at foreground.
>> I want a unified sceme for all protein .
>> pls suggest.
>> thanks!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] strange mouse button problem since version 1.8 with PyMOL for Linux

2016-04-27 Thread Thomas Holder

Hi Christoph,

This sounds like a serious picking bug, possibly related to your graphics 
driver. Please send further details directly to me (I'll send an update to the 
list once we've figured it out).

Thanks,
  Thomas

On 27 Apr 2016, at 05:24, Christoph Parthier  wrote:

> Hi,
> 
> I have a strange issue with (incentive) PyMOL version >= 1.8 for Linux 
> running under Scientic Linux 6.x (64-bit, current OPENGL driver for 
> NVIDIA Quadro graphics cards).
> 
> Independent of the mouse mode in PyMOL (2-Button/3-Button) selecting 
> (left mouse button), ID-ing (right mouse button) or centering (middle 
> mouse button) residues, from time to time the wrong residues are 
> selected/IDd/centered which are not even in close proximity to the 
> intended residue (or just hidden by too narrow slab settings).
> Furthermore this doesn't happen consistently, about 2-3 out of 10 mouse 
> clicks (still annoying...), possibly with minimal mouse movement 
> inbetween but still pointing at the same residue. Interestingly,  the 
> same 'wrong' residues keep popping up, when getting selected erroneously 
> (but I can't get figure out any 'systematic' behind it yet). The 
> behaviour appears with any molecule loaded (also the '1tii' built-into 
> the cartoon demo of PyMOL).
> 
> Interesting also, I do not observe this behaviour with PyMOL 1.7.4.3. 
> and also not when running PyMOL 1.8.x via remote login 
> (X-windows-powered SSH), which might indicate a local graphics/mouse 
> driver problem?
> 
> Any comments are welcome!
> 
> Thanks,
> Christoph

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] query

2016-04-27 Thread H. Adam Steinberg

Scrolling the mouse will not move the molecule, it will reduce the fog that 
pymol puts in the image, making it less gray.

Sent from my iPhone

> On Apr 27, 2016, at 6:45 AM, ankita mehta  wrote:
> 
> No, I can not do this becos i have to show the complex that is protein in a 
> fix orientation.
> Suggest some alternative..
> Thanks!
> 
>> On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:
>> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and 
>> down! 
>> Usually (if you have not changed any settings), SCROLLING UP should solve 
>> your problem.
>> 
>> Cheers.
>> 
>>> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta  
>>> wrote:
>>> Hii,
>>> I want to save the image in pymol
>>> I am using white background but it gives me dull colouring of the protein 
>>> which is at the background than the protein part at foreground.
>>> I want a unified sceme for all protein .
>>> pls suggest.
>>> thanks!
>>> 
>>> --
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> 
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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread Tsjerk Wassenaar

Hi,

You need

for i in ${pdb_array[@]}
do
...
done

Cheers,

Tsjerk
On Apr 27, 2016 4:44 PM, "James Starlight"  wrote:

> so As I tried to do it but it was not worked :-O)
>
> #pdbs list
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> #where to save
> pdb_array_store=$template/pymol/
>
>
> # A simple FETCHER: download pdbs to the folder and pre-process them!
> #mkdir ${pdb_array_store}
> for i in `cat ${pdb_array}` ; do wget
> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
> done
>
> result
> cat: 1UBI: No such file or directory
>
> 2016-04-27 12:29 GMT+02:00 James Starlight :
> > Please give me an example of the list of 3 pdbs instead of just cat $1 :)
> >  as well as proper syntax of how to save each pdb after fetching in
> > pymol using same command line
> > Forgot to mention important points:
> > 1) that list should be physically in my script like in python
> > 2) I use pymol because I will need to process each of the pdb- e,g to
> > remove from them ligands or water etc
> >
> > Thanks!
> >
> > 2016-04-27 12:18 GMT+02:00 James Starlight :
> >> Please give me an example of the list of 3 pdbs instead of cat $1  as
> >> well as how to save syntax of how to save each pdb
> >>
> >>
> >> Thanks!
> >>
> >> J
> >>
> >> 2016-04-27 12:09 GMT+02:00 Jordan Willis :
> >>> If you really want to use pymol, this works
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
> >>>
> >>>
> >>> Then on the command line
> chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> On Apr 27, 2016, at 2:55 AM, Jordan Willis 
> wrote:
> >>>
> >>> Must you use pymol?
> >>>
> >>>
> >>> Try directly from the PDB
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>>
> >>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
> done
> >>>
> >>>
> >>>
> >>>
> >>> Then on the command line
> chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> J
> >>>
> >>> On Apr 27, 2016, at 2:41 AM, James Starlight 
> wrote:
> >>>
> >>> Dear Pymol users!
> >>>
> >>> I need to add a few strings to my simple bash script which will creat
> >>> a list of pdb files and than will call pymol without GUI from the
> >>> terminal to fetch all the pdbs and save it to the desired location.
> >>> For one pdb it should be smth like
> >>>
> >>> pdbs="1f88"
> >>>
> >>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
> >>> ${tmp}/pymol_${pdbs}.log
> >>>
> >>> will be thankful for the correction of this string as well as example
> >>> how it can be adapted for a list of pdbs in bash.
> >>>
> >>> Thanks!
> >>>
> >>> J
> >>>
> >>>
> --
> >>> Find and fix application performance issues faster with Applications
> Manager
> >>> Applications Manager provides deep performance insights into multiple
> tiers
> >>> of
> >>> your business applications. It resolves application problems quickly
> and
> >>> reduces your MTTR. Get your free trial!
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> >>> ___
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> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>> Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >>>
> >>>
> >>>
>
>
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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight

so As I tried to do it but it was not worked :-O)

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


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

result
cat: 1UBI: No such file or directory

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

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Re: [PyMOL] query

2016-04-27 Thread ankita mehta

No, I can not do this becos i have to show the complex that is protein in a
fix orientation.
Suggest some alternative..
Thanks!

On Wed, Apr 27, 2016 at 4:01 PM, Dheeraj Prakaash  wrote:

> Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
> down!
> Usually (if you have not changed any settings), SCROLLING UP should solve
> your problem.
>
> Cheers.
>
> On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta 
> wrote:
>
>> Hii,
>> I want to save the image in pymol
>> I am using white background but it gives me dull colouring of the protein
>> which is at the background than the protein part at foreground.
>> I want a unified sceme for all protein .
>> pls suggest.
>> thanks!
>>
>>
>> --
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> ___
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>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
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Re: [PyMOL] query

2016-04-27 Thread Dheeraj Prakaash

Try pointing your (mouse) cursor in the Pymol Viewer and scrolling up and
down!
Usually (if you have not changed any settings), SCROLLING UP should solve
your problem.

Cheers.

On Wed, Apr 27, 2016 at 6:15 PM, ankita mehta 
wrote:

> Hii,
> I want to save the image in pymol
> I am using white background but it gives me dull colouring of the protein
> which is at the background than the protein part at foreground.
> I want a unified sceme for all protein .
> pls suggest.
> thanks!
>
>
> --
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> Manager
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> tiers of
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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight

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

Thanks!

2016-04-27 12:18 GMT+02:00 James Starlight :
> Please give me an example of the list of 3 pdbs instead of cat $1  as
> well as how to save syntax of how to save each pdb
>
>
> Thanks!
>
> J
>
> 2016-04-27 12:09 GMT+02:00 Jordan Willis :
>> If you really want to use pymol, this works
>>
>> #!/bin/bash
>> #myscript.bash
>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> On Apr 27, 2016, at 2:55 AM, Jordan Willis  wrote:
>>
>> Must you use pymol?
>>
>>
>> Try directly from the PDB
>>
>> #!/bin/bash
>> #myscript.bash
>>
>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
>>
>>
>>
>>
>> Then on the command line
>>>chmod +x myscript.bash; ./myscript.bash mylist.txt
>>
>>
>> J
>>
>> On Apr 27, 2016, at 2:41 AM, James Starlight  wrote:
>>
>> Dear Pymol users!
>>
>> I need to add a few strings to my simple bash script which will creat
>> a list of pdb files and than will call pymol without GUI from the
>> terminal to fetch all the pdbs and save it to the desired location.
>> For one pdb it should be smth like
>>
>> pdbs="1f88"
>>
>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
>> ${tmp}/pymol_${pdbs}.log
>>
>> will be thankful for the correction of this string as well as example
>> how it can be adapted for a list of pdbs in bash.
>>
>> Thanks!
>>
>> J
>>
>> --
>> Find and fix application performance issues faster with Applications Manager
>> Applications Manager provides deep performance insights into multiple tiers
>> of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> ___
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>>

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[PyMOL] query

2016-04-27 Thread ankita mehta

Hii,
I want to save the image in pymol
I am using white background but it gives me dull colouring of the protein
which is at the background than the protein part at foreground.
I want a unified sceme for all protein .
pls suggest.
thanks!
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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread Jordan Willis

If you really want to use pymol, this works 

#!/bin/bash
#myscript.bash
for i in `cat $1` ; do pymol -d "fetch $i" -c ; done


Then on the command line 
>chmod +x myscript.bash; ./myscript.bash mylist.txt


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

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Re: [PyMOL] Bash scripting and pymol

2016-04-27 Thread Jordan Willis

Must you use pymol?


Try directly from the PDB

#!/bin/bash
#myscript.bash

for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done




Then on the command line 
>chmod +x myscript.bash; ./myscript.bash mylist.txt


J

> On Apr 27, 2016, at 2:41 AM, James Starlight  wrote:
> 
> Dear Pymol users!
> 
> I need to add a few strings to my simple bash script which will creat
> a list of pdb files and than will call pymol without GUI from the
> terminal to fetch all the pdbs and save it to the desired location.
> For one pdb it should be smth like
> 
> pdbs="1f88"
> 
> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
> ${tmp}/pymol_${pdbs}.log
> 
> will be thankful for the correction of this string as well as example
> how it can be adapted for a list of pdbs in bash.
> 
> Thanks!
> 
> J
> 
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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[PyMOL] Bash scripting and pymol

2016-04-27 Thread James Starlight

Dear Pymol users!

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

pdbs="1f88"

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

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

Thanks!

J

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[PyMOL] strange mouse button problem since version 1.8 with PyMOL for Linux

2016-04-27 Thread Christoph Parthier

Hi,

I have a strange issue with (incentive) PyMOL version >= 1.8 for Linux 
running under Scientic Linux 6.x (64-bit, current OPENGL driver for 
NVIDIA Quadro graphics cards).

Independent of the mouse mode in PyMOL (2-Button/3-Button) selecting 
(left mouse button), ID-ing (right mouse button) or centering (middle 
mouse button) residues, from time to time the wrong residues are 
selected/IDd/centered which are not even in close proximity to the 
intended residue (or just hidden by too narrow slab settings).
Furthermore this doesn't happen consistently, about 2-3 out of 10 mouse 
clicks (still annoying...), possibly with minimal mouse movement 
inbetween but still pointing at the same residue. Interestingly,  the 
same 'wrong' residues keep popping up, when getting selected erroneously 
(but I can't get figure out any 'systematic' behind it yet). The 
behaviour appears with any molecule loaded (also the '1tii' built-into 
the cartoon demo of PyMOL).

Interesting also, I do not observe this behaviour with PyMOL 1.7.4.3. 
and also not when running PyMOL 1.8.x via remote login 
(X-windows-powered SSH), which might indicate a local graphics/mouse 
driver problem?

Any comments are welcome!

Thanks,
Christoph







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Re: [PyMOL] Dynamic reloading of plugin

Re: [PyMOL] query

Re: [PyMOL] strange mouse button problem since version 1.8 with PyMOL for Linux

Re: [PyMOL] query

Re: [PyMOL] Bash scripting and pymol

Re: [PyMOL] Bash scripting and pymol

Re: [PyMOL] query

Re: [PyMOL] query

Re: [PyMOL] Bash scripting and pymol

[PyMOL] query

Re: [PyMOL] Bash scripting and pymol

Re: [PyMOL] Bash scripting and pymol

[PyMOL] Bash scripting and pymol

[PyMOL] strange mouse button problem since version 1.8 with PyMOL for Linux

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