pymol-users Mailing List for PyMOL Molecular Graphics System

Thats great input.

Thanks alot, will check.

Martin

On 27.04.16 20:36, Sampson, Jared M. wrote:
> 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 <tho...@sc...> 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 <ma...@bl...> 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.
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

Yes thanks it works!

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

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

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




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

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

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

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

Here the realization of that for only 1 reference:

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



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

Thanks for help!

J,

2016-04-28 15:48 GMT+02:00 David Hall <li...@co...>:
> You need to add “,async=0” to your fetch calls.
>
> http://pymolwiki.org/index.php/Fetch
>
>
>
>> On Apr 28, 2016, at 4:51 AM, James Starlight <jms...@gm...> wrote:
>>
>> Hi,
>>
>> My script is
>>
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> pdb_array_store=$template/pymol
>>
>>
>> # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them!
>> mkdir ${pdb_array_store}
>> for i in ${pdb_array[@]}; do
>> pdb_tit=$(basename "$i")
>> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
>> ${pdb_tit}" -c ;
>> rm ${pdb_array_store}/*.log
>> done
>>
>>
>> while executing it sends error
>>
>> PyMOL>fetch 5A2H; save
>> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
>> 5A2H
>> please wait ...
>> Selector-Error: Invalid selection name "5A2H".
>> ( 5A2H )<--
>> Save: wrote "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
>> PyMOL: normal program termination.
>>
>> if I change save selection just to 'polymer' it saved empty pdbs-
>> where might be an error here?
>>
>> Thanks!
>>
>> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <ts...@gm...>:
>>> Hi,
>>>
>>> You need
>>>
>>> for i in ${pdb_array[@]}
>>> do
>>> ...
>>> done
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Apr 27, 2016 4:44 PM, "James Starlight" <jms...@gm...> wrote:
>>>>
>>>> so As I tried to do it but it was not worked :-O)
>>>>
>>>> #pdbs list
>>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>>> #where to save
>>>> pdb_array_store=$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 <jms...@gm...>:
>>>>> 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 <jms...@gm...>:
>>>>>> 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 <jwi...@gm...>:
>>>>>>> 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 <jwi...@gm...>
>>>>>>> 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 <jms...@gm...>
>>>>>>> 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
>>>>>>> _______________________________________________
>>>>>>> PyMOL-users mailing list (PyM...@li...)
>>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>>> Archives:
>>>>>>> http://www.mail-archive.com/pym...@li...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

You need to add “,async=0” to your fetch calls.

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



> On Apr 28, 2016, at 4:51 AM, James Starlight <jms...@gm...> wrote:
> 
> Hi,
> 
> My script is
> 
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> pdb_array_store=$template/pymol
> 
> 
> # A simple FETCHER via PYMOL: download pdbs to the folder and pre-process them!
> mkdir ${pdb_array_store}
> for i in ${pdb_array[@]}; do
> pdb_tit=$(basename "$i")
> pymol -d "fetch $i; save ${pdb_array_store}/${pdb_tit}_proc.pdb,
> ${pdb_tit}" -c ;
> rm ${pdb_array_store}/*.log
> done
> 
> 
> while executing it sends error
> 
> PyMOL>fetch 5A2H; save
> /projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb,
> 5A2H
> please wait ...
> Selector-Error: Invalid selection name "5A2H".
> ( 5A2H )<--
> Save: wrote "/projects/clouddyn/md_bench/script_amber/inputs/pymol/5A2H_proc.pdb".
> PyMOL: normal program termination.
> 
> if I change save selection just to 'polymer' it saved empty pdbs-
> where might be an error here?
> 
> Thanks!
> 
> 2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <ts...@gm...>:
>> Hi,
>> 
>> You need
>> 
>> for i in ${pdb_array[@]}
>> do
>> ...
>> done
>> 
>> Cheers,
>> 
>> Tsjerk
>> 
>> On Apr 27, 2016 4:44 PM, "James Starlight" <jms...@gm...> wrote:
>>> 
>>> so As I tried to do it but it was not worked :-O)
>>> 
>>> #pdbs list
>>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>>> #where to save
>>> pdb_array_store=$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 <jms...@gm...>:
>>>> 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 <jms...@gm...>:
>>>>> 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 <jwi...@gm...>:
>>>>>> 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 <jwi...@gm...>
>>>>>> 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 <jms...@gm...>
>>>>>> 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
>>>>>> _______________________________________________
>>>>>> PyMOL-users mailing list (PyM...@li...)
>>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>> Archives:
>>>>>> http://www.mail-archive.com/pym...@li...
>>>>>> 
>>>>>> 
>>>>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> 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
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi,

My script is

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


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


while executing it sends error

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

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

Thanks!

2016-04-27 16:53 GMT+02:00 Tsjerk Wassenaar <ts...@gm...>:
> Hi,
>
> You need
>
> for i in ${pdb_array[@]}
> do
> ...
> done
>
> Cheers,
>
> Tsjerk
>
> On Apr 27, 2016 4:44 PM, "James Starlight" <jms...@gm...> wrote:
>>
>> so As I tried to do it but it was not worked :-O)
>>
>> #pdbs list
>> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
>> #where to save
>> pdb_array_store=$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 <jms...@gm...>:
>> > 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 <jms...@gm...>:
>> >> 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 <jwi...@gm...>:
>> >>> 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 <jwi...@gm...>
>> >>> 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 <jms...@gm...>
>> >>> 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
>> >>> _______________________________________________
>> >>> PyMOL-users mailing list (PyM...@li...)
>> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >>> Archives:
>> >>> http://www.mail-archive.com/pym...@li...
>> >>>
>> >>>
>> >>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...

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 <tho...@sc...> 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 <ma...@bl...> 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.
> 
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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 <h.a...@gm...> 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 <meh...@gm...> 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 <dh...@gm...> 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 <meh...@gm...> 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.

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 <cpa...@go...> 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

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

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 <meh...@gm...> 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 <dh...@gm...> 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 <meh...@gm...> 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
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Hi,

You need

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

Cheers,

Tsjerk
On Apr 27, 2016 4:44 PM, "James Starlight" <jms...@gm...> 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 <jms...@gm...>:
> > 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 <jms...@gm...>:
> >> 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 <jwi...@gm...>:
> >>> 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 <jwi...@gm...>
> 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 <jms...@gm...>
> 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
> >>> _______________________________________________
> >>> PyMOL-users mailing list (PyM...@li...)
> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>> Archives:
> http://www.mail-archive.com/pym...@li...
> >>>
> >>>
> >>>
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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 <jms...@gm...>:
> 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 <jms...@gm...>:
>> 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 <jwi...@gm...>:
>>> 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 <jwi...@gm...> 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 <jms...@gm...> 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
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>>
>>>

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 <dh...@gm...> 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 <meh...@gm...>
> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

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 <meh...@gm...>
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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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 <jms...@gm...>:
> 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 <jwi...@gm...>:
>> 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 <jwi...@gm...> 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 <jms...@gm...> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>

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!

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 <jwi...@gm...> 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 <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 <jms...@gm... <mailto:jms...@gm...>> 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 <" rel="nofollow">https://ad.doubleclick.net/ddm/clk/302982198;130105516;z>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 

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 <jms...@gm...> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

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

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

Thank you both for taking the time to work this out, and explain how and why it works!



> On Apr 26, 2016, at 8:14 AM, Thomas Holder <tho...@sc...> wrote:
> 
> Hi Adam and Annemarie,
> 
> There are no alt location in these files. In the slash notation, the second item is the segment identifier, which for mmCIF files in the label_asym_id field (the third item, chain, is the auth_asym_id field). For this example, the label_asym_id (segi) should be easier to match up between the two structures than the auth_asym_id (chain).
> 
> # To illustrate the arrangement of label_asym_ids:
> 
> fetch 3j5r 3j5q, async=0
> as ribbon
> set grid_mode
> spectrum segi
> label guide and resn ALA, segi
> set_view (\
>    -0.985940218,   -0.146149188,   -0.081017971,\
>     0.152838722,   -0.984706044,   -0.083635844,\
>    -0.067555539,   -0.094843410,    0.993197739,\
>     0.000000000,    0.000000000, -619.393493652,\
>     0.042427063,   -0.005607605,    6.552642822,\
>   516.705444336,  722.081604004,  -20.000000000 )
> 
> # So I would swap segi A and C for one of the structures to bring
> # the chains into the same order. The chain identifier (third item in
> # slash notation) doesn't affect sorting in this case, since the segi
> # has higher priority.
> 
> stored.remap = {'A': 'C', 'C': 'A'}
> alter 3j5q, segi = stored.remap.get(segi, segi)
> sort
> 
> # illustrate that the order is the same now:
> 
> spectrum segi
> label guide and resn ALA, segi
> 
> # Now the morphing should work as expected:
> 
> morph mout, 3j5r, 3j5q, refinement=0
> 
> Hope that helps.
> 
> See also:
> http://pymolwiki.org/index.php/Selection_Macros
> 
> Cheers,
>  Thomas
> 
> On 26 Apr 2016, at 08:24, harold steinberg <h.a...@gm...> wrote:
> 
>> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
>> 
>> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other.    I have tried it all the ways I can think of, I tried all possible combinations.
>> 
>> These are .cif files not .pdb files.
>> 
>> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
>> 
>>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
>>> 
>>> Yes, you want to keep atoms that have no alternative conformation  (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>>> therefore you specify:
>>> 
>>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors , bottom of page
>>> 
>>> best regards 
>>> 
>>> 		Annemarie
>>> 
>>> _______________________________
>>> 
>>> Dr. Annemarie Honegger PhD
>>> Department 
>>> of Biochemistry
>>> Zürich University
>>> Winterthurerstrasse 190
>>> CH-8057 Zürich
>>> Switzerland
>>> 
>>> e-Mail: hon...@bi...
>>> 
>>> websites
>>> http://www.bioc.uzh.ch/plueckthun
>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm...> wrote:
>>>> 
>>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>>> 
>>>> 
>>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
>>>>> 
>>>>> Hi Annemarie,
>>>>> 
>>>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>>>> 
>>>>> 
>>>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
>>>>>> 
>>>>>> Hi Adam
>>>>>> 
>>>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
>>>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>>>> 
>>>>>> best regards
>>>>>> 
>>>>>> 		Annemarie
>>>>>> _______________________________
>>>>>> 
>>>>>> Dr. Annemarie Honegger PhD
>>>>>> Department 
>>>>>> of Biochemistry
>>>>>> Zürich University
>>>>>> Winterthurerstrasse 190
>>>>>> CH-8057 Zürich
>>>>>> Switzerland
>>>>>> 
>>>>>> e-Mail: hon...@bi...
>>>>>> 
>>>>>> websites
>>>>>> http://www.bioc.uzh.ch/plueckthun
>>>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> Message: 6
>>>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>>>> From: harold steinberg <h.a...@gm...>
>>>>>>> Subject: [PyMOL] morph issues
>>>>>>> To: pymol-users <pym...@li...>
>>>>>>> Message-ID: <0E8...@gm...>
>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>> 
>>>>>>> Hi all,
>>>>>>> 
>>>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>>>> 
>>>>>>> In the structures that do not morph correctly a sample selection is:
>>>>>>> /3j5r/A/B/ILE`573/CD1
>>>>>>> /3j5q/C/E/ILE`573/CD1
>>>>>>> 
>>>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>>>> 
>>>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>>>> /3lut//D/GLY`338/CA
>>>>>>> 
>>>>>>> Is that what is messing up the morph?
>>>>> 
>>>>> H. Adam Steinberg
>>>>> 7904 Bowman Rd
>>>>> Lodi, WI 53555
>>>>> 608/592-2366
>>>>> 
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

OK, after some trial and error I have found out a way that works.

The two structures have the corresponding chains in different orders and with different chain labels:

You can copy-paste the following commands into Pymol to follow that I did:

#--------------------------------------------------------------------------------------------------------------------------------
# get the structures from the pdb:

load http://www.rcsb.org/pdb/files/3j5r.pdb
load http://www.rcsb.org/pdb/files/3j5q.pdb

hide all
show ribbon
util.cbc

# chain labels are not the same in both molecules, 
# chain A in 3j5r corresponds to chain B in 3j5q, B to E, C to D, D to G
# chains A,C,F and A in 3j5q are additional small domains of unknown sequence
# the order in the pdb file is B-A-C-D for 3j5r and D-B-E-G in 3j5q
# additional "UNK" residues in 3j5q confuse the issue

remove resn UNK

# morphing a single chain, /3j5r//A to /3j5q//B 

create objA, /3j5r//A
create objB, /3j5q//B

morph objC, objA, objB

# this works!!!

delete objA objB objC

#-----------------------------------

# now all 4 chains: if I do

morph objD, 3j5r, 3j5q

# the wrong chains morph into each other

delete objD

#-----------------------------------

# give corresponding chains the same chain label

alter /3j5q//B, chain="A"
alter /3j5q//E, chain="B"
alter /3j5q//D, chain="C"
alter /3j5q//G, chain="D"

util.cbc

morph objE, 3j5r, 3j5q

# to change the chain identifiers is not enough!!!

delete objE

#-----------------------------------

# is it possible to take objects apart and put them back to
extract 3j5rA, /3j5r//A
extract 3j5rB, /3j5r//B
extract 3j5rC, /3j5r//C
extract 3j5rD, /3j5r//D
delete 3j5r


extract 3j5qA, /3j5q//A
extract 3j5qB, /3j5q//B
extract 3j5qC, /3j5q//C
extract 3j5qD, /3j5q//D
delete 3j5q

create 3j5r, 3j5rA or 3j5rB or 3j5rC or 3j5rD
create 3j5q, 3j5qA or 3j5qB or 3j5qC or 3j5qD

morph objF, 3j5r, 3j5q

# still something strange happening, I am loosing atoms in chain B and D
delete objF

#-----------------------------------

morph objG, 3j5rA, 3j5qA
morph objH, 3j5rB, 3j5qB
morph objI, 3j5rC, 3j5qC
morph objJ, 3j5rD, 3j5qD

# OK, this works
#--------------------------------------------------------------------------------------------------------------------------------


although I do not understand haow you managed to get segment identifiers into your selections


best regards
		Annemarie
_______________________________

Dr. Annemarie Honegger PhD
Department 
of Biochemistry
Zürich University
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland

e-Mail: hon...@bi...

websites
http://www.bioc.uzh.ch/plueckthun
http://www.bioc.uzh.ch/plueckthun/antibody
http://www.bioc.uzh.ch/plueckthun/nanowelt






> On 26 Apr 2016, at 14:24, harold steinberg <h.a...@gm...> wrote:
> 
> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
> 
> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other.    I have tried it all the ways I can think of, I tried all possible combinations.
> 
> These are .cif files not .pdb files.
> 
> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
> 
>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote:
>> 
>> Yes, you want to keep atoms that have no alternative conformation  (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>> therefore you specify:
>> 
>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors <" rel="nofollow">http://www.pymolwiki.org/index.php/Property_Selectors> , bottom of page
>> 
>> best regards 
>> 
>> 		Annemarie
>> 
>> _______________________________
>> 
>> Dr. Annemarie Honegger PhD
>> Department 
>> of Biochemistry
>> Zürich University
>> Winterthurerstrasse 190
>> CH-8057 Zürich
>> Switzerland
>> 
>> e-Mail: hon...@bi... <mailto:hon...@bi...>
>> 
>> websites
>> http://www.bioc.uzh.ch/plueckthun <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun>
>> http://www.bioc.uzh.ch/plueckthun/antibody <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun/antibody>
>> http://www.bioc.uzh.ch/plueckthun/nanowelt <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun/nanowelt>
>> 
>> 
>> 
>> 
>> 
>> 
>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>>> 
>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>> 
>>> 
>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>>>> 
>>>> Hi Annemarie,
>>>> 
>>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>>> 
>>>> 
>>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote:
>>>>> 
>>>>> Hi Adam
>>>>> 
>>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
>>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>>> 
>>>>> best regards
>>>>> 
>>>>> 		Annemarie
>>>>> _______________________________
>>>>> 
>>>>> Dr. Annemarie Honegger PhD
>>>>> Department 
>>>>> of Biochemistry
>>>>> Zürich University
>>>>> Winterthurerstrasse 190
>>>>> CH-8057 Zürich
>>>>> Switzerland
>>>>> 
>>>>> e-Mail: hon...@bi... <mailto:hon...@bi...>
>>>>> 
>>>>> websites
>>>>> http://www.bioc.uzh.ch/plueckthun <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun>
>>>>> http://www.bioc.uzh.ch/plueckthun/antibody <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun/antibody>
>>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Message: 6
>>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>>> From: harold steinberg <h.a...@gm...>
>>>>>> Subject: [PyMOL] morph issues
>>>>>> To: pymol-users <pym...@li...>
>>>>>> Message-ID: <0E8...@gm...>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>>> 
>>>>>> In the structures that do not morph correctly a sample selection is:
>>>>>> /3j5r/A/B/ILE`573/CD1
>>>>>> /3j5q/C/E/ILE`573/CD1
>>>>>> 
>>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>>> 
>>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>>> /3lut//D/GLY`338/CA
>>>>>> 
>>>>>> Is that what is messing up the morph?
>>>>>> 
>>>>>> 
>>>>>> H. Adam Steinberg
>>>>>> 7904 Bowman Rd
>>>>>> Lodi, WI 53555
>>>>>> 608/592-2366
>>>>>> 
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> 
>>>>>> ------------------------------
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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
>>>>>> 
>>>>>> ------------------------------
>>>>>> 
>>>>>> _______________________________________________
>>>>>> PyMOL-users mailing list
>>>>>> PyM...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>> 
>>>>>> 
>>>>>> End of PyMOL-users Digest, Vol 119, Issue 16
>>>>>> ********************************************
>>>>> 
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> 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
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list (PyM...@li...)
>>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> 
>>>> H. Adam Steinberg
>>>> 7904 Bowman Rd
>>>> Lodi, WI 53555
>>>> 608/592-2366
>>>> 
>>> 
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>> 
>> 
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 

Hi Adam and Annemarie,

There are no alt location in these files. In the slash notation, the second item is the segment identifier, which for mmCIF files in the label_asym_id field (the third item, chain, is the auth_asym_id field). For this example, the label_asym_id (segi) should be easier to match up between the two structures than the auth_asym_id (chain).

# To illustrate the arrangement of label_asym_ids:

fetch 3j5r 3j5q, async=0
as ribbon
set grid_mode
spectrum segi
label guide and resn ALA, segi
set_view (\
    -0.985940218,   -0.146149188,   -0.081017971,\
     0.152838722,   -0.984706044,   -0.083635844,\
    -0.067555539,   -0.094843410,    0.993197739,\
     0.000000000,    0.000000000, -619.393493652,\
     0.042427063,   -0.005607605,    6.552642822,\
   516.705444336,  722.081604004,  -20.000000000 )

# So I would swap segi A and C for one of the structures to bring
# the chains into the same order. The chain identifier (third item in
# slash notation) doesn't affect sorting in this case, since the segi
# has higher priority.

stored.remap = {'A': 'C', 'C': 'A'}
alter 3j5q, segi = stored.remap.get(segi, segi)
sort

# illustrate that the order is the same now:

spectrum segi
label guide and resn ALA, segi

# Now the morphing should work as expected:

morph mout, 3j5r, 3j5q, refinement=0

Hope that helps.

See also:
http://pymolwiki.org/index.php/Selection_Macros

Cheers,
  Thomas

On 26 Apr 2016, at 08:24, harold steinberg <h.a...@gm...> wrote:

> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
> 
> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other.    I have tried it all the ways I can think of, I tried all possible combinations.
> 
> These are .cif files not .pdb files.
> 
> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
> 
>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
>> 
>> Yes, you want to keep atoms that have no alternative conformation  (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>> therefore you specify:
>> 
>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors , bottom of page
>> 
>> best regards 
>> 
>> 		Annemarie
>> 
>> _______________________________
>> 
>> Dr. Annemarie Honegger PhD
>> Department 
>> of Biochemistry
>> Zürich University
>> Winterthurerstrasse 190
>> CH-8057 Zürich
>> Switzerland
>> 
>> e-Mail: hon...@bi...
>> 
>> websites
>> http://www.bioc.uzh.ch/plueckthun
>> http://www.bioc.uzh.ch/plueckthun/antibody
>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>> 
>> 
>> 
>> 
>> 
>> 
>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm...> wrote:
>>> 
>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>> 
>>> 
>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
>>>> 
>>>> Hi Annemarie,
>>>> 
>>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>>> 
>>>> 
>>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
>>>>> 
>>>>> Hi Adam
>>>>> 
>>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
>>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>>> 
>>>>> best regards
>>>>> 
>>>>> 		Annemarie
>>>>> _______________________________
>>>>> 
>>>>> Dr. Annemarie Honegger PhD
>>>>> Department 
>>>>> of Biochemistry
>>>>> Zürich University
>>>>> Winterthurerstrasse 190
>>>>> CH-8057 Zürich
>>>>> Switzerland
>>>>> 
>>>>> e-Mail: hon...@bi...
>>>>> 
>>>>> websites
>>>>> http://www.bioc.uzh.ch/plueckthun
>>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Message: 6
>>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>>> From: harold steinberg <h.a...@gm...>
>>>>>> Subject: [PyMOL] morph issues
>>>>>> To: pymol-users <pym...@li...>
>>>>>> Message-ID: <0E8...@gm...>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>>> 
>>>>>> In the structures that do not morph correctly a sample selection is:
>>>>>> /3j5r/A/B/ILE`573/CD1
>>>>>> /3j5q/C/E/ILE`573/CD1
>>>>>> 
>>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>>> 
>>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>>> /3lut//D/GLY`338/CA
>>>>>> 
>>>>>> Is that what is messing up the morph?
>>>> 
>>>> H. Adam Steinberg
>>>> 7904 Bowman Rd
>>>> Lodi, WI 53555
>>>> 608/592-2366
>>>> 

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.

Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other.    I have tried it all the ways I can think of, I tried all possible combinations.

These are .cif files not .pdb files.

No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.

> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
> 
> Yes, you want to keep atoms that have no alternative conformation  (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
> therefore you specify:
> 
> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors <" rel="nofollow">http://www.pymolwiki.org/index.php/Property_Selectors> , bottom of page
> 
> best regards 
> 
> 		Annemarie
> 
> _______________________________
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: hon...@bi... <mailto:hon...@bi...>
> 
> websites
> http://www.bioc.uzh.ch/plueckthun <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun>
> http://www.bioc.uzh.ch/plueckthun/antibody <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun/antibody>
> http://www.bioc.uzh.ch/plueckthun/nanowelt <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun/nanowelt>
> 
> 
> 
> 
> 
> 
>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>> 
>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>> 
>> 
>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
>>> 
>>> Hi Annemarie,
>>> 
>>> Thank you for the answer. Do you know the command to remove the alternative conformation?
>>> 
>>> 
>>>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi... <mailto:hon...@bi...>> wrote:
>>>> 
>>>> Hi Adam
>>>> 
>>>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
>>>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>>>> 
>>>> best regards
>>>> 
>>>> 		Annemarie
>>>> _______________________________
>>>> 
>>>> Dr. Annemarie Honegger PhD
>>>> Department 
>>>> of Biochemistry
>>>> Zürich University
>>>> Winterthurerstrasse 190
>>>> CH-8057 Zürich
>>>> Switzerland
>>>> 
>>>> e-Mail: hon...@bi... <mailto:hon...@bi...>
>>>> 
>>>> websites
>>>> http://www.bioc.uzh.ch/plueckthun <" rel="nofollow">http://www.bioc.uzh.ch/plueckthun>
>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> 
>>>>> 
>>>>> Message: 6
>>>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>>>> From: harold steinberg <h.a...@gm...>
>>>>> Subject: [PyMOL] morph issues
>>>>> To: pymol-users <pym...@li...>
>>>>> Message-ID: <0E8...@gm...>
>>>>> Content-Type: text/plain; charset="utf-8"
>>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>>>> 
>>>>> In the structures that do not morph correctly a sample selection is:
>>>>> /3j5r/A/B/ILE`573/CD1
>>>>> /3j5q/C/E/ILE`573/CD1
>>>>> 
>>>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>>>> 
>>>>> In files that the morph does work this letter is missing (it?s a blank space):
>>>>> /3lut//D/GLY`338/CA
>>>>> 
>>>>> Is that what is messing up the morph?
>>>>> 
>>>>> 
>>>>> H. Adam Steinberg
>>>>> 7904 Bowman Rd
>>>>> Lodi, WI 53555
>>>>> 608/592-2366
>>>>> 
>>>>> -------------- next part --------------
>>>>> An HTML attachment was scrubbed...
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> 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
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> PyM...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>> 
>>>>> 
>>>>> End of PyMOL-users Digest, Vol 119, Issue 16
>>>>> ********************************************
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>> 
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.


> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
> 
> Hi Annemarie,
> 
> Thank you for the answer. Do you know the command to remove the alternative conformation?
> 
> 
>> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
>> 
>> Hi Adam
>> 
>> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
>> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
>> 
>> best regards
>> 
>> 		Annemarie
>> _______________________________
>> 
>> Dr. Annemarie Honegger PhD
>> Department 
>> of Biochemistry
>> Zürich University
>> Winterthurerstrasse 190
>> CH-8057 Zürich
>> Switzerland
>> 
>> e-Mail: hon...@bi...
>> 
>> websites
>> http://www.bioc.uzh.ch/plueckthun
>> http://www.bioc.uzh.ch/plueckthun/antibody
>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>> 
>> 
>> 
>> 
>> 
>>> 
>>> 
>>> Message: 6
>>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>>> From: harold steinberg <h.a...@gm...>
>>> Subject: [PyMOL] morph issues
>>> To: pymol-users <pym...@li...>
>>> Message-ID: <0E8...@gm...>
>>> Content-Type: text/plain; charset="utf-8"
>>> 
>>> Hi all,
>>> 
>>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>>> 
>>> In the structures that do not morph correctly a sample selection is:
>>> /3j5r/A/B/ILE`573/CD1
>>> /3j5q/C/E/ILE`573/CD1
>>> 
>>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>>> 
>>> In files that the morph does work this letter is missing (it?s a blank space):
>>> /3lut//D/GLY`338/CA
>>> 
>>> Is that what is messing up the morph?
>>> 
>>> 
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>> 
>>> -------------- next part --------------
>>> An HTML attachment was scrubbed...
>>> 
>>> ------------------------------
>>> 
>>> ------------------------------------------------------------------------------
>>> 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
>>> 
>>> ------------------------------
>>> 
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> 
>>> 
>>> End of PyMOL-users Digest, Vol 119, Issue 16
>>> ********************************************
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

Hi Annemarie,

Thank you for the answer. Do you know the command to remove the alternative conformation?


> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
> 
> Hi Adam
> 
> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
> 
> best regards
> 
> 		Annemarie
> _______________________________
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: hon...@bi...
> 
> websites
> http://www.bioc.uzh.ch/plueckthun
> http://www.bioc.uzh.ch/plueckthun/antibody
> http://www.bioc.uzh.ch/plueckthun/nanowelt
> 
> 
> 
> 
> 
>> 
>> 
>> Message: 6
>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>> From: harold steinberg <h.a...@gm...>
>> Subject: [PyMOL] morph issues
>> To: pymol-users <pym...@li...>
>> Message-ID: <0E8...@gm...>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi all,
>> 
>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>> 
>> In the structures that do not morph correctly a sample selection is:
>> /3j5r/A/B/ILE`573/CD1
>> /3j5q/C/E/ILE`573/CD1
>> 
>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>> 
>> In files that the morph does work this letter is missing (it?s a blank space):
>> /3lut//D/GLY`338/CA
>> 
>> Is that what is messing up the morph?
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> 
>> ------------------------------
>> 
>> ------------------------------------------------------------------------------
>> 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
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> 
>> 
>> End of PyMOL-users Digest, Vol 119, Issue 16
>> ********************************************
> 
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366