Re: [PyMOL] Bash scripting and pymol
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 :
> 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!
>> >>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> >>> ___
>> >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >>> Archives:
>> >>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> >>>
>> >>>
>> >>>
>>
>>
>> --
>> 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 (PyMOL-users@lists.sourceforge.net)
>> Info Page:
Re: [PyMOL] Bash scripting and pymol
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 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 :
>> 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!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>>
>>>
>>>
>>> --
>>> Find and fix application performance issues faster with Applications
>>> Manager
>>> Applications Manager provides deep performance insights into multiple
>>> tiers of
[PyMOL] okay
-- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
