VMD-L Mailing List

From: Ryan Woltz (rlwoltz_at_ucdavis.edu)
Date: Wed Jun 26 2024 - 18:41:17 CDT

Dear all,

      I forgot to mention that there is one edit to Diego's script.

the line:

set sel [atomselect top "resid 190-350"]

should read:

set sel [atomselect top "resid 190 to 350"]

With this edit the script seems to work for me

Thank you again,

Ryan

On Wed, Jun 26, 2024 at 4:29 PM Ryan Woltz <rlwoltz_at_ucdavis.edu> wrote:

> Dear Diego and Gianluca,
>
> Thank you both for your help. For anyone searching for this in the future,
> modifying Diego's script seems to be the safest way to go. I made a list
> using ls mode-*.pdb which organizes the names as expected. However, glob in
> tcl to make a matching name list seems to make a random list of names. Here
> is the output from a [glob model-*.pdb] ###same as ls in bash
>
> model_0_unrelaxed_alphafold2_multimer_v3_model_1_seed_002.r4.pdb
> model_0_unrelaxed_alphafold2_multimer_v3_model_5_seed_003.r1.pdb
> model_0_unrelaxed_alphafold2_multimer_v3_model_2_seed_007.r2.pdb
> model_0_unrelaxed_alphafold2_multimer_v3_model_3_seed_010.r1.pdb
> model_0_unrelaxed_alphafold2_multimer_v3_model_1_seed_003.r2.pdb
>
> So I'd advise to create a list in a file using Gianluca's advice and
> import that list into vmd with the read command and Diego's script. If you
> do not need to load in a specific order and just need to keep track of the
> file names Diego's script works as is.
>
> Thank you both for your assistance once again as both solutions was very
> helpful.
>
> Ryan
>
> On Wed, Jun 26, 2024 at 2:10 PM Gianluca Interlandi <
> gianluca_at_u.washington.edu> wrote:
>
>> > vmd models-*.pdb -e modify.tcl
>>
>> I believe that the "*" on the command line acts the same as globbing. You
>> can type
>>
>> ls models-*.pdb
>>
>> and this should give you the sequence how the "*" is replaced. If for
>> example your models are numbered: models-1.pdb, models-2.pdb, ...,
>> models-10.pdb, ..., models-100.pdb, ..., models-1000.pdb, and you want
>> them to be read in increasing sequence, you may need to use:
>>
>> vmd models-?.pdb models-??.pdb models-???.pdb models-????.pdb -e
>> modify.tcl
>>
>> But if you named them models-0001.pdb ... models-1000.pdb, then you
>> shoudn't have to.
>>
>> Gianluca
>>
>> On Wed, 26 Jun 2024, Ryan Woltz wrote:
>>
>> > Dear community,
>> > I think I can do this task with UCSF chimera and maybe it is
>> better suited but I have all the
>> > scripts already written for vmd and I like the results. I have 1000
>> models I need to import into vmd
>> > then save residues 190-350 and save each one with the same name. The
>> name of the pdb is important to
>> > preserve because I have a table with associated values to help rank the
>> pdbs. I have scripts to
>> > import and modify and save, however, I'm seeking advice on the safest
>> method to preserve the name. I
>> > can either
>> >
>> > A) develop a bash script loop to open vmd with a single pdb modify then
>> save. i.e. for i - 1 to 1000
>> > - do vmd model-$i.pdb -e modify.tcl done (where i is the model number
>> and modify.tcl selects and
>> > saves the desired region). The problem with this is that it'll be very
>> heavy and time consuming
>> > opening vmd that many times for a bigger batch of models. Also I don't
>> know how to import the
>> > model-$i.pdb name into the tcl so that it saves with the same name.
>> >
>> > B) (preferred since all my scripts currently use this) open vmd with
>> all the models as frames. i.e.
>> > vmd models-*.pdb -e modify.tcl. this is what I normally do to analyze
>> my pdbs and have many scripts
>> > either measuring bond distances, rmsd, or saving sections but the pdb
>> names are associated with the
>> > frame number. I can create a separate array that collects the file
>> names (glob function) then moves
>> > through the array at the same rate of the frames. My concern with this
>> is "vmd model-*.jpdb" and the
>> > tcl function "glob" might have a different sorting order. My model
>> names are actually quite long and
>> > complex with main deviations happening at a "." "r" or "0-9". My
>> question for this one is does "*" in
>> > the vmd loading protocol prioritize letters/numbers/special characters
>> the same as "glob"? I've run
>> > into this filename sorting issue a long time ago with a different
>> program so I'm quite paranoid about
>> > this now.
>> >
>> > Thanks for suggestions,
>> >
>> > Ryan
>> >
>> >
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> https://urldefense.com/v3/__http://gianluca.today/research/__;!!DZ3fjg!5nI0S76f-WE-musAfCgh2NqRkch88iXyRE9ovL6jELH3jhhf_o6FSYJGdsF3Ma4gR7T5apHktQMArO5C2TluSg$
>>
>> Department of Bioengineering
>> University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
>