Problem with t-coffee finding local pdb files as templates

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Esteban López Tavera

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Aug 23, 2022, 11:06:19 AM8/23/22
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Dear T-coffee team,

I'm running t-coffee locally (T-COFFEE Version_13.45.0.4846264), with mode expresso, using a database I made from a small set of sequences. I have the corresponding pdb files, some from structure models and some crystal structures, which I'd like to be used as templates.

My command looks like this:
t_coffee -in=my_input_seqs.fa -mode=expresso\
 -blast=LOCAL\
 -pdb_db=<Absolute path to my db>\
 -pdb_type=dnm\
 -output=score_html,clustalw_aln,fasta_aln -outorder=input\
 -run_name=test -cache=$PWD -pdb_min_sim 85 -pdb_min_cov 90


I have set the environment variables accordingly:
  • PDB_DIR=<absolute path to where the template pdb files are located>
  • NO_REMOTE_PDB_DIR=1
  • PDB_ENTRY_TYPE_FILE=<Path to a txt file with my template ids, all as  prot diffraction, in the same format as the actual pdb_entry_type>
The pdb files are named in the format id_in_the_database.pdb
I also tried copying all the pdb files to the current directory.

Yet, I'm still getting the following after it fails to retrieve any template:

**<PROTEIN_ID> [PDB NOT RELEASED or WITHDRAWN]
<Sequence_ID> No Template Selected

And as a consequence, for all my sequences I get:

Method  cannot be applied to [<sequence_id1> vs <sequence_id2>], proba_pair will be used instead.

Could you help me figure out how to use my pdb files as templates?

Best,
Esteban




Athanasios Baltzis

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Aug 24, 2022, 4:56:11 AM8/24/22
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Dear Esteban,

I cannot reproduce the issue you mentioned using the latest tcoffee commit (https://github.com/cbcrg/tcoffee). Please update your tcoffee version.

Best,
Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)
  


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Esteban López Tavera

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Aug 24, 2022, 10:03:10 AM8/24/22
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Thank you, Athanasios.

I have updated it, but the problem persists.

This is the code that I'm running:
export PDB_DIR="/Users/esteban/t_coffee_test/test_pdbs"
echo PDB_DIR=$PDB_DIR
echo PDB_DIR contents: $(ls $PDB_DIR)
export NO_REMOTE_PDB_DIR=1
t_coffee -version

t_coffee -in=reduced_CBP21_nopipe_ren.fa -mode=expresso -blast=LOCAL\
 -pdb_db="/Users/esteban/t_coffee_test/test_db/test_db.fa"\
 -pdb_type=dnm\
 -output=score_html,clustalw_aln,fasta_aln -outorder=input\
 -run_name=test -cache=update -pdb_min_sim 50 -pdb_min_cov 90


And this is the first chunk of output that I'm getting:
PDB_DIR=/Users/esteban/t_coffee_test/test_pdbs
PDB_DIR contents: AOM11.pdb CBP21.pdb CELS2.pdb QIS10.pdb SC10D.pdb
PROGRAM: T-COFFEE Version_13.45.60.cd84d2a (Version_13.45.60.cd84d2a)

PROGRAM: T-COFFEE Version_13.45.60.cd84d2a (Version_13.45.60.cd84d2a)
-full_log          S    [0]
-genepred_score    S    [0]     nsd
-run_name          S    [1]     test
-mem_mode          S    [0]     mem
-extend            D    [1]     1
-extend_mode       S    [0]     very_fast_triplet
-max_n_pair        D    [0]     10
-seq_name_for_quadruplet    S    [0]     all
-compact           S    [0]     default
-clean             S    [0]     no
-do_self           FL    [0]     0
-do_normalise      D    [0]     1000
-template_file     S    [1]     EXPRESSO
-setenv            S    [0]     0
-export            S    [0]     0
-template_mode     S    [0]
-flip              D    [0]     0
-remove_template_file    D    [0]     0
-profile_template_file    S    [1]     EXPRESSO
-in                S    [1]     reduced_CBP21_nopipe_ren.fa
-seq               S    [0]
-aln               S    [0]
-method_limits     S    [0]
-method            S    [1]     sap_pair
-lib               S    [0]
-profile           S    [0]
-profile1          S    [0]
-profile2          S    [0]
-pdb               S    [0]
-relax_lib         D    [0]     1
-filter_lib        D    [0]     0
-shrink_lib        D    [0]     0
-out_lib           W_F    [0]     no
-out_lib_mode      S    [0]     primary
-lib_only          D    [0]     0
-outseqweight      W_F    [0]     no
-seq_source        S    [0]     ANY
-cosmetic_penalty    D    [0]     0
-gapopen           D    [0]     0
-gapext            D    [0]     0
-fgapopen          D    [0]     0
-fgapext           D    [0]     0
-nomatch           D    [0]     0
-newtree           W_F    [0]     default
-tree              W_F    [0]     NO
-usetree           R_F    [0]
-tree_mode         S    [0]     nj
-distance_matrix_mode    S    [0]     ktup
-distance_matrix_sim_mode    S    [0]     idmat_sim1
-quicktree         FL    [0]     0
-outfile           W_F    [0]     default
-maximise          FL    [1]     1
-output            S    [1]     score_html    clustalw_aln    fasta_aln
-len               D    [0]     0
-infile            R_F    [0]
-matrix            S    [0]     default
-tg_mode           D    [0]     1
-profile_mode      S    [0]     cw_profile_profile
-profile_comparison    S    [0]     profile
-dp_mode           S    [0]     linked_pair_wise
-ktuple            D    [0]     1
-ndiag             D    [0]     0
-diag_threshold    D    [0]     0
-diag_mode         D    [0]     0
-sim_matrix        S    [0]     vasiliky
-transform         S    [0]
-extend_seq        FL    [0]     0
-outorder          S    [1]     input
-inorder           S    [0]     aligned
-seqnos            S    [0]     off
-case              S    [0]     keep
-cpu               D    [0]     0
-ulimit            D    [0]     -1
-maxnseq           D    [0]     -1
-maxlen            D    [0]     -1
-sample_dp         D    [0]     0
-weight            S    [0]     default
-seq_weight        S    [0]     no
-align             FL    [1]     1
-mocca             FL    [0]     0
-domain            FL    [0]     0
-start             D    [0]     0
-len               D    [0]     0
-scale             D    [0]     0
-mocca_interactive    FL    [0]     0
-method_evaluate_mode    S    [0]     default
-color_mode        S    [0]     new
-aln_line_length    D    [0]     0
-evaluate_mode     S    [0]     triplet
-get_type          FL    [0]     0
-clean_aln         D    [0]     0
-clean_threshold    D    [1]     1
-clean_iteration    D    [1]     1
-clean_evaluate_mode    S    [0]     t_coffee_fast
-extend_matrix     FL    [0]     0
-prot_min_sim      D    [0]     0
-prot_max_sim      D    [100]     100
-psiJ              D    [0]     3
-psitrim_mode      S    [0]     regtrim
-psitrim_tree      S    [0]     codnd
-psitrim           D    [100]     100
-prot_min_cov      D    [90]     90
-pdb_type          S    [1]     dnm
-pdb_min_sim       D    [50]     50
-pdb_max_sim       D    [100]     100
-pdb_min_cov       D    [90]     90
-pdb_blast_server    W_F    [0]     EBI
-blast             W_F    [1]     LOCAL
-pdb_db            W_F    [1]     /Users/esteban/t_coffee_test/test_db/test_db.fa
-protein_db        W_F    [0]     uniref50
-method_log        W_F    [0]     no
-struc_to_use      S    [0]
-cache             W_F    [1]     update
-print_cache       FL    [0]     0
-align_pdb_param_file    W_F    [0]     no
-align_pdb_hasch_mode    W_F    [0]     hasch_ca_trace_bubble
-external_aligner    S    [0]     NO
-msa_mode          S    [0]     tree
-et_mode           S    [0]     et
-master            S    [0]     no
-blast_nseq        D    [0]     0
-lalign_n_top      D    [0]     10
-iterate           D    [0]     0
-trim              D    [0]     0
-split             D    [0]     0
-trimfile          S    [0]     default
-split             D    [0]     0
-split_nseq_thres    D    [0]     0
-split_score_thres    D    [0]     0
-check_pdb_status    D    [0]     0
-clean_seq_name    D    [0]     0
-seq_to_keep       S    [0]
-dpa_master_aln    S    [0]
-dpa_maxnseq       D    [0]     0
-dpa_min_score1    D    [0]
-dpa_min_score2    D    [0]
-dpa_keep_tmpfile    FL    [0]     0
-dpa_debug         D    [0]     0
-multi_core        S    [0]     templates_jobs_relax_msa_evaluate
-n_core            D    [0]     1
-thread            D    [0]     1
-max_n_proc        D    [0]     1
-lib_list          S    [0]
-prune_lib_mode    S    [0]     5
-tip               S    [0]     none
-rna_lib           S    [0]
-no_warning        D    [0]     0
-run_local_script    D    [0]     0
-proxy             S    [0]     unset
-email             S    [0]
-clean_overaln     D    [0]     0
-overaln_param     S    [0]
-overaln_mode      S    [0]
-overaln_model     S    [0]
-overaln_threshold    D    [0]     0
-overaln_target    D    [0]     0
-overaln_P1        D    [0]     0
-overaln_P2        D    [0]     0
-overaln_P3        D    [0]     0
-overaln_P4        D    [0]     0
-exon_boundaries    S    [0]
-display           D    [0]     100

INPUT FILES
    Input File (S) reduced_CBP21_nopipe_ren.fa  Format fasta_seq
    Input File (M) sap_pair

Identify Master Sequences [no]:

Master Sequences Identified
Looking For Sequence Templates:

    Template Type: [EXPRESSO] Mode Or File: [EXPRESSO] [Start
!    Process: >AMO81812 [LOCAL/blast//Users/esteban/t_coffee_test/test_db/test_db.fa][COMPUTE CACHE]
        **CBP21 [PDB NOT RELEASED or WITHDRAWN]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
        **CBP21 [PDB NOT RELEASED or WITHDRAWN]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
         >AMO81812 No Template Selected
!    Process: >QXJ62528 [LOCAL/blast//Users/esteban/t_coffee_test/test_db/test_db.fa][COMPUTE CACHE]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
         >QXJ62528 No Template Selected
!    Process: >QXX84031 [LOCAL/blast//Users/esteban/t_coffee_test/test_db/test_db.fa][COMPUTE CACHE]
        **CBP21 [PDB NOT RELEASED or WITHDRAWN]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
        **CBP21 [PDB NOT RELEASED or WITHDRAWN]
        **AOM11 [PDB NOT RELEASED or WITHDRAWN]
         >QXX84031 No Template Selected

...
Then further down, many lines like this, one for each pair:

pid 15360 -- Method  cannot be applied to [AMO81812 vs QXJ62528], proba_pair will be used instead

So, it seems like t_coffee is assigning correctly the templates, but then it fails to find the corresponding structures, which are in the PDB_DIR.

Best,
Esteban 

Cedric Notredame

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Aug 24, 2022, 10:25:56 AM8/24/22
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Dear Esteban, Dear all

I think I know what is the issue: Expresso assumes you are working on public PDBs and it checks them against a list downloaded from PDB and stored in ~/.t_coffee/cache/pdb_entry_type.txt, since your PDBS are not public, it complains.

There are two workaround:

1- the correct one, a bit more involved: use 3D-Coffee instead of Expresso. 3D-Coffee is like Expresso without BLAST. You will need to build your your own template files that bind sequences and PDBs

><seq name> _P_ <PDB>

as many lines as needed

Then run t_coffee -in=reduced_CBP21_nopipe_ren.fa -template_file <your template file> -method sap_pair

you can add other structural pairwise methods, mustang_pair, TMalign_pair are the main ones I would recommand. In our hand TMalign_pair + sap_pair is often the best.

OR, quick and dirty

2-update ~/.t_coffee/cache/pdb_entry_type.txt by concatenating a list of all your PDBs following the original format (one entry per list)

111d    nuc     diffraction
111l    prot    diffraction
111m    prot    diffraction
112d    nuc     diffraction
112l    prot    diffraction

You may want to run the cat in your script to avoid your pdb_entry_file being updated. Note that I have not had time to check it. YOu may want to add TWO PDBs manualy and see if it works


All of these decision were taken before AF2... In the next release I will make Expresso more tolerant to unrealeased PDBs. Thanks for pointing this out.

Cheers,

Cedric


PS: I am also preparing a fix for the missing binaries. More on this soon.

To view this discussion on the web visit https://groups.google.com/d/msgid/tcoffee/1e0d445d-da9a-4c89-826a-187474e0ed53n%40googlegroups.com.
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Esteban López Tavera

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Aug 24, 2022, 11:16:48 AM8/24/22
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Thank you, Cedric!

I tried the dirty workaround (for now) and it seems to be running nicely now.

Just for reference, I had to make sure all pdbs have ids no longer than 5 characters. I guess that's related to what you just mentioned about expresso expecting public PDBs. Also, in the pdb_entry_type.txt file, the pdb ids need to be lowercase.

Indeed, most of my pdb files come from AF2, lol.

Thanks again!

Best,
Esteban

Tyler Starr

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Nov 29, 2022, 8:52:47 PM11/29/22
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Hi Esteban,

I'm trying to follow this thread to solve a similar problem (using local pdb structure files that aren't available yet from public PDB because unpublished). Could you clarify what was the final command you used once updated the pdb_entry_type.txt file as indicated?

My cache'd pdb_entry_type.txt file is:
neoc    prot     diffraction
mers    prot    diffraction
hku4    prot    diffraction

My templates.txt file is:
>hMERS_EMC-2012_JX869059/377-5929 _P_ mers
>HKU4_NC009019/382-5979 _P_ hku4
>NeoCoV_KC869678/380-589 _P_ neoc

and mers.pdb, hku4.pdb, and neoc.pdb are pdb files in the same directory that I'm working within

And I've tried running command various ways including the original type of expresso command you were trying as well as the shorter -method=sap_pair recommended above. Because of your tips on four-digit ids and lowercase ids, I was able to get any clear bugs about pdb imports to go away, but there is still no positive indication that it is actually using sap_pair to modulate those sequences for which I'm trying to provide structures -- for example, in the list of all-against-all methods, two sequences for which I want there to be pdbs loaded to use sap_pair, I am getting e.g. 

-- Method  cannot be applied to [HKU4_NC009019_382-597 vs hMERS_EMC-2012_JX869059_377-592], proba_pair will be used instead

Curious what type of command syntax ended up working for you in the end once the database issues were addressed.

Thanks,
Tyler

Tyler Starr

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Nov 29, 2022, 8:55:55 PM11/29/22
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One problem for me could be the version I'm using -- Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211)

I installed via conda. Not sure if it's easy to make newer versions available from conda for simplicity of installation?

Cedric Notredame

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Nov 30, 2022, 4:11:39 AM11/30/22
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Hello Tyler,

I am not entirely sure what is the issue. We did the conda distribution quite some time ago and are not actively maintaining it. In fact I think there are two such distro including one we did not do and that was not maintained. We have it high on our todolist to look into this or something equivalent for easier uptake. The most trustworthy way would be compiling the latest github beta or download from the website. I think updating will help, 12 is pretty old and predates our use of AF2 structures.

http://tcoffee-packages.s3-website.eu-central-1.amazonaws.com/#Beta/Latest/

Version_13.45.60.cd84d2a


If it does not work, in your template file you should specify the absolute path of your structures files. I think it should work. I would recommend doing this anyway as you may end up with alternative structures of the same sequences. This would specify your things in a permanent way.

All these structure based things in T-Coffee were based on the unformulated assumption that AF2 would never happen... but now that it has, we clearly need to do a bit of thinking, which is not so bad :)

Cheers,

Cedric

Charlotte Crauwels

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Dec 8, 2022, 5:02:08 AM12/8/22
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Hello,

I'm having some issues running 3Dcoffee using AF models:

I'm running the following command:
t_coffee  try.fasta   -method TMalign_pair -template_file a_pdb1.template_list -output=fasta_aln

try.fasta:
>P089
MDVLSPGQGNNTTSPPAPFETGGNTTGISDVTVSYQVITSLLLGTLIFCAVLGNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVLNKWTLGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNKRTPRRAAALISLTWLIGFLISIPPMLGWRTPEDRSDPDACTISKDHGYTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRKTVKKVEKTGADTRHGASPAPQPKKSVNGESGSRNWRLGVESKAGGALCANGAVRQGDDGAALEVIEVHRVGNSKEHLPLPSEAGPTPCAPASFERKNERNAEAKRKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCESSCHMPTLLGAIINWLGYSNSLLNPVIYAYFNKDFQNAFKKIIKCKFCRQ
>P282
MEEPGAQCAPPPPAGSETWVPQANLSSAPSQNCSAKDYIYQDSISLPWKVLLVMLLALITLATTLSNAFVIATVYRTRKLHTPANYLIASLAVTDLLVSILVMPISTMYTVTGRWTLGQVVCDFWLSSDITCCTASILHLCVIALDRYWAITDAVEYSAKRTPKRAAVMIALVWVFSISISLPPFFWRQAKAEEEVSECVVNTDHILYTVYSTVGAFYFPTLLLIALYGRIYVEARSRILKQTPNRTGKRLTRAQLITDSPGSTSSVTSINSRVPDVPSESGSPVYVNQVKVRVSDALLEKKKLMAARERKATKTLGIILGAFIVCWLPFFIISLVMPICKDACWFHLAIFDFFTWLGYLNSLINPIIYTMSNEDFKQAFHKLIRFKCTS
>P309
MDFLNSSDQNLTSEELLNRMPSKILVSLTLSGLALMTTTINSLVIAAIIVTRKLHHPANYLICSLAVTDFLVAVLVMPFSIVYIVRESWIMGQVVCDIWLSVDITCCTCSILHLSAIALDRYRAITDAVEYARKRTPKHAGIMITIVWIISVFISMPPLFWRHQGTSRDDECIIKHDHIVSTIYSTFGAFYIPLALILILYYKIYRAAKTLYHKRQASRIAKEEVNGQVLLESGEKSTKSVSTSYVLEKSLSDPSTDFDKIHSTVRSLRSEFKHEKSWRRQKISGTRERKAATTLGLILGAFVICWLPFFVKELVVNVCDKCKISEEMSNFLAWLGYLNSLINPLIYTIFNEDFKKAFQKLVRCRC

a_pdb1.template_list:
> P089 _P_ p089.pdb
> P282 _P_ p282.pdb
> P309 _P_ p309.pdb


Note that try.fasta, a_pdb1.template_list, and my .pdb files are in the same directory as the one from which I call the command stated above.

I keep having the following output:
Master Sequences Identified
Looking For Sequence Templates:

        Template Type: [a_pdb1.template_list] Mode Or File: [a_pdb1.template_list] [Start]
INPUT SEQUENCES: 3 SEQUENCES  [PROTEIN]
  Input File try.fasta Seq P089 Length  422 type PROTEIN Struct Unchecked
  Input File try.fasta Seq P282 Length  390 type PROTEIN Struct Unchecked
  Input File try.fasta Seq P309 Length  366 type PROTEIN Struct Unchecked

        Multi Core Mode (read): 1 processor(s):

        --- Process Method/Library/Aln Stry.fasta
        xxx Retrieved Stry.fasta
        --- Process Method/Library/Aln MTMalign_pair
pid 8257 -- Method TMalign cannot be applied to [P089 vs P282], proba_pair will be used instead

pid 8257 -- Method TMalign cannot be applied to [P089 vs P309], proba_pair will be used instead

pid 8257 -- Method TMalign cannot be applied to [P282 vs P309], proba_pair will be used instead

        xxx Retrieved MTMalign_pair

        All Methods Retrieved

MANUAL PENALTIES: gapopen=0 gapext=0

        Library Total Size: [6750]

Library Relaxation: Multi_proc [1]

!               [Relax Library][TOT=    3][  0 %]^M!            [Relax Library][TOT=    3][ 66 %]^M!            [Relax Library][TOT=    3][100 %]

Relaxation Summary: [6750]--->[3384]



UN-WEIGHTED MODE: EVERY SEQUENCE WEIGHTS 1

MAKE GUIDE TREE
        [MODE=nj][DONE]

PROGRESSIVE_ALIGNMENT [Tree Based]
Group    1: P089
Group    2: P282
Group    3: P309

#Single Thread

        Group    4: [Group    2 (   1 seq)] with [Group    1 (   1 seq)]-->[Len=  442][PID:8250]
        Group    5: [Group    3 (   1 seq)] with [Group    4 (   2 seq)]-->[Len=  446][PID:8250]


and so on with at the end, an alignment.
But as proba_pair is used instead of TM_pair, I guess it is not using the structures and just aligning the sequences?

Could you please indicate what I do wrong?

Thanks a lot.

Kind regards,
Charlotte

Cedric Notredame

unread,
Dec 8, 2022, 5:41:30 AM12/8/22
to tco...@googlegroups.com
Dear Charlotte

Please update to the lates beta if you have not done so

For the files, please provide the relative./ or the absolute path.

It should then work 

Cheers 

Cedric 

###################################
Dr Cedric Notredame

Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain

Ph#     + 34 93 316 02 71
Fax#    + 34 93 316 00 99
Mobile# + 34 66 250 47 82

email   cedric.n...@crg.eu
url     www.tcoffee.org
blog    cedricnotredame.blogspot.com
ORC-ID: 0000-0003-1461-0988
###################################

On 8 Dec 2022, at 11:02, Charlotte Crauwels <charlotte....@gmail.com> wrote:

Hello,

Charlotte Crauwels

unread,
Dec 9, 2022, 5:30:40 AM12/9/22
to Tcoffee
Dear Cedric,

I'm working on a supercomputer , I can't thus just update the version (now working on T-COFFEE Version_13.45.0.4846264 (2020-10-15 17:52:11 - Revision 5becd5d - Build 620)). Is there no work around to make it work on this version? I have tried with the absolute and relative paths but it didn't change anything to my output.

command: 
t_coffee -in=$SEQUENCE -method=TMalign_pair -template_file=$TEMPLATE

where:
SEQUENCE=/scratch/brussel/106/vsc10611/TCOFFEE/toy.fasta
TEMPLATE=/scratch/brussel/106/vsc10611/TCOFFEE/a_pdb1.template_list

toy.fasta contains:
>112L_1|Chain A|T4 LYSOZYME|Enterobacteria phage T4 (10665)
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKPELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL
>111M_1|Chain A|MYOGLOBIN|Physeter catodon (9755)
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG
>111L_1|Chain A|T4 LYSOZYME|Enterobacteria phage T4 (10665)
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKNELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL

and a_pdb1.template_list contains
> 112L_1|Chain A|T4 LYSOZYME|Enterobacteria phage T4 (10665) _P_ /scratch/brussel/106/vsc10611/TCOFFEE/PDB_DIR/112l.pdb
> 111M_1|Chain A|MYOGLOBIN|Physeter catodon (9755) _P_ /scratch/brussel/106/vsc10611/TCOFFEE/PDB_DIR/111m.pdb
> 111L_1|Chain A|T4 LYSOZYME|Enterobacteria phage T4 (10665) _P_ /scratch/brussel/106/vsc10611/TCOFFEE/PDB_DIR/111l.pdb

scratch/brussel/106/vsc10611/TCOFFEE/PDB_DIR indeed contains 3 files:
112l.pdb, 111m.pdb and 111l.pdb.

If you're convinced this issue can be fixed with the latest release, I will ask for an update.

But perhaps I should try the "quick and dirty" work around that you suggested above as it seems it worked for Esteban (see above):
could you give me the command I should use?

Thank you for your help.

Best,
Charlotte
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