April 2006 - modeller_usage

Concatenating models
by Alex Brown 24 Apr '06

24 Apr '06

Hi. A simple question - is it possible to concatenate (add) two models, using a MODELLER script, to create a single file ? I know that two files can be added together using Unix commands or using a text editor, but then the atom numbers are duplicated (I'm not sure this is a problem tho'). Cheers, Alex Brown

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General Question
by Brandon Guida 24 Apr '06

24 Apr '06

Does anyone know whats going on here? I am trying to exit stage 2 but when I add that constriant to the model-single.py file all I get is the following log file and no models being built. As soon as I remove the exit command I get model the models. Here is the log file: check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 23 atom names : C +N atom indices : 175 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 23 atom names : C CA +N O atom indices : 175 171 0 176 Dynamically allocated memory at finish [B,kB,MB]: 2152131 2101.690 2.052 Starting time : 2006/04/23 16:51:44.937 Closing time : 2006/04/23 16:51:47.203 Total CPU time [seconds] : 2.20

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rotameric state in MUTATE_MODEL
by Sridhar Acharya 21 Apr '06

21 Apr '06

Hello MODELLERs, I want to know what rotameric state of the mutant residues that the MUTATE_MODEL option of MODELLER generates? What rotameric configuration does the program generates. Is it the most optimum that is possible for the model or is it generated based on some other scoring scheme? Is there any control on the rotameric state of the mutant residue. thanks in advance for your suggessions. sridhar

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Re:plotting dope values
by Prabhakar. G. 21 Apr '06

21 Apr '06

hi, there is a perl script for parsing the dope scrores in the below link http://salilab.org/modeller/wiki/Plotdope run the script, get the output and then plot it using the gnuplot prabhakar On 4/21/06, modeller_usage-request(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. help (biocompr) > 2. CHAINS_all Updates (Alex Brown) > 3. Re: CHAINS_all Updates (Modeller Caretaker) > > > > ---------- Forwarded message ---------- > From: "biocompr" <biocompr(a)163.com> > To: modeller_usage(a)salilab.org > Date: Thu, 20 Apr 2006 01:22:45 +0800 (CST) > Subject: [modeller_usage] help > hi: > I find the question in the past posts ,bu i do not find the answer. > > I am new user to the modeler, I have started with the basic tutorial, I > have difficulty with plotting the dope scores with GNU plot, > when I plot the two dat files '1bdma_dope.dat','TVLDH_dope.dat'(from the > tutorials folder) I get the graph plotted(Dope score vs Residue Index), but > the two graphs are not aligned, as shown in the tutorial html file. how to > align the graphs. hope someone could help me with this silly doubt. > > Thank you very much. > > > > > > > > > > > > > > 你知道中国每年耗费多少一次性筷子吗？ > 450亿双！相当于170万立方米的木材，大约需要砍伐2500万棵大树！ <http://www.126.com/> > > ---------- Forwarded message ---------- > From: "Alex Brown" <alexander.brown(a)tech.mrc.ac.uk> > To: <modeller_usage(a)salilab.org> > Date: Thu, 20 Apr 2006 13:31:02 +0100 > Subject: [modeller_usage] CHAINS_all Updates > > Hi. > > > > I was wondering if it is possible to get updates to the CHAINS_all.seq > database. > > > > If not, where can I get hold of an updated PIR-formatted file of PDB > sequences with values in the resolution field? > > > > Many thanks, > > > > Alex Brown > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Alex Brown <alexander.brown(a)tech.mrc.ac.uk> > Date: Thu, 20 Apr 2006 14:28:28 -0700 > Subject: Re: [modeller_usage] CHAINS_all Updates > Alex Brown wrote: > > I was wondering if it is possible to get updates to the CHAINS_all.seq > > database. > > > > If not, where can I get hold of an updated PIR-formatted file of PDB > > sequences with values in the resolution field? > > You can rebuild the databases yourself from the original PDB files. See > the relevant page in the Modeller wiki: > http://salilab.org/modeller/wiki/Rebuilding_sequence_databases > > Alternatively, you can download updates, when available, from our > supplemental data file download page, which is linked from that wiki > page and from the main 'download & installation' page. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > -- Prabhakar.G Project Assistant, Bioinformatics and Data Management, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411 007 Maharastra India

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CHAINS_all Updates
by Alex Brown 20 Apr '06

20 Apr '06

Hi. I was wondering if it is possible to get updates to the CHAINS_all.seq database. If not, where can I get hold of an updated PIR-formatted file of PDB sequences with values in the resolution field? Many thanks, Alex Brown

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help
by biocompr 19 Apr '06

19 Apr '06

hi: I find the question in the past posts ,bu i do not find the answer. I am new user to the modeler, I have started with the basic tutorial, I have difficulty with plotting the dope scores with GNU plot, when I plot the two dat files '1bdma_dope.dat','TVLDH_dope.dat'(from the tutorials folder) I get the graph plotted(Dope score vs Residue Index), but the two graphs are not aligned, as shown in the tutorial html file. how to align the graphs. hope someone could help me with this silly doubt. Thank you very much.

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ASGL Files
by Alex Brown 18 Apr '06

18 Apr '06

Hi. Some of the MODELLER commands are able to produce ASGL output files - files that can be used with ASGL scripts to produce plots, although by the looks of them, they could be used for other plotting programs. However, they are largely undocumented in the MODELLER manual. Could anyone tell me what data the following files contain (from alignment.compare_structures): posdif.asgl (per residue rmsd ??), dihs.asgl, dpsdif.asgl, and poscmp.asgl Many thanks, Alex Brown

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Running two versions of MODELLER
by Alex Brown 13 Apr '06

13 Apr '06

Hi. Is it possible to run two versions of MODELLER on the same machine ?? I am having a problem with a model in 8.2, and would like to re-run some modelling scripts in an older version I used a while back (probably 6.?) Cheers, Alex

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one question about modeller
by biocompr 13 Apr '06

13 Apr '06

hi i download the soft GNUPLOT ,and how use it to show 'TvLDH.profile' to the picture 'DOPE score profiles for the model and templates'? thank you

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Problem with MODELLER6v2
by Ludovic Pétain 12 Apr '06

12 Apr '06

Hello. Here is my script (for MODELLER6v2): INCLUDE SET ATOM_FILES_DIRECTORY='' SET ALNFILE='GPR43_ES_HSA#2.ali' SET KNOWNS='rhodo_1u19' SET SEQUENCE='GPR43_ES_HSA' SET OUTPUT_CONTROL=1 1 1 1 1 SET STARTING_MODEL=1 SET ENDING_MODEL=1 CALL ROUTINE='model' #Redefine the special_restraints routine to disable energy optimization on the residues 123 to 143 SUBROUTINE ROUTINE='special_restraints' DELETE_RESTRAINT RESIDUE_IDS='123' '124' END_SUBROUTINE #energy optimization ENERGY OUTPUT='SHORT' OPTIMIZE OPTIMIZATION_METHOD=1,MAX_ITERATIONS=10 But I when I run the script, here is the error message : No ":" in ATOM:RESID[CHAINID] atom identifier I have replaced several times the string after 'RESIDUE_IDS=' ( for example: '123 :','124 :' ), but it doesn't change anything. Thanks by advance. Ludovic PETAIN EUROSCREEN SA Tel +32 71 348 500 Fax +32 71 348 519 Direct +32 71 348 5XX http://www.euroscreen.com This message contains information that may be confidential and privileged and is intended solely for the use of the intended recipient. Unless you are the intended recipient (or authorized to receive for the intended recipient), you may not use, copy or disclose to anyone the message and any attachments or any information contained in the message. If you have received this message in error, please notify Euroscreen at +32 71 348 500 or by reply e-mail and destroy all copies of this message and any attachments.

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