April 2002 - modeller_usage

RE: How to do modeling with non-standard residue?
by Bozidar Jerkovic 12 Apr '02

12 Apr '02

Hi, There is an example in the manual in the FAQ section. Manual is available on-line. Good luck, Bozidar -----Original Message----- From: Kong Lesheng [mailto:lesheng@bic.nus.edu.sg] Sent: Monday, April 08, 2002 6:02 AM To: bozidar(a)salilab.org Subject: How to do modeling with non-standard residue? Dear Dr. Bozidar, I'm a user of the wonderful program-Modeller. I'm currently working on homology modelling on conotoxin. Post-translational modification is very popular in conotoxin. Conotoxins are very small peptides(6-40). I think during the modelling's simulted annealling, I should consider post-translational modification. How to do modeling with non-standard residue(such as GAMMA-CARBOXY-GLUTAMIC ACID)? Thank you very much! With best regards, Kong Lesheng -- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6774 7149 Fax: (65)6778 2466

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RE: Questions
by Bozidar Jerkovic 12 Apr '02

12 Apr '02

Hi, You clearly have problem with permissions. <1> Should I run the "mod model-default" every time when I log in the shell with ROOT? A: If you installed MODELLER as a root, all you need to do is to make sure that user (you) has the permissions to execute/write files installed by the root in your home dir (or wherever the MODELLER is installed). <2> Should I run "source ~/.cshrc" each time before running "mod model-default"? A: No, that's not necessary because .cshrc is executed every time you login. Thanks, Bozidar -----Original Message----- From: Yao Jian Chao [mailto:jcyao@eee.hku.hk] Sent: Thursday, April 11, 2002 5:23 AM To: Bozidar Subject: Questions Dear Sir: I encounter several problems when I first ran the model-default.top file in the tutorial-model directory. 1: If I log in the tcsh with my home directory,I cannot run the command "mod model-default".The reminder is "mod" command cannot be found. 2: If I log in the tcsh with root directory,I can run "mod model-default" after I run "source ~/.cshrc".When I log out and log in again with my home directory,the run "mod model-default",the error reminder is: " /usr/local/bin/modeller6v1/bin/mod6v1: ./model-default.log: Permission denied " 3: When I log in with root directory again, I only could run "mod model-default" after I run "source ~/.cshrc" again. So, my questions are: <1> Should I run the "mod model-default" every time when I log in the shell with ROOT? <2> Should I run "source ~/.cshrc" each time before running "mod model-default"? The following is the login script of mine for your reference. ### begin MODELLER6v1 ###################################################### setenv MODINSTALL6v1 /usr/local/modeller/modeller6v1 setenv EXECUTABLE_TYPE6v1 i386-absoft setenv LIBS_LIB6v1 $MODINSTALL6v1/modlib/libs.lib setenv KEY_MODELLER6v1 XXX alias mod mod6v1 set path=($path $MODINSTALL6v1/bin) limit stacksize unlimited ### end MODELLER6v1 This following is the environment variables of mine. ######################################################## TERM=xterm DISPLAY=:0.0 HOME=/root SHELL=/bin/tcsh USER=root LOGNAME=root PATH=/usr/local/sbin:/usr/sbin:/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/ local/bin:/usr/local/sbin:/usr/bin/X11:/usr/X11R6/bin:/root/bin:/usr/loc al/modeller/modeller6v1/bin HOSTTYPE=i386-linux VENDOR=intel OSTYPE=linux MACHTYPE=i386 SHLVL=1 PWD=/home/jcyao/modeller/modeller6v1/examples/tutorial-model GROUP=root HOST=csg389-p-jcyao HOSTNAME=csg389-p-jcyao LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd =40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32 :*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31: *.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*. Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio= 01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png= 01;35:*.tif=01;35: KDEDIR=/usr LANG=en_US SUPPORTED=zh_CN.GB2312:zh_CN:zh:zh_TW.Big5:zh_TW:zh:en_US:en LESSOPEN=|/usr/bin/lesspipe.sh %s QTDIR=/usr/lib/qt-2.3.1 MODINSTALL6v1=/usr/local/modeller/modeller6v1 EXECUTABLE_TYPE6v1=i386-absoft LIBS_LIB6v1=/usr/local/modeller/modeller6v1/modlib/libs.lib KEY_MODELLER6v1=XXX ######################################################################## # YAO Jianchao Department of Electrical and Electronic Engineering The University of Hong Kong Pokfulam Road Hong Kong

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problem in running model script
by giulio＠unimo.it 11 Apr '02

11 Apr '02

Dear Sir, I'm having a problem running the homology modeling script. Here is the error message: delete__442E> One or more atoms absent from MODEL: O: 240: C: 240: N: 241: CA: 241: splinel_223E> Array too small. Increase MPRMCNS current maximum, current need: 810000 810002 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 It seems that the program is looking for residue number 241 as an aminoacid instead of a block residue (.) I do not understand why, everything look fine in the alignment file (at least to me) Attached are the script and the alignment. Any held will be very appreciated. Sincerely, Giulio Rastelli ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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How to run the tutorial-model
by Jianchao YAO 11 Apr '02

11 Apr '02

Dear Sir: I encounter several problems when I first ran the model-default.top file in the tutorial-model directory. 1: If I log in the tcsh with my home directory,I cannot run the command "mod model-default".The reminder is "mod" command cannot be found. 2: If I log in the tcsh with root directory,I can run "mod model-default" after I run "source ~/.cshrc".When I log out and log in again with my home directory,the run "mod model-default",the error reminder is: " /usr/local/bin/modeller6v1/bin/mod6v1: ./model-default.log: Permission denied " 3: When I log in with root directory again, I only could run "mod model-default" after I run "source ~/.cshrc" again. So, my questions are: <1> Should I run the "mod model-default" every time when I log in the shell with ROOT? <2> Should I run "source ~/.cshrc" each time before running "mod model-default"? The following is the login script of mine for your reference. ### begin MODELLER6v1 ###################################################### setenv MODINSTALL6v1 /usr/local/modeller/modeller6v1 setenv EXECUTABLE_TYPE6v1 i386-absoft setenv LIBS_LIB6v1 $MODINSTALL6v1/modlib/libs.lib setenv KEY_MODELLER6v1 XXX alias mod mod6v1 set path=($path $MODINSTALL6v1/bin) limit stacksize unlimited ### end MODELLER6v1 This following is the environment variables of mine. ######################################################## TERM=xterm DISPLAY=:0.0 HOME=/root SHELL=/bin/tcsh USER=root LOGNAME=root PATH=/usr/local/sbin:/usr/sbin:/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/usr/bin/X11:/usr/X11R6/bin:/root/bin:/usr/local/modeller/modeller6v1/bin HOSTTYPE=i386-linux VENDOR=intel OSTYPE=linux MACHTYPE=i386 SHLVL=1 PWD=/home/jcyao/modeller/modeller6v1/examples/tutorial-model GROUP=root HOST=csg389-p-jcyao HOSTNAME=csg389-p-jcyao LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35: KDEDIR=/usr LANG=en_US SUPPORTED=zh_CN.GB2312:zh_CN:zh:zh_TW.Big5:zh_TW:zh:en_US:en LESSOPEN=|/usr/bin/lesspipe.sh %s QTDIR=/usr/lib/qt-2.3.1 MODINSTALL6v1=/usr/local/modeller/modeller6v1 EXECUTABLE_TYPE6v1=i386-absoft LIBS_LIB6v1=/usr/local/modeller/modeller6v1/modlib/libs.lib KEY_MODELLER6v1=XXX ######################################################################### Evan

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problem with template selection using compare
by michael hanlon (BITS) 10 Apr '02

10 Apr '02

Running v6.1 on RedHat7.2 on a PIII Trying to use the following script for template selection: READ_RESTYP_LIB RESTYP_LIB_FILE = '${MODINSTALL6v1}/modlib/restyp.lib' READ_ALIGNMENT FILE = '${MODINSTALL6v1}/modlib/CHAINS_all.seq',; ALIGN_CODES = '1bmdA' '5mdhA' '7mdhA' 4mdhA MALIGN MALIGN3D COMPARE ID_TABLE DENDROGRAM but I get the error: read_al_375E> Unknown residue type,position,sequence: 1 4 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I tried adding the first line of the script to force reading of the default residue types (in case that was the problem), but it didn't help. Any help much appreciated Mike -----Original Message----- From: Voula Kanelis [mailto:kanelis@sauron.psf.sickkids.on.ca] Sent: 10 April 2002 14:29 To: modeller_usage(a)salilab.org Subject: phospo-serine residues Hello, I am currently using Modeller 4 and need a phosphoserine residue. Unfortunately, this residue is not defined in the modlib files and I do not have access to CHARM or QUANTA to be able to create it (a problem to be fixed shortly - hopefully). Does anyone have such a residue defined and would be willing to share? Thanks in advance, Voula Kanelis --

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problem with sequence search
by michael hanlon (BITS) 09 Apr '02

09 Apr '02

I'm running v6 on ReDHat 7.2 on a PIII. I tried the following script for a sequence search: SET OUTPUT_CONTROL = 1 1 1 1 0 SET SEARCH_RANDOMIZATIONS = 20 SET SEARCH_CHAINS_LIST = '${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod' SEQUENCE_SEARCH FILE = './TvLDH.ali', ALIGN_CODES = 'TvLDH' DATA_FILE = ON but get the following error, the last bit of which seems to indicate that 1xnb cannot be found, and yet it's there alright: TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 20 TOP_________> 3 3 SET SEARCH_CHAINS_LIST = '${MODINSTALL6v0}/modlib/CHAINS_; 3.0_40_XN.cod' TOP_________> 4 4 SEQUENCE_SEARCH FILE = './TvLDH.ali', ALIGN_CODES = 'TvLD; H' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v0}/modlib/CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL {MODINSTALL6v0}/modlib//CHAINS_all.seq read_se_367E> Sequence not found; code: P1;1xnb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Any ideas? Mike Dr. Mike Hanlon Molecular Biology Computing Support BBSRC Bioscience IT Services West Common Harpenden Herts AL5 2JE Phone: 01582 714904 Email: molbio.support(a)bbsrc.ac.uk Web: http://www.molbiol.bbsrc.ac.uk

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List security update
by Bozidar Jerkovic 08 Apr '02

08 Apr '02

Hi all, Since the spammers didn't give up I needed to act again. This time I have implemented restrictions on posting messages. From now on only the subscribers can post to the list. I also increased a number of keywords that are monitored for spam content, so please make sure that you don't use any stock market terminology when posting to the list. Thanks for your patience once again... Best, Bozidar

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None
by Bozidar Jerkovic 08 Apr '02

08 Apr '02

from bozidar please ignore

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None
by Bozidar Jerkovic 08 Apr '02

08 Apr '02

Wall Street

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Re: MODELLER
by Bozidar Jerkovic 08 Apr '02

08 Apr '02

Hi, Can you please send me your .top and .log and all input files and I'll run it here. I can't actually see which part of .top fails. I presume it's "CALL ROUTINE = 'loop' # do loop modeling", but I don't wanna guess. Best, Bozidar On 8/4/02 3:24 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> wrote: > Dear Bozidar, > > > I downloaded the last version of MODELLER and I am running into some > problems. For the time being, I use MODELLER mostly for loop modeling. Using > the > previous version(mod6a), I used to create a top file like this, and everything > worked ok: > > INCLUDE > SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for debugging. > SET SEQUENCE = '1dysA_47-50' > SET LOOP_MODEL = '1dysA_47-50.pdb' > SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest > # refine2 - medium > # refine1 - most thorough > SET LOOP_STARTING_MODEL = 1 > SET LOOP_ENDING_MODEL = 3 # number of loop models > SET RAND_SEED = -38901 # change for different starting models > CALL ROUTINE = 'loop' # do loop modeling > > # Pick model residues that need to be refined. > > SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you also want to > optimize the environment: > # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 > PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS = 'initialize' > RETURN > END_SUBROUTINE > > > With the newest version of MODELLER that I downloaded last week, doesn't work > anymore. I receive an error message in the end of.log file like this: > > act10___551E> No such routine: > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: 28478873 > 27811.400 27.160 > Starting time : 2002/04/08 > 14:20:40.274 > Closing time : 2002/04/08 > 14:20:51.421 > Total CPU time [seconds] : 11.00 > > > Could you help me please regarding this matter? Could you also tell me if > there is any dependency needed(some libraries, fortran, etc)? I am using > RedHat > 7.2 with kernal 2.4.7-10 > > > > Thanks, > > Adrian Canutescu

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