- modeller_usage - salilab.org

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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(OTCBB: WSCH) Special Investment Update
by leeuwen＠163.net 08 Apr '02

08 Apr '02

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model coordinate uncertainty
by margot 08 Apr '02

08 Apr '02

Dear modelling community, thanks to Michael Buck for his reply, unfortunately the only one. I would assume that there are many modeling problems where it is inherently impossible to derive at a single "best" set of constraints and consequently a single model best satisfying these constraints. I can't believe that there is no general procedure to derive at some mesure of uncertainty associated with the coordinates of a given residue based on a) degree of conservation among template(s) and target, and, b) the local properties of the fold, and, c) variations in the restriants that follow from a) and b). Any helpful thoughts out there? Michael: I'm not sure that I understand what a correlation between an uncertainty (statistical scatter) and error (systematic bias) tells me, or how the quanity you call "model error" is defined. In my case, the problem is a lot greater anyhow, as precise beginnings and endings of secondary structure motifs in target and template are highly likely to vary substantially (beta fold, low to moderate homology). Cheers, margot

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(OTCBB: WSCH) Special Investment Update
by traiber＠ok.ru 04 Apr '02

04 Apr '02

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List update email
by Bozidar 03 Apr '02

03 Apr '02

Hi again, Sorry about the disclosed list of recipients in the previous email. I hit the wrong button. There in no reason for worry, since the email was send to the modeller_usage people only. Thanks, Bozidar

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Stock
by Bozidar Jerkovic 03 Apr '02

03 Apr '02

Please ignore. Thanks, Bozidar

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Re: CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in the Stock Market: QY
by Bozidar Jerkovic 02 Apr '02

02 Apr '02

Dear Radha, No that will not be necessary. If I run into some problematic email addresses I will contact the owners of those individually. Best, Bozidar On 2/4/02 8:57 PM, "RATHNACHALAM_RADHAKRISHNAN(a)Lilly.com" <RATHNACHALAM_RADHAKRISHNAN(a)Lilly.com> wrote: > Dear Bozidar, > > Do we have to "subscribe" again? Thanks. > radha > > > Bozidar Jerkovic <bozidar(a)salilab.org> > Sent by: owner-modeller_usage(a)salilab.org > > 04/02/02 06:52 PM > > To: Allen Smith <easmith(a)beatrice.rutgers.edu>, > owner-modeller_usage(a)salilab.org > cc: modeller_usage(a)salilab.org, Andrej Sali > <sali(a)rockefeller.edu> > Subject: CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in > the Stock Market: QY > > > > > Hi all, > > Due to an increased influx of a junk mail that the list has been > experiencing lately I propose that we go from the open to a 'members-only' > list. In addition to closing the list, the subscribers will have to be > manually approved as well. > > If you have any suggestions please feel free to contact me. > > I expect to have everything implemented in a week time, so please try to > ignore the junk mail for that time. > > Thanks for your patience, > Bozidar (list owner) > > > > >

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CHANGE IN A SUBSCRIPTION POLICY Re: (Fwd) Investors in the Stock Market: QY
by Bozidar Jerkovic 02 Apr '02

02 Apr '02

Hi all, Due to an increased influx of a junk mail that the list has been experiencing lately I propose that we go from the open to a 'members-only' list. In addition to closing the list, the subscribers will have to be manually approved as well. If you have any suggestions please feel free to contact me. I expect to have everything implemented in a week time, so please try to ignore the junk mail for that time. Thanks for your patience, Bozidar (list owner)

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model coordinate uncertainty
by margot 02 Apr '02

02 Apr '02

Hello modelling community, ist there any accepted algorithm to generate coordinate uncertainties for homology models (or ensembles of models)? If anyone knows of anything published on that matter I'd be grateful for the reference, as well as unpublished insightful material. And another question: Is there any additional bulletin board dealing with protein (biomolecule) modelling in a broader sense than Modeller usage? thanks, margot

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