- modeller_usage - salilab.org

Cluster PDBs
by Wang Yanli 29 Sep '08

29 Sep '08

Dear modeller, I had build 500 models, and want cluster the build models. I had try the Cluster_PDBs(http://www.salilab.org/modeller/wiki/Cluster%20PDBs), but I just got the average-structure. I want analysis the clusters of the build models. How to do it? Thanks very much!

2 1

Re: [modeller_usage] Need help in not modeling the propep feature in final model
by Modeller Caretaker 29 Sep '08

29 Sep '08

Saravanan wrote: > I am modeling a protein in which two subunits are linked by a "propep" > which is not present in crystal structurei.e, its cleaved when protein > is active. I want to generate models without the "PROPEP". > > Crystal Structure available looks like this: (chain a and b) > > aaaaaaaaaabbbbbbbbbbb > > Model sequence is like this : (chain a and b and p-propep) > > aaaaaaaaaaapppppppppppppppbbbbbbbbbbb > > Model structure should be like this : (chain a and b AND propep chain p > should not present) > > aaaaaaaaaaabbbbbbbbbbb I don't think I fully understand your question, because the model structure always has the same sequence as the "model sequence", by definition. If you don't want to have the propep sequence in your model, just don't include it in the model sequence in your alignment. If, on the other hand, you want to build a model containing the propep sequence but you don't want to write it into the output PDB file, you can either edit the output PDB file by hand, or you can use selection() to select the non-propep parts and then selection.write() to write out a PDB. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

1 0

W> MODEL atom not classified: GLY:OXT GLY
by Joaquim Rui Rodrigues 24 Sep '08

24 Sep '08

Dear Modellers, I am trying to build some missing loops in a PDB structure with modeller 9v4. For this, I am using the script found in examples/automodel/model-loop-define.py for which I only changed residue_range's, and alnfile, knowns and sequence. The protein is a dimer, and both subunits end with a Gly residue. I am getting this warning at the DOPE potential assessment: >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: GLY:OXT GLY iatmcls_286W> MODEL atom not classified: GLY:OXT GLY A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/ modeller_usage/2004/msg00169.html). This file seems to be used for loop modelling, but not for DOPE evaluation, as suggested in the log file: openf___224_> Open ${LIB}/atmcls-mf I have also tried to use the dope_loopmodel class, instead of loopmodel. Here, I get the same warnings for both stages (loop modelling and DOPE assessment). How can I avoid such messages? Should I somehow edit atmcls-mf.lib? Many thanks, Rui Rodrigues -- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

2 1

from ylwang: loop conformation sampling
by Wang Yanli 19 Sep '08

19 Sep '08

Dear modeller, Firt, thanks for Ben Webb's help on my question, I follow your advice and found that error in MASS line. Now, I want to ask questioins about loop conformation. A loop in involved in the ligand binding and also involved in the dimmer interface. In the templet, the loop is short, but for my protein, it is longer than templet by 12 residues. The protein can be monomer or dimmer, but only be funcational in dimmer form. So, I want study: 1: the impact of dimmer on the loop conformation. 2: the impact of ligand on the loop conformation. Can I do loop-refine process times for dimmer and monomer to the study 1 issue 1? And Can I do modeller by "modeling ligands in the binding site" to study the issue 2? Or, is there other ways for my issue. I had read some paper about "ligand-supported homology model", but can't understand it well. It seems a method, but no tool-package availble? Any advices, please! -- PH.D Student Shanghai Key Lab. of Chemical Biology School of Pharmacy East China University of Science and Technology

2 1

how to constrain automodel to remain closer to the template
by Jake Gunn-Glanville 19 Sep '08

19 Sep '08

I have been modeling a protein with a template I am quite confident in, and a loop that I would like to use a separate template for. When I generate 200 models, they all seem to show a great deal of structural diversity. Curious, I developed 20 models of a solved structure against itself, and found a bit of diversity in all of these resulting models as well. Is there a good way to constrain automodel so that it diverses less from the templates when thre are no obvious residue clashes forcing it to make adjustments? -- Jacob Glanville Informatics Associate Rinat Biotherapeutics & Bioinnovation Center; Pfizer Inc. 415 497 3552

2 1

How to introduce a covalent bond in a model?
by DimitryASuplatov 19 Sep '08

19 Sep '08

Hello, I want to link N-end of the chain alpha with C-end of the chain beta in my peptide. Terminal acids are quite near to each other (4 A), thus it is possible. I have made up some workarounds like switching the chains in pdb and seq files before making the alignment for modeller etc.; I dont like it though. I suggest that there should be some universal function built-in modeller for this kind of purpose. Do you know how to manage this? Thank you. I appreciate your help. SDA

2 1

CHARMM atom type is not recognized (not in RADII_LIB): 15.999
by Wang Yanli 09 Sep '08

09 Sep '08

Hi, Modeller When I add the ligand (Allosamidin) as new residue type. I use insightII to generate the rtf file, ad add information in *.lib files. But I still get bellow error. How can I do? Thanks! env.libs.topology.read(file='$(LIB)/top_heav.lib') File "/home/ylwang/bin/modeller9v4/modlib/modeller/topology.py", line 23, in read return self.append(file) File "/home/ylwang/bin/modeller9v4/modlib/modeller/topology.py", line 27, in append return _modeller.mod_topology_read(self._modpt, self.__libs.modpt, file) _modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): 15.999

2 1

(My) problems with BLK
by Francesco Pietra 08 Sep '08

08 Sep '08

I posted to a wrong list of Modeller, so I got no answer. Here the latest from my efforts, trying with a single chain to simplify. My pdb file ends like: HETATM 3346 CLA BLK A 859 78.668 51.520 63.082 1.00 26.90 CLA END In the ali file, CLA is represented as a dot "." in both the structure and the sequence, without "/", i.e., CLA is in the same chain. Models are built as if they had good DOPE score, though the log file complains: iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: CLA --> CT2 This message is written only for the first such atom. Although I am unfamiliar with CHARMM (I use Amber), I understand that my setting of BLK is incorrect, CLA is represented by a wrong atom type (CT2 stands for some carbon?). I tried variants, vainly. I looked at toppar files on the web, being unable to find the ten-entries long range and 1-4 non-bonded soft sphere terms for CLA to introduce in my /modlib/modeller/radii.lib. Such parameterization is available for SOD (just to talk about a single-atom ion) both on the toppar files and in Modeller itself, just in the radii.lib and radii14.lib. What I am trying is to represent CLA (chloride ion) as accurately as possible, even if I am aware that the effective spatial situation depends on the environment (in particular the balance between ionic and covalent bonding) so that any set of literature data for CLA will hardly fit accurately my situation. Thanks francesco

2 3

Re: [modeller_usage] how to fix some residues not lying in allowed regions of Ramachandran plot
by Frederico Arnoldi 07 Sep '08

07 Sep '08

Dear Ruchi, >On ssessing the stereochemical > quality of the model, I found that it had 28 outliers residues (phi, psi), that > were lying in disallowed regions of Ramachandran plot. Most of these residues > are functionally important and hence can not be ignored. Will it be fine to > select each of these residues and model them using loop modelling? I am not the greatest expert in the area, but, maybe, I could try to help you with somethings. You said you are working with a tetrameric model. It must be a very large model. The first point I think you should pay attention is: How large is it? Which percentage 28 residues represents? Of course 28 residues are not irrelevant, but I think you should put it on the right scale. In a 280 residues model it could mean your model is not good. On the hand, in a 2800 residues (we are talking about a tetrameric model), it just represent 1%. Any way, the suggestion you have already received in the first answer is one manner to correct "mismodelled" residues. But don't forget the begining, your template. Even, making more models. Another point is that residues in disallowed regions generally means mismodelled residues, but them can also be related with important functions and these "wrong" angles are indicative of functionally important positions (there are a few papers discussing it, but I am not really updated). Check the template. Do these residues have "allowed" angles? And in other homologous structures? I hope my email help more than confuse you. Good luck, Fred The _________________________________________________________________ Receba GRÁTIS as mensagens do Messenger no seu celular quando você estiver offline. Conheça o MSN Mobile! http://mobile.live.com/signup/signup2.aspx?lc=pt-br

1 0

how to fix some residues not lying in allowed regions of Ramachandran plot
by rsachdeva＠imtech.res.in 03 Sep '08

03 Sep '08

Dear All, I built 200 tetrameric models of my protein using 2 templates. I selected best model as the one having the least DOPE score. On ssessing the stereochemical quality of the model, I found that it had 28 outliers residues (phi, psi), that were lying in disallowed regions of Ramachandran plot. Most of these residues are functionally important and hence can not be ignored. Will it be fine to select each of these residues and model them using loop modelling? Or can anyone please suggest me some other (better) way of fixing such bad residues? With Regards Ruchi

2 1