- modeller_usage - salilab.org

Problem for a protein model
by Bishwajit Das 24 Jan '11

24 Jan '11

I am doing a protein model name RFX5 in a modeller in windows operating system,but i can't understand which command i use and how i search a template and doing model.Please tell me the command name and example also. -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

2 1

Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 9
by Ashish Runthala 24 Jan '11

24 Jan '11

Respected Sir, I tried your approach. It works. But still it wasn't working out the way i want it. Is it possible that you can find the "final max quality" for a model decoy with its native state experimental structure. salign_iterative does work properly for 2 crystal structures but how to make it work for both template/Native State & Model structure. Thanks, Ashish ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Saturday, January 22, 2011 2:59:16 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 9 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://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. Regarding Salign (Ashish Runthala) 2. model_addrsr.py (Koushik A C) 3. Re: model_addrsr.py (Modeller Caretaker) 4. Re: Regarding Salign (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Fri, 21 Jan 2011 08:41:47 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: [modeller_usage] Regarding Salign To: modeller <modeller_usage(a)salilab.org> Message-ID: <32062261.262361295579507848.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 I checked salign too. It considers penalties on primary sequence and then moves to the structural alignment of considered structures before adding target sequence according to generated structural topology. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them. Thanks, Ashish ------------------------------ Message: 2 Date: Fri, 21 Jan 2011 13:23:40 +0530 (IST) From: Koushik A C <011113027(a)sastra.edu> Subject: [modeller_usage] model_addrsr.py To: modeller_usage(a)salilab.org Message-ID: <992863059.70038.1295596420282.JavaMail.root(a)mail.sastra.edu> Content-Type: text/plain; charset="utf-8" Hi, I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!!

2 1

Problem modelling protein dimer close to DNA ...
by Sergio Garay 24 Jan '11

24 Jan '11

Dear Modeller's Users: I'm trying to model a protein dimer interacting with a small DNA molecule. Following the manual instructions I was able to build my dimer using: >P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer * But I have some problems to add my DNA molecule as an additional restraint: I added to my script: env.io.hetatm = True And I also added my DNA molecule (all the DNA atoms were named HETATM) into the template pdb and modified my alignment in this way: >P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer ---------- --->alignment of extra dna residues (I'm not sure is this is right) / ---------------------------------------------------- ---> 1st strand of DNA ............. / ---------------------------------------------------- ---> 2nd strand of DNA ............. * Modeller worked without any warning but my dimer pass through the DNA molecule, so this is not working. Any help would be very appreciated. Sergio -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1

error message while ploting DOPE score
by hari krishna 24 Jan '11

24 Jan '11

Hi, i need help regarding the error that i'm getting while modeling protein. i have the ploting values from evaluate model and template. and i'm attempting to plot those value, but i'm getting error message: File "plot_profiles.py", line 1, in ? import pylab Importerror: No module named pylab could you please help to overcome this problem. -- *Thanks & regards* *N.Harikrishna,*

2 1

Regarding Salign
by Ashish Runthala 21 Jan '11

21 Jan '11

I checked salign too. It considers penalties on primary sequence and then moves to the structural alignment of considered structures before adding target sequence according to generated structural topology. But will you pass me the script lines which aligns structures at 1,2,3,4Angstroms. My another doubt is that how the considered structures are considered all together for each of these distance cutoffs. Is this like nC2 combination based structural alignment satisfaction of restraint matrix generated. Show me where these 1,2,3,4 Angstroms are available in salign_iterative. I couldn't find them. Thanks, Ashish

2 1

model_addrsr.py
by Koushik A C 21 Jan '11

21 Jan '11

Hi, I am not able to model beta sheets even if i am using model_addrsr,py file. Can anyone please help me out..!!

2 1

query
by bharat lakhani 17 Jan '11

17 Jan '11

Hi sir When i am running modeller on solaris, following error is coming up Traceback (most recent call last): File "compare.py", line 8, in ? from modeller import * File "/export/home/bhageerathH/bin/modeller9v8/modlib/modeller/__init__.py", line 72, in ? import _modeller ImportError: ld.so.1: python2.3: fatal: /export/home/bhageerathH/bin/modeller9v8/lib/sun4/_modeller.so: wrong ELF data format: ELFDATA2MSB thank you

2 1

Loop Modeling
by bharat lal 14 Jan '11

14 Jan '11

Hi, I have a question regarding modeling the loop of an already determined structure of a protein de novo. I want to change the entire sequence of the loop regions of the protein with random sequences and also I want to extend the length of the loops in the protein structure. I have searched through a lot of papers but I am not able to find any specific paper about such an approach.. So, I want to know can Modeller help in solving this problem and also I will be highly obliged if anybody can refer me to some good paper on De novo loop modeling .. Looking forward for a positive and fast reply,..... Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

2 2

Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6
by bharat lal 13 Jan '11

13 Jan '11

Thanks for ur help But I am still not able to generate any model as after doing the alignment of the two sequences like teh way u said. Its giving the error "Sequence Difference between the alignement and pdb" . Here is my alignment file :- >P1;template structureX:template:1 :A: 230 :: : : : ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFF-----------NYKTRAEVK FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM DELYK * >P1;target sequence:target: : : : : : : : ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFTDGYDFNDSKANYKTRAEVK FEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIED GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGM DELYK * The error is :- Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3567011 3483.409 3.402 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 101) Alignment RTIFFNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNG PDB RTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADK Match ***** * * * * Alignment residue type 12 (N, ASN) does not match pdb residue type 9 (K, LYS), for align code template (atom file template), pdb residue number "101", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 template --------------------------------------------------- I am using model-loop.py script to generate the models. i want to know one more thing that how this script will model the structure of the loop sequence since the pdb coordinates are not present in the template file ... Regards --------- BHARAT

2 1

MD Simulation
by asmat salim 11 Jan '11

11 Jan '11

Hi, We have constructed homology models based on templates of low sequence identity (27-28%). It was an enzyme and we also did some ligand-enzyme interaction study using Modeller. We did some superpositions of template and target structure and the deviation was below 1 Angstrom. We have submitted this to a journal and got a few comments. I need your advise in this regard. As you will notice that these are related to deducing and improving the quality of a homology model, I would be grateful if I can get a few tips in order to further improve the model quality in light of the listed parameters. A few of the points are concept based i.e. sequence identity and homology. Kindly comment on those. Here is the summary: RMSD related: The backbone could deviate from the true structure by a few angstroms and the impact of such deviation for enzyme catalysis could be huge. Therefore, the application of such models is often limited. Trying to deduce the specific interactions between the active site residues and a substrate based on such a model is thus questionable. The rmsd between the model and the template was ~1 angstrom is not the evidence of high quality of the models. The term rmsd is being mis-understood. In structure prediction, the rmsd between a homology model of the target protein and the X-ray structure of the same target protein was often calculated as the indication of the quality of the models, but not the rmsd between the model and the X-ray structure of the template. Sequence Related: The multiple alignment was only used for the phylogenetic analysis, whereas the pairwise alignments were used as a starting point to create the models. This procedure is conceptually wrong, since the alignment created by PSI-BLAST is not necessarily the best one. In fact, PSI-BLAST makes a pairwise alignment to find the most similar sequences, not to find the best alignment between the sequences. Moreover, with such a low sequence similarity (less than 30%) the best procedure to be sure of a good starting alignment is to perform a multiple alignment, and in case to use also predictions of the position of secondary structure elements, etc in order to improve as much as possible the quality of the alignment (see refs. to the CASP competitions). Then, the alignment between template(s) and model should be extrapolated by the multiple sequence alignment. Homolgy Definition: The term "homology" simply indicates the presence of a common evolutionary origin between two biological entities: therefore, two proteins are homologous or not. Somebody said that talking about "X% of homology" would be more or less the same as talking about a women who is "X% pregnant". Instead, it is correct to say that two proteins have X% of their amino acids identical. Energy Minimization: The authors do not have the energy minimized structure, which is a must for carrying out interaction analyses and if not done, leads to incorrect interpretations. They have assumed the program Modeller provides a proper energy-minimized structure with 'automodel' environment. However, published literature that use Modeller in such an environment still have been found to energy minimize the structure and only then use further. Thank you asmat

2 1