Re: [ccp4bb] How to generate a complete viirus PDB
Hi, In continuation to the previous suggestion about using the 'Oligomer Generator' in viperdb. To use viperdb, your pdb needs to be in the viper format. So download any pdb (example this one : http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1z14) and then superpose your monomer onto this reference viper format pdband then upload your 'moved' pdb into the Oligomer generator 'browse' option. Then select the T number and the option for 60mer, 30mer etc. If this is an already published pdb then just input the id in the homepage and then the next page will have options for you to download a whole capsid or half capsid. -Tina On Thu, Apr 25, 2013 at 2:48 AM, Bradley Kearney bmkea...@ncsu.edu wrote: Hi Hong, ** ** I would recommend that you check out the services at the VIPERdb website http://viperdb.scripps.edu. It looks like the oligomer tool ( http://viperdb.scripps.edu/oligomer_multi.php) might be useful for what you want to do. They have many of the virus structures from the PDB already processed for you, or you could upload your own PDB coordinate file. ** ** Brad ** ** --- Bradley Kearney, Research Associate The Scripps Research Institute Department of Integrative Structural and Computational Biology Jack Johnson Laboratory ** ** ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Guan Hong Hsiang *Sent:* Wednesday, April 24, 2013 11:19 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] How to generate a complete viirus PDB ** ** Dear all: I have one subunit PDB of one virus with a NCS record. Which program should I use to generate a complete virus PDB using the NCS? Thank you Hong Hsiang
[ccp4bb] phasing with EM map using Amore
Hi, I am trying to use a cryo-EM map as a MR model for an Xtal data set. I have calculated structure factors for my map using SFALL. And then used rotcross function and translation function searches (from AMORE) to determine the MR solution. So, finally I got X, Y, Z fractional coordinates and Euler alpha, beta , gamma. Usually I start with a coordinate file (pdb) as a model whereas my initial model is a map. So how am I supposed to apply this solution to the mtz file from my initial map? Is there is a program/script available that can be used to apply those rotations and translation to structure factors ? Or am I proceeding in the wrong direction? I tried to use Phaser and Molrep but it did not give a solution. Any help would be highly appreciated. Thank you. -Sujata Halder
Re: [ccp4bb] strict structure based alignment
Hi, SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver) will do a structure based alignment and outputs a table of rmsd but will not give you a alignment file as such. -Sujata On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth christian.r...@bbz.uni-leipzig.de wrote: Dear all, I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also the sequence into account. I tried also Rapido, but this does only a pairwise comparison. Superpose does align it nicely (ccp4 based or Coot based) but there seems to be no option to print the sequence alignment in a file and it is again just a pairwise comparison . Is there an other program which does something similar? Best Regards Christian
Re: [ccp4bb] color for metal ions
thanks everybody. On Mon, May 21, 2012 at 1:51 PM, mjvdwo...@netscape.net wrote: There is a really nice web site that shows how colors are perceived by various color-blind readers. One of the journals I recently published in recommends it for consideration. If you are interested, have a look. The web site is made especially for people who publish scientific articles with color illustrations. It is not hard to be considerate. http://jfly.iam.u-tokyo.ac.jp/html/color_blind/ Mark -Original Message- From: Artem Evdokimov artem.evdoki...@gmail.com To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Sun, May 20, 2012 2:54 pm Subject: Re: [ccp4bb] color for metal ions As long as you are considerate of the needs of colorblind people, I would vote that anything goes. Artem On May 20, 2012 3:17 PM, sujata halder halder.suj...@gmail.com wrote: Hi all, I was wondering if there is a rule for coloring metal ions a specific color. I am using pymol and was not sure if I have to use a specific color for calcium or magnesium ions for publication figures. Thanks, Sujata
[ccp4bb] color for metal ions
Hi all, I was wondering if there is a rule for coloring metal ions a specific color. I am using pymol and was not sure if I have to use a specific color for calcium or magnesium ions for publication figures. Thanks, Sujata
Re: [ccp4bb] Sodium ion vs. Water
Hi, I decided to give the server a try...and the output is: FILE NOT FOUND: /prod/tmp/individual_validation/output_wasp/25854/bindividual6Na.ion Either my pdb does not have any metal ions or this server is currently not working. Sujata On Tue, Aug 2, 2011 at 5:04 PM, Sean Seaver s...@p212121.com wrote: Hi Christina, The WASP server seems to working at this location (about half way down the page): http://www.jcsg.org/prod/scripts/validation/sv2.cgi I hope that helps. Take Care, Sean P212121 http://store.p212121.com/
Re: [ccp4bb] Library description for Pentacoordinated phosphate.
Hi, phenix.elbow might work... from the phenix website: To run eLBOW on a PDB file (containing one molecule) phenix.elbow input_file.pdb To run eLBOW on a PDB file containing protein and ligands. This will only process the ligands that are unknown to phenix.refine. phenix.elbow input_file.pdb --do-all -Tina On Fri, Jun 10, 2011 at 10:33 AM, pravinkumar jagtap pravinja...@gmail.comwrote: Dear CCP4 users, I am trying to get library description for a ligand having a pentacoordinated phosphate in it (for modeling a transition state) but unable to do so as Sketcher in CCP4 programms fails with an error message of ERROR: nt = 4 for 10 ERRROR: in subroutine CMP_CRD_M ERRROR: in subroutine CALC_POLCRD ERRROR: in subroutine CREATE_BLCRD and the PRODRUG server fails with an error message Error in GROMOS atom names/types. In Prodrug server, this mainly seems due to the fact that it cant handle more than 4 connections/atom. I dont know about sketcher. Can anybody advice how to do get library for such a ligand? Thanks in advance for any suggestion. With regards, Pravin Kumar.
Re: [ccp4bb] how convert SF to intensities
Hi, Use SFALL to convert coordinates to structure factors...and then use mtz2various to convert to intensities...use the scalepack format under mtz2various. On Thu, May 12, 2011 at 3:13 PM, Fulvio Saccoccia fulvio.saccoc...@uniroma1.it wrote: Dear ccp4 users, I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF. Does anyone know how can I do? Thanks in advance Fulvio Saccoccia
