Re: [ccp4bb] PISA

Dear Jon Thanks for the suggestion and that works for me to calculate the interface area and other parameters I need. Many thanks! Best regards Sam On Wed, 20 Jan 2021 at 22:38, Jon Cooper wrote: > Dear Sam > > I can only suggest trying the old trick of editing the pdb file and giving > all

Re: [ccp4bb] PISA

Dear Sam I can only suggest trying the old trick of editing the pdb file and giving all the DNA bases the same residue number. As you are using the old gui you might be able to do the same with pdbset or pdbcur, or maybe a graphics program. Cheers, Jon Cooper Sent from ProtonMail mobile -

[ccp4bb] PISA

Dear community I ran PISA from CCP4i to analyze a protein-ssDNA complex with non-standard modified nucleotides. It turns out that PISA identifies each nucleotide in the DNA chain as a ligand (i.e. I have 7 DNA bases and PISA calls out 7 ligands). May I solicit your experience if there is a way to

Re: [ccp4bb] PISA command line

Hi Wolfram, I just tried running pisa 5jju  -analyse 5jju.pdb pisa 5jju -list interfaces with  PISA v.2.1.1 built 05-04-2017   with SSM v.1.4.0, SRS v.1.0.0, MMDB v.2,0.17 on Ubuntu 16.04 and that seems to work as expected. Hope this helps, Folmer On 2018-07-06 19:54, wtempel wrote: Hi, h

[ccp4bb] PISA command line

Hi, has anyone of you performed a PISA command line analysis using the version distributed with CCP4 on ubuntu-16.04? My attempt to "-list interfaces" after seemingly successful "-analysis" resulted in a core dump: PISA v.2.1.1 built 05-04-2017 with SSM v.1.4.0, SRS v.1.0.0, MMDB v.2,0.17 Ses

[ccp4bb] PISA values

Dear all I have a dimer that is related to each other by a crystallographic symmetry. My questions are: a. how reliable are the delta G values given by PISA? Has there been an experimental study? b. For a dissociation delta G of say, around 30 kcal/mol, is it possible to estimate the sort of

[ccp4bb] PISA server @ CCP4

Dear All, CCP4 releases new PISA web-server at the following URL: http://www.ccp4.ac.uk/pisa . As always, constructive criticism, bug reports and feature requests are welcome. Enjoy! Eugene Krissinel. -- Scanned by iCritical.

Re: [ccp4bb] PISA and ligands with non-natural amino acids

Dear Herman, I am looking at protein complexes with ligands containing non-natural amino acids. When I run PISA, I get the total area of the ligand, as well as the area of the ligand-protein interface, but hydrogen bonds and salt links are not recognized. I therefore do not think the calculated

[ccp4bb] PISA and ligands with non-natural amino acids

Dear Bulletin board, I am looking at protein complexes with ligands containing non-natural amino acids. When I run PISA, I get the total area of the ligand, as well as the area of the ligand-protein interface, but hydrogen bonds and salt links are not recognized. I therefore do not think the ca

Re: [ccp4bb] PISA interface question

On 05/13/2013 06:34 PM, Evgeny Osipov wrote: Hello everybody, I am trying to evaluate solvatation energy of my protein and. Unfortunately the protein highly glycosilated and it seems that PISA does not take into account hydrogen bonds between mannose from one molecule and symmetry related molecul

[ccp4bb] PISA interface question

Hello everybody, I am trying to evaluate solvatation energy of my protein and. Unfortunately the protein highly glycosilated and it seems that PISA does not take into account hydrogen bonds between mannose from one molecule and symmetry related molecule. Is there any way to tell PISA to use lig

Re: [ccp4bb] Pisa application

On 08/08/2012 09:00 AM, Jose Duarte wrote: To my knowledge PISA by itself is not able to do interface prediction To my understanding PISA is not *intended* to do interface prediction

Re: [ccp4bb] Pisa application

Hi Careina, I asked the exactly same question in this year's CCP4 summer school @APS, and the answer I got was "no ... PISA is not for predicting...". Cheers, Xun Sent from my iPad On Aug 8, 2012, at 2:33 AM, Careina Edgooms wrote: > Dear ccp4ers > > I just wonder whether anybody

Re: [ccp4bb] Pisa application

Perhaps IBIS does what you want? http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi "IBIS ... infers/predicts interacting partners and binding sites by homology " -- David On 8 August 2012 07:33, Careina Edgooms wrote: > Dear ccp4ers > > I just wonder whether anybody knows if the PISA softwa

Re: [ccp4bb] Pisa application

Hi Careina To my knowledge PISA by itself is not able to do interface prediction. In any case there are a few methods available for protein-protein interface prediction. See for example this nice compilation: http://rosettadesigngroup.com/blog/58/10-protein-protein-interface-prediction-server

Re: [ccp4bb] Pisa application

Maybe Nat Protoc. 2011 Aug 11;6(9):1341-54. doi: 10.1038/nprot.2011.367. Predic

[ccp4bb] Pisa application

Dear ccp4ers I just wonder whether anybody knows if the PISA software could be used/modified to detect potential interfaces of interaction of different proteins? This would be very useful as a tool to validate protein-protein interactions detected by in vivo methods such as yeast 2 hybrid scree

Re: [ccp4bb] PISA question

Tongqing Thank you for highlighting an issue with a recent release of the PDBePisa service. The option to return the atom detail as well as the residue detail within the PISA service was accidentally missed from the production service during a major update of features. I am sorry that this

Re: [ccp4bb] PISA question

.ac.uk > Subject: Re: [ccp4bb] PISA question > To: CCP4BB@JISCMAIL.AC.UK > Date: Tuesday, 23 August, 2011, 17:50 > Dear Tongqing > > No there is no such option in CCP4's PISA, but I put this > on the list for further developments. Regrettably PDBe > changed the interface after

Re: [ccp4bb] PISA question

Dear Tongqing No there is no such option in CCP4's PISA, but I put this on the list for further developments. Regrettably PDBe changed the interface after I moved out and I cannot help you with that. However, you may ask them to put that option back. Sorry, Eugene. On 23 Aug 2011, at 17:16,

[ccp4bb] PISA question

Dear CCP4bb, We are trying to get some detailed interface information from an antibody:antigen complex, PDBePISA used to have an option to select atomic level details, now the new web interface only gives residue level information. Is there a way to run PISA (in the CCP4 package) with a differe

Re: [ccp4bb] PISA server

Thanks for all the replies. Like I said, it eventually did upload the structure after 20 minutes and I had no problems in analyzing the interface. I did try two different computers, my home computer on Friday night and the lab one on Saturday afternoon. At home it failed to load the structure, b

Re: [ccp4bb] PISA server

I did not see anything terribly wrong with PISA after I suggested PDBe to turn off PISA's job logging. Because of the latency of distributed file system, the log was jammed from time to time, which resulted in 10-minute delay with getting to the service (PISA is configured to try log for 10 minu

Re: [ccp4bb] PISA server

Hello! I was actually wrong with my statement to PISA - it worked always fine, another server had made trouble the last month. Sorry for this! Thanks and best wishes Kornelius On Mon, 28 Mar 2011 10:53:23 +0100 Eleanor Dodson wrote: > I have found it erratic, and sometimes terribly slow, but

Re: [ccp4bb] PISA server

I have found it erratic, and sometimes terribly slow, but that may be due to local network problems.. But it was working last week.. Eleanor On 03/26/2011 05:28 PM, Miri Hirshberg wrote: Sat., March 26th 2011 EBI Dear Dan, I've just checked (Sat. 17:25 British times), and uploading my

[ccp4bb] PISA server

Sat., March 26th 2011 EBI Dear Dan, I've just checked (Sat. 17:25 British times), and uploading my own structure worked (I tried it from outside EBI network). You have probably experienced some temporary hiccup of the system. Hope it would work for you now, and don't hesitate to inform us

Re: [ccp4bb] PISA server

It has eventually loaded but has taken nearly 20minutes.

Re: [ccp4bb] PISA server

it seems that it's stuck since long time. I asked there for help six week ago but have not received any answer. Cheers Kornelius On Sat, 26 Mar 2011 16:58:26 + Daniel Bonsor wrote: > Is the PISA server having problems? I can not seem to upload any structure. > > Thanks > > Dan --

[ccp4bb] PISA server

Is the PISA server having problems? I can not seem to upload any structure. Thanks Dan

Re: [ccp4bb] PISA ligand handling: Summary

To recap it turns out that the element symbol does supersede the atom and residue name which seems to provide a sneaky workaround to the unrecognized ligand issue in PISA. However this information does come with the disclaimer that it does not replace electrostatic calculations such as CHARMM or A

[ccp4bb] PISA ligand handling

Hi all, I have sort of an oddball question regarding how PISA reads the ligand file into the program for calculations. Does the element symbol of the PDB file take precedence over the atom name or residue name? Specifically, if a ligand contains either atom names or residue names that are inconsi

Re: [ccp4bb] PISA parameters for surface area calculation

Dear Rafael -- I am using PISA to calculate the surface interface of a homdimeric protein. Does anyone know where I can find the parameters (probe radius, atomic radii, etc) PISA uses to calculate surface area? not sure, but would that help?: http://www.ebi.ac.uk/msd-srv/prot_int/picite.ht

[ccp4bb] PISA parameters for surface area calculation

Hi, I am using PISA to calculate the surface interface of a homdimeric protein. Does anyone know where I can find the parameters (probe radius, atomic radii, etc) PISA uses to calculate surface area? Cheers, Rafael.

Re: [ccp4bb] PISA standalone

It is scheduled for 6.1 It works for me, but you need to sort out things like having the latest SSM and MMDB libraries and a few environment variables to set. Email me if you want to beta test it for us ;-) Martyn On Tue, 2007-11-27 at 11:19 +0100, Patrick Hollerein wrote: > Hello CCP4 people

[ccp4bb] PISA standalone

Hello CCP4 people! I was wondering about the status of the PISA standalone version. The powerpoint slides of the CCP4 meeting in march 2007 ( http://www.ccp4.ac.uk/dev/CCP4_meeting_270307/session_8/3_pisa.ppt ) say that the standalone version by Eugene Krissinel is finished and includes screensho