ProBiS Algorithm Frequently Asked Questions

Fri, Mar 10, 2017 at 3:43 PM

Q: se_enkrat_brez_attachmentov

If this is not the error you were looking for, ten could you please send me zipped directory with all files?

Best rgards,
Janez

--
Dr. Janez Kon

National Institute of Chemistry
Department of Molecular odeling
Hajdrihova 19
SI-1000 Ljubljana
SLOVENIA
P: + 386-1476-02-73
E:=C2=A0konc@cmm.ki.si
W:=C2=A0http://insilab.org
Dear Sir or Madam,

I would like to use your program Probis for a binding site comparison. I followed the steps in the Users manual. However, when running the step

../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
I get the following error: std::bad_alloc
and I optain not example.nosql file. I tried both the precompiled 64bit linux version and the source code compiled on my machine. Both give the same error. I would be grateful for any help.
Kind regards, Nadine Homeyer
------------------------------------------------------------------------ Dr. Nadine Homeyer
Drug Discovery Unit =C2=A6 Sir James Black Centre Division of Biological Chemistry and Drug Discovery School of Life Sciences
University of Dundee Dow Street Dundee DD1 5EH United Kingdom
E-Mail: n.homeyer@dundee.ac.uk


The University of Dundee is a registered Scottish Charity, No: SC015096
---------- From: Janez Konc Date: Wed, Mar 15, 2017 at 8:32 PM To: "Nadine Homeyer (Staff)"

Dear Nadine,
The command should be on one line like this:
../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
Your example streatches two lines.
If this is not the error you were looking for, then could you please send me zipped directory with all files?
Best regards, Janez
--=20 Dr. Janez Konc
National Institute of Chemistry Department of Molecular Modeling Hajdrihova 19 SI-1000 Ljubljana SLOVENIA P: + 386-1-476-02-73 <(01)%20476%2002%2073> E: konc@cmm.ki.si W: http://insilab.org
---------- From: Nadine Homeyer (Staff) Date: Thu, Mar 16, 2017 at 7:02 PM To: Janez Konc Cc: "Jonathan Downward (Staff)"

Hi Janez,

I am aware that the command needs to be in one line. Probably the E-Mail program broke into two parts.

/local_software/probis_source/probis/probis -surfdb -local -sfile srfs.txt -f1 ../probis_bsite_files_30/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql

I have attached a sample dataset. The commands are generated by a python script in the folder probis_analyis_30.

I would be highly grateful for your help with this.

Kind regards,
Nadine




------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 15 March 2017 19:32 *To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis

---------- From: Janez Konc Date: Thu, Mar 16, 2017 at 8:37 PM To: "Nadine Homeyer (Staff)" Cc: "Jonathan Downward (Staff)"

Hi Nadine,
The solution is to add chain_id's as the second column in the srfs.txt file. Attached is modified srfs.txt file from your example that works.
Best regards, Janez
---------- From: Nadine Homeyer (Staff) Date: Fri, Mar 17, 2017 at 10:25 AM To: Janez Konc

Hi Janez,

with your suggested modification I am now able to generate nosql-files successfully, thanks. However, in these nosql files there are only data for some alignments shown. I would like to do an all against all comparison. For this I need alignments even if they are bad, for all protein binding sites. Is there a cutoff value I can set differently to prevent that only some alignments are not shown/generated?

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 16 March 2017 19:37:04 *To:* Nadine Homeyer (Staff) *Cc:* Jonathan Downward (Staff)

---------- From: Janez Konc Date: Fri, Mar 17, 2017 at 10:43 AM To: "Nadine Homeyer (Staff)"

Use this option:
-param PAR_FILE Read parameters from the specified parameter file.
Regards, Janez

---------- From: Nadine Homeyer (Staff) Date: Fri, Mar 17, 2017 at 10:51 AM To: Janez Konc

Hi Janez,

thank you for your help. However, unfortunately the output did not change with the param option.
probis -surfdb -local -sfile srfs.txt -param parameters.inp -f1 ../probis_bsite_files_50/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql
Where the srfs.txt file contains all the srf files to compare with.

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 09:43:47

---------- From: Janez Konc Date: Fri, Mar 17, 2017 at 2:07 PM To: "Nadine Homeyer (Staff)"

Hi Nadine,
This took me a while. Add the -noprune -nofp options to the command line!
Regards, Janez
---------- From: Nadine Homeyer (Staff) Date: Fri, Mar 17, 2017 at 2:33 PM To: Janez Konc

Hi Janez,

great, that worked, thank you.

Kind regards
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 13:07:53

---------- From: Nadine Homeyer (Staff) Date: Fri, Mar 17, 2017 at 2:44 PM To: Janez Konc

Hi Janez,

I have been happy to early. It is true for my first sample case but not for the others. You can use the files I sent you. The protein 1a8i gets comparisons with all others, which is fine. But, the other proteins have only comparisons with a fraction of the other proteins in their nosql file.

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:33:44 *To:* Janez Konc

---------- From: Nadine Homeyer (Staff) Date: Fri, Mar 17, 2017 at 6:49 PM To: Janez Konc

Hi Janez,

did you have time to have a look? Can you tell if this is something general, i.e. an all against all comparison is not possible in general? Or if it is something system dependent? Thank you for your help!

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:44:54

---------- From: Janez Konc Date: Mon, Mar 20, 2017 at 8:07 AM To: "Nadine Homeyer (Staff)"

Hi Nadine,
Add this line to the parameters.inp file to raise the similarity threshold:
THRMSD 1.8
In some rare cases it might still not output all lines, regard those proteins as non-similar.
Best regards, Janez







--=20 Dr. Janez Konc
National Institute of Chemistry Department of Molecular Modeling Hajdrihova 19 SI-1000 Ljubljana SLOVENIA P: + 386-1-476-02-73 E: konc@cmm.ki.si W: http://insilab.org
--001a114039f44d445005502d9ac2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
DESTINATION: PROBIS_ALGOITHM
TITLE: =C2=A0se_enkrat_brez_attchmentov

Forwarded converstion
Subject: Usage of Probis------------------------

From: Nadine Homeyer (Staff) <n.homeyer@dudee.ac.uk>
Date: Fri, Mar 10, 2017 at 3:43 PM
To: &quo;konc@cmm.ki.si" <konc@cmm.ki.si>






Fri, Mar 10, 2017 at 3:

Q: std

Dear Sir or Madam,

I would like to use your program Probis for a binding site comparison=.I followed the steps in the Users manual. However, when running the s=tep

../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
I get the following error: std::bad_alloc
and I optain not example.nosql file. I tried both the precompiled 64bit linux version and the source code compiled on my machine. Both give the same error. I would be grateful for any help.
Kind regards, Nadine Homeyer
------------------------------------------------------------ ------------ Dr. Nadine Homeyer
Drug Discovery Unit =C2=A6 Sir James Black Centre Division of Biological Chemistry and Drug Discovery School of Life Sciences
University of Dundee Dow Street Dundee DD1 5EH United Kingdom
E-Mail: n.homeyer@dundee.ac.uk


The University of Dundee is a registered Scottish Charity, No: SC0150=96
Hi Janez,

I am aware that the command needs to be in one line. Probably the E-Mail program broke into two parts.

/local_software/probis_source/probis/probis -surfdb -local -sfile srfs.txt -f1 ../probis_bsite_files_30/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql

I have attached a sample dataset. The commands are generated by a python script in the folder probis_analyis_30.

I would be highly grateful for your help with this.

Kind regards,
Nadine




------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 15 March 2017 19:32 *To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Dear Nadine,
The command should be on one line like this:
../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
Your example streatches two lines.
If this is not the error you were looking for, then could you please send me zipped directory with all files?
Best regards, Janez
Hi Janez,

with your suggested modification I am now able to generate nosql-files successfully, thanks. However, in these nosql files there are only data=forsome alignments shown. I would like to do an all against all comparison=.For this I need alignments even if they are bad, for all protein bindin=gsites. Is there a cutoff value I can set differently to prevent that on=lysome alignments are not shown/generated?

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 16 March 2017 19:37:04 *To:* Nadine Homeyer (Staff) *Cc:* Jonathan Downward (Staff)
*Subject:* Re: Usage of Probis
Hi Nadine,
The solution is to add chain_id's as the second column in the srfs.txt file. Attached is modified srfs.txt file from your example that works.
Hi Janez,

thank you for your help. However, unfortunately the output did not chang=ewith the param option.
probis -surfdb -local -sfile srfs.txt -param parameters.inp -f1 ../probis_bsite_files_50/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql
Where the srfs.txt file contains all the srf files to compare with.

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 09:43:47
*To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Use this option:
-param PAR_FILE Read parameters from the specified parameter file.
Regards, Janez
Hi Janez,

did you have time to have a look? Can you tell if this is something general, i.e. an all against all comparison is not possible in general? Orif it is something system dependent? Thank you for your help!

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:44:54
*To:* Janez Konc *Subject:* Re: Usage of Probis

Hi Janez,

I have been happy to early. It is true for my first sample case but not for the others. You can use the files I sent you. The protein 1a8i gets comparisons with all others, which is fine. But, the other proteins have only comparisons with a fraction of the other proteins in their nosql files.

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:33:44 *To:* Janez Konc *Subject:* Re: Usage of Probis

Hi Janez,

great, that worked, thank you.

Kind regards
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 13:07:53 *To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Hi Nadine,
This took me a while. Add the -noprune -nofp options to the command line!
Hi Nadine,
Add this line to the parameters.inp file to raise the similarity threshold:
THRMSD 1.8
In some rare cases it might still not output all lines, regard those proteins as non-similar.
Best regards, Janez




Fri, Mar 10, 2017 at 3:

Q: std

Dear Sir or Madam,

I would like to use your program Probis for a binding site comparison=.I followed the steps in the Users manual. However, when running the s=tep

../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
I get the following error: std::bad_alloc
and I optain not example.nosql file. I tried both the precompiled 64bit linux version and the source code compiled on my machine. Both give the same error. I would be grateful for any help.
Kind regards, Nadine Homeyer
------------------------------------------------------------ ------------ Dr. Nadine Homeyer
Drug Discovery Unit =C2=A6 Sir James Black Centre Division of Biological Chemistry and Drug Discovery School of Life Sciences
University of Dundee Dow Street Dundee DD1 5EH United Kingdom
E-Mail: n.homeyer@dundee.ac.uk


The University of Dundee is a registered Scottish Charity, No: SC0150=96
Hi Janez,

I am aware that the command needs to be in one line. Probably the E-Mail program broke into two parts.

/local_software/probis_source/probis/probis -surfdb -local -sfile srfs.txt -f1 ../probis_bsite_files_30/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql

I have attached a sample dataset. The commands are generated by a python script in the folder probis_analyis_30.

I would be highly grateful for your help with this.

Kind regards,
Nadine




------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 15 March 2017 19:32 *To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Dear Nadine,
The command should be on one line like this:
../probis -ncpu 8 -surfdb -local -sfile srfs.txt -f1 1phrA.srf -c1 A -nosql example.nosql
Your example streatches two lines.
If this is not the error you were looking for, then could you please send me zipped directory with all files?
Best regards, Janez
Hi Janez,

with your suggested modification I am now able to generate nosql-files successfully, thanks. However, in these nosql files there are only data=forsome alignments shown. I would like to do an all against all comparison=.For this I need alignments even if they are bad, for all protein bindin=gsites. Is there a cutoff value I can set differently to prevent that on=lysome alignments are not shown/generated?

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 16 March 2017 19:37:04 *To:* Nadine Homeyer (Staff) *Cc:* Jonathan Downward (Staff)
*Subject:* Re: Usage of Probis
Hi Nadine,
The solution is to add chain_id's as the second column in the srfs.txt file. Attached is modified srfs.txt file from your example that works.
Hi Janez,

thank you for your help. However, unfortunately the output did not chang=ewith the param option.
probis -surfdb -local -sfile srfs.txt -param parameters.inp -f1 ../probis_bsite_files_50/1j04_LLP_1000_A.srf -c1 A -nosql 1j04_LLP_1000_A.nosql
Where the srfs.txt file contains all the srf files to compare with.

Kind regards,
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 09:43:47
*To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Use this option:
-param PAR_FILE Read parameters from the specified parameter file.
Regards, Janez
Hi Janez,

did you have time to have a look? Can you tell if this is something general, i.e. an all against all comparison is not possible in general? Orif it is something system dependent? Thank you for your help!

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:44:54
*To:* Janez Konc *Subject:* Re: Usage of Probis

Hi Janez,

I have been happy to early. It is true for my first sample case but not for the others. You can use the files I sent you. The protein 1a8i gets comparisons with all others, which is fine. But, the other proteins have only comparisons with a fraction of the other proteins in their nosql files.

Kind regards,
Nadine ------------------------------ *From:* Nadine Homeyer (Staff) *Sent:* 17 March 2017 13:33:44 *To:* Janez Konc *Subject:* Re: Usage of Probis

Hi Janez,

great, that worked, thank you.

Kind regards
Nadine ------------------------------ *From:* janez.konc2@gmail.com on behalf of Janez Konc *Sent:* 17 March 2017 13:07:53 *To:* Nadine Homeyer (Staff) *Subject:* Re: Usage of Probis
Hi Nadine,
This took me a while. Add the -noprune -nofp options to the command line!
Hi Nadine,
Add this line to the parameters.inp file to raise the similarity threshold:
THRMSD 1.8
In some rare cases it might still not output all lines, regard those proteins as non-similar.
Best regards, Janez