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2020-03-05 14:25:48 -0500 answered a question Topology of pathway differences between pathway-tools and .owl file

Hi, it looks like the problem is not with our biopax output but with how that particular pathway is represented within o

2020-02-12 12:20:15 -0500 answered a question Problem with Regulatory Overview with Web Ptools 23.5 on Centos 7

Hi Greg, This sounds similar to a bug we'd already noticed (for some organisms on our biocyc website) but hadn't yet go

2020-02-11 22:15:41 -0500 edited question Problem with Regulatory Overview with Web Ptools 23.5 on Centos 7

Problem with Regulatory Overview with Web Ptools 23.5 on Centos 7 Hi, I've run into a strange problem with the Regulat

2020-01-08 13:47:08 -0500 answered a question how I can edit the different comparments of my PGDB

Hi Beatriz, CCO-PM-BAC-NEG is the plasma membrane for a Gram-negative bacterium (if your organism is not a Gram-negativ

2020-01-02 19:02:24 -0500 edited answer Getting "Object is not coercible to a frame for KB METACYC 22.0" Error when creating PGDB using Pathologic

Hi Chris, SRI is currently shut down for the holidays, so most likely no-one will be able to look into this until after

2019-12-27 02:40:31 -0500 answered a question Is it possible to obtain older versions of Pathway Tools?

I'm sorry, we do not make older versions of the software available. In fact, we have just released version 23.5, so if

2019-12-27 02:35:12 -0500 answered a question Getting "Object is not coercible to a frame for KB METACYC 22.0" Error when creating PGDB using Pathologic

Hi Chris, SRI is currently shut down for the holidays, so most likely no-one will be able to look into this until after

2019-12-21 22:37:48 -0500 commented answer SBML Import

I've been told that the 23.5 release (which is in the process of being released as we speak) will have sbml import enabl

2019-12-20 20:22:49 -0500 commented answer SBML Import

I'm not sure. I've forwarded your question to some other developers, but you may need to wait until after the holidays.

2019-12-20 20:20:40 -0500 commented answer SBML Import

I'm not sure. I've forwarded your question to some other developers, but you may need to wait until after the holidays.

2019-12-20 10:53:49 -0500 answered a question SBML Import

Are you using Windows? This capability seems to be disabled for Windows (I can see the command there, on my Mac). I pe

2019-11-27 12:53:29 -0500 answered a question No reactions for this EC number are present in MetaCyc database

I'm not sure why you say that. EC# 2.3.1.274 corresponds to RXN-9590 in MetaCyc. I'm not sure what other reaction this

2019-11-18 13:22:18 -0500 edited answer Reactions not found in MetaCyc

Hi Beatriz, Reactions shouldn't be blocked by adding nutrients. Is Co2+ a biomass metabolite in your .fba file? Did you

2019-11-15 02:08:48 -0500 answered a question Using Pathway tools for unannotated genome

No, sorry. In order to get useful information, you should annotate the genome before feeding it in to Pathway Tools. O

2019-10-24 16:28:49 -0500 edited answer remove pathways from a PGDB

Hi Beatriz, Go to the page for the pathway, right-click on the pathway name, and select Edit -> Delete Frame. If th

2019-10-24 16:28:01 -0500 answered a question remove pathways from a PGDB

Hi Beatriz, Go to the page for the pathway, right-click on the pathway name, and select Edit -> Delete Frame. If the

2019-10-03 12:36:27 -0500 commented question Make reaction assignments to polypeptides classified in the "No match" category

I'm assuming you figured out that you need to right-click on the protein name, not the gene name...

2019-10-03 12:35:14 -0500 commented answer Make reaction assignments to polypeptides classified in the "No match" category

When you are right-clicking on the reaction, I assume that is the reaction in MetaCyc. Other options won't appear in th

2019-10-02 12:38:06 -0500 answered a question Make reaction assignments to polypeptides classified in the "No match" category

Hi Beatriz, There are 2 possible ways to manually assign a protein to a reaction. You can right-click on the reaction

2019-05-28 23:02:25 -0500 received badge  Supporter (source)
2019-05-09 12:14:25 -0500 answered a question Pathologic GenBank File Import Weirdness- Ptools v.23

Are you sure the locus_tags aren't also the PGDB accessions? I think we're trying to do that now, where possible, to li

2018-12-16 19:57:04 -0500 answered a question Publish PGDB on GitHub?

Hi Rudy, I'm not quite sure what you are asking. If you are asking if you can somehow publish the PGDB through the Reg

2018-11-08 17:32:38 -0500 answered a question Running the www server with SSL?

The value of the WWW-Server-SSL-Certificate parameter should be the name of PEM encoded file containing both the server

2018-10-31 12:22:26 -0500 commented answer How to export regulation table from MetaCyc

If you just select the slot Regulated-By from the pulldown menu, because the values of that slot are all objects, it aut

2018-10-29 13:03:46 -0500 answered a question error in 22.5: aclssl.so undefined symbol

Here's what our sysadmin has to say: We need more information about what version of Linux they're running. However, bas

2018-10-27 00:22:12 -0500 commented answer How to export regulation table from MetaCyc

We can't create links to the SAQP with fields already filled out. That's why I included the first screenshot, so you'd

2018-10-27 00:19:58 -0500 commented answer How to export regulation table from MetaCyc

We can't create links to the SAQP with fields already filled out. That's why I included the screenshot, so you'd see ho

2018-10-26 11:06:55 -0500 commented answer How to export regulation table from MetaCyc

Unfortunately, in order to get the most out of the advanced query features, you need to both really understand the under

2018-10-26 00:57:34 -0500 edited answer How to export regulation table from MetaCyc

Will this give you what you want? I get a table that looks like this (you can also request it in tab-delimited text fo

2018-10-26 00:49:35 -0500 answered a question How to export regulation table from MetaCyc

Will this give you what you want? I get a table that looks like this (you can also request it in tab-delimited text fo

2018-09-24 11:56:13 -0500 edited answer checkpoint file error

The checkpoint file should be in your home directory, and will be named .ptools-enz-editor.ckp. If you can't find it th

2018-09-24 11:52:47 -0500 answered a question checkpoint file error

The checkpoint file should be in your home directory, and will be named .ptools-enz-editor.ckp. If you can't find it th

2018-08-24 22:26:34 -0500 answered a question Ubuntu 18.04 LTS "Bionic Beaver" incompatible with ptools v.22

Here are the instructions another developer gave me: Open a terminal, or cd to your home directory. cd to pathway-tool

2018-08-13 16:40:35 -0500 answered a question How can we rebuild the PGDBs with our data?

I believe that on the website, the only thing you can do to save the image is to take a screen snapshot. With the downl

2018-06-12 23:37:58 -0500 answered a question return value of pathway-components

Looking at the code, the 2nd integer is the number of reactions in the first component. Why just the first? Why was th

2018-06-12 12:08:19 -0500 commented answer Exporting to a BioPAX File

We have fixed the problem with this pathway, so biopax3 output for it should now be included in our next release.

2018-06-09 18:42:37 -0500 commented answer Exporting to a BioPAX File

PWY-6887 is actually a super-pathway, since it contains the ent-kaurine biosynthesis pathway. If that sub-pathway is no

2018-06-04 20:49:28 -0500 commented answer Exporting to a BioPAX File

Nothing about whether a pathway can be exported to biopax would effect whether or not it could be predicted by pathologi

2018-06-01 23:05:47 -0500 answered a question Exporting to a BioPAX File

This is not a problem with superpathways in general. It seems to be a problem with this particular pathway. If there i

2018-05-23 00:40:14 -0500 edited answer Modify all instances of interactions between a particular transcription factor and all target promoters?

Sure, it's easy using the Lisp API: (loop for regframe in (get-slot-values 'TF 'regulates) do (put-slot-value reg

2018-05-23 00:38:40 -0500 answered a question Modify all instances of interactions between a particular transcription factor and all target promoters?

Sure, it's easy using the Lisp API: (loop for regframe in (get-slot-values 'TF 'regulates) do (put-slot-value regframe

2018-05-09 09:34:12 -0500 answered a question Display read depth

You as a user of the database can upload a data file and display it as a track on the genome browser on both web and des

2018-04-25 17:41:20 -0500 answered a question Pathologic tool ceased at creating gene frames

Hi, have you looked at your terminal window to see if there is any error reported there? In general for this kind of qu

2018-04-19 13:05:25 -0500 answered a question It would be useful to create smart tables from a list of EC numbers

I agree that this sounds useful. Unfortunately, EC numbers are not represented as objects in any organism database (we

2018-03-06 01:08:09 -0500 commented answer Pathologic: Is there a way not to show progress windows

FYI, in our 22.0 release, due out in a month or two, we do a better job of suppressing all the progress windows in batch

2018-02-08 11:58:43 -0500 received badge  Commentator
2018-02-08 11:58:43 -0500 commented answer metabolite list highlight

If I understand your question correctly, you are right -- all our cellular overview diagrams are organism-specific.

2018-02-06 19:15:32 -0500 answered a question metabolite list highlight

We don't have a direct command to do that for compounds, however it is quite straightforward. Just upload your file of

2017-12-13 15:09:08 -0500 answered a question Pathologic: Is there a way not to show progress windows

When running pathologic in batch mode, you shouldn't get any progress windows, but I don't believe there is currently an

2017-11-28 14:41:40 -0500 commented answer Information from the DIAGRAM-INFO slot

Send an email to ptools-support@ai.sri.com.